Alternative splicing

Last updated
Alternative splicing produces three protein isoforms. Protein A includes all of the exons, whereas Proteins B and C result from exon skipping. DNA alternative splicing.gif
Alternative splicing produces three protein isoforms. Protein A includes all of the exons, whereas Proteins B and C result from exon skipping.

Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to produce different splice variants. For example, some exons of a gene may be included within or excluded from the final RNA product of the gene. [1] This means the exons are joined in different combinations, leading to different splice variants. In the case of protein-coding genes, the proteins translated from these splice variants may contain differences in their amino acid sequence and in their biological functions (see Figure).

Contents

Biologically relevant alternative splicing occurs as a normal phenomenon in eukaryotes, where it increases the number of proteins that can be encoded by the genome. [1] In humans, it is widely believed that ~95% of multi-exonic genes are alternatively spliced to produce functional alternative products from the same gene [2] but many scientists believe that most of the observed splice variants are due to splicing errors and the actual number of biologically relevant alternatively spliced genes is much lower. [3] [4]

Discovery

Alternative splicing was first observed in 1977. [5] [6] The adenovirus produces five primary transcripts early in its infectious cycle, prior to viral DNA replication, and an additional one later, after DNA replication begins. The early primary transcripts continue to be produced after DNA replication begins. The additional primary transcript produced late in infection is large and comes from 5/6 of the 32kb adenovirus genome. This is much larger than any of the individual adenovirus mRNAs present in infected cells. Researchers found that the primary RNA transcript produced by adenovirus type 2 in the late phase was spliced in many different ways, resulting in mRNAs encoding different viral proteins. In addition, the primary transcript contained multiple polyadenylation sites, giving different 3' ends for the processed mRNAs. [7] [8] [9]

In 1981, the first example of alternative splicing in a transcript from a normal, endogenous gene was characterized. [7] The gene encoding the thyroid hormone calcitonin was found to be alternatively spliced in mammalian cells. The primary transcript from this gene contains 6 exons; the calcitonin mRNA contains exons 1–4, and terminates after a polyadenylation site in exon 4. Another mRNA is produced from this pre-mRNA by skipping exon 4, and includes exons 1–3, 5, and 6. It encodes a protein known as CGRP (calcitonin gene related peptide). [10] [11] Examples of alternative splicing in immunoglobin gene transcripts in mammals were also observed in the early 1980s. [7] [12]

Since then, many other examples of biologically relevant alternative splicing have been found in eukaryotes. [1] The "record-holder" for alternative splicing is a D. melanogaster gene called Dscam, which could potentially have 38,016 splice variants. [13]

In 2021, it was discovered that the genome of adenovirus type 2, the adenovirus in which alternative splicing was first identified, was able to produce a much greater variety of splice variants than previously thought. [14] By using next generation sequencing technology, researchers were able to update the human adenovirus type 2 transcriptome and document the presence of 904 splice variants produced by the virus through a complex pattern of alternative splicing. Very few of these splice variants have been shown to be functional, a point that the authors raise in their paper.

"An outstanding question is what roles the menagerie of novel RNAs play or whether they are spurious molecules generated by an overloaded splicing machinery." [14]

Modes

Traditional classification of basic types of alternative RNA splicing events. Exons are represented as blue and yellow blocks, introns as lines in between. Alt splicing bestiary2.jpg
Traditional classification of basic types of alternative RNA splicing events. Exons are represented as blue and yellow blocks, introns as lines in between.
Relative frequencies of types of alternative splicing events differ between humans and fruit flies. Splice types frequency.jpg
Relative frequencies of types of alternative splicing events differ between humans and fruit flies.

Five basic modes of alternative splicing are generally recognized. [1] [2] [16] [15]

In addition to these primary modes of alternative splicing, there are two other main mechanisms by which different mRNAs may be generated from the same gene; multiple promoters and multiple polyadenylation sites. Use of multiple promoters is properly described as a transcriptional regulation mechanism rather than alternative splicing; by starting transcription at different points, transcripts with different 5'-most exons can be generated. At the other end, multiple polyadenylation sites provide different 3' end points for the transcript. Both of these mechanisms are found in combination with alternative splicing and provide additional variety in mRNAs derived from a gene. [1] [16]

Schematic cutoff from 3 splicing structures in the murine hyaluronidase gene. Directionality of transcription from 5' to 3' is shown from left to right. Exons and introns are not drawn to scale. Hyaluronidase3.gif
Schematic cutoff from 3 splicing structures in the murine hyaluronidase gene. Directionality of transcription from 5' to 3' is shown from left to right. Exons and introns are not drawn to scale.


These modes describe basic splicing mechanisms, but may be inadequate to describe complex splicing events. For instance, the figure to the right shows 3 spliceforms from the mouse hyaluronidase 3 gene. Comparing the exonic structure shown in the first line (green) with the one in the second line (yellow) shows intron retention, whereas the comparison between the second and the third spliceform (yellow vs. blue) exhibits exon skipping. A model nomenclature to uniquely designate all possible splicing patterns has recently been proposed. [15]

Mechanisms

General splicing mechanism

Spliceosome A complex defines the 5' and 3' ends of the intron before removal A complex.jpg
Spliceosome A complex defines the 5' and 3' ends of the intron before removal

When the pre-mRNA has been transcribed from the DNA, it includes several introns and exons. (In nematodes, the mean is 4–5 exons and introns; in the fruit fly Drosophila there can be more than 100 introns and exons in one transcribed pre-mRNA.) The exons to be retained in the mRNA are determined during the splicing process. The regulation and selection of splice sites are done by trans-acting splicing activator and splicing repressor proteins as well as cis-acting elements within the pre-mRNA itself such as exonic splicing enhancers and exonic splicing silencers.

The typical eukaryotic nuclear intron has consensus sequences defining important regions. Each intron has the sequence GU at its 5' end. Near the 3' end there is a branch site. The nucleotide at the branchpoint is always an A; the consensus around this sequence varies somewhat. In humans the branch site consensus sequence is yUnAy. [18] The branch site is followed by a series of pyrimidines – the polypyrimidine tract – then by AG at the 3' end. [16]

Splicing of mRNA is performed by an RNA and protein complex known as the spliceosome, containing snRNPs designated U1, U2, U4, U5, and U6 (U3 is not involved in mRNA splicing). [19] U1 binds to the 5' GU and U2, with the assistance of the U2AF protein factors, binds to the branchpoint A within the branch site. The complex at this stage is known as the spliceosome A complex. Formation of the A complex is usually the key step in determining the ends of the intron to be spliced out, and defining the ends of the exon to be retained. [16] (The U nomenclature derives from their high uridine content).

The U4,U5,U6 complex binds, and U6 replaces the U1 position. U1 and U4 leave. The remaining complex then performs two transesterification reactions. In the first transesterification, 5' end of the intron is cleaved from the upstream exon and joined to the branch site A by a 2',5'-phosphodiester linkage. In the second transesterification, the 3' end of the intron is cleaved from the downstream exon, and the two exons are joined by a phosphodiester bond. The intron is then released in lariat form and degraded. [1]

Regulatory elements and proteins

Splicing repression Splicing repression.jpg
Splicing repression

Splicing is regulated by trans-acting proteins (repressors and activators) and corresponding cis-acting regulatory sites (silencers and enhancers) on the pre-mRNA. However, as part of the complexity of alternative splicing, it is noted that the effects of a splicing factor are frequently position-dependent. That is, a splicing factor that serves as a splicing activator when bound to an intronic enhancer element may serve as a repressor when bound to its splicing element in the context of an exon, and vice versa. [20] The secondary structure of the pre-mRNA transcript also plays a role in regulating splicing, such as by bringing together splicing elements or by masking a sequence that would otherwise serve as a binding element for a splicing factor. [21] [22] Together, these elements form a "splicing code" that governs how splicing will occur under different cellular conditions. [23] [24]

There are two major types of cis-acting RNA sequence elements present in pre-mRNAs and they have corresponding trans-acting RNA-binding proteins. Splicing silencers are sites to which splicing repressor proteins bind, reducing the probability that a nearby site will be used as a splice junction. These can be located in the intron itself (intronic splicing silencers, ISS) or in a neighboring exon (exonic splicing silencers, ESS). They vary in sequence, as well as in the types of proteins that bind to them. The majority of splicing repressors are heterogeneous nuclear ribonucleoproteins (hnRNPs) such as hnRNPA1 and polypyrimidine tract binding protein (PTB). [16] [23] Splicing enhancers are sites to which splicing activator proteins bind, increasing the probability that a nearby site will be used as a splice junction. These also may occur in the intron (intronic splicing enhancers, ISE) or exon (exonic splicing enhancers, ESE). Most of the activator proteins that bind to ISEs and ESEs are members of the SR protein family. Such proteins contain RNA recognition motifs and arginine and serine-rich (RS) domains. [16] [23]

Splicing activation Splicing activation.jpg
Splicing activation

In general, the determinants of splicing work in an inter-dependent manner that depends on context, so that the rules governing how splicing is regulated form a splicing code. [24] The presence of a particular cis-acting RNA sequence element may increase the probability that a nearby site will be spliced in some cases, but decrease the probability in other cases, depending on context. The context within which regulatory elements act includes cis-acting context that is established by the presence of other RNA sequence features, and trans-acting context that is established by cellular conditions. For example, some cis-acting RNA sequence elements influence splicing only if multiple elements are present in the same region so as to establish context. As another example, a cis-acting element can have opposite effects on splicing, depending on which proteins are expressed in the cell (e.g., neuronal versus non-neuronal PTB). The adaptive significance of splicing silencers and enhancers is attested by studies showing that there is strong selection in human genes against mutations that produce new silencers or disrupt existing enhancers. [25] [26]

Examples

Exon skipping: Drosophiladsx

Alternative splicing of dsx pre-mRNA Dsx splicing.jpg
Alternative splicing of dsx pre-mRNA

Pre-mRNAs from the D. melanogaster gene dsx contain 6 exons. In males, exons 1,2,3,5,and 6 are joined to form the mRNA, which encodes a transcriptional regulatory protein required for male development. In females, exons 1,2,3, and 4 are joined, and a polyadenylation signal in exon 4 causes cleavage of the mRNA at that point. The resulting mRNA is a transcriptional regulatory protein required for female development. [27]

This is an example of exon skipping. The intron upstream from exon 4 has a polypyrimidine tract that doesn't match the consensus sequence well, so that U2AF proteins bind poorly to it without assistance from splicing activators. This 3' splice acceptor site is therefore not used in males. Females, however, produce the splicing activator Transformer (Tra) (see below). The SR protein Tra2 is produced in both sexes and binds to an ESE in exon 4; if Tra is present, it binds to Tra2 and, along with another SR protein, forms a complex that assists U2AF proteins in binding to the weak polypyrimidine tract. U2 is recruited to the associated branchpoint, and this leads to inclusion of exon 4 in the mRNA. [27] [28]

Alternative acceptor sites: DrosophilaTransformer

Alternative splicing of the Drosophila Transformer gene product. Transformer splicing.gif
Alternative splicing of the DrosophilaTransformer gene product.

Pre-mRNAs of the Transformer (Tra) gene of Drosophila melanogaster undergo alternative splicing via the alternative acceptor site mode. The gene Tra encodes a protein that is expressed only in females. The primary transcript of this gene contains an intron with two possible acceptor sites. In males, the upstream acceptor site is used. This causes a longer version of exon 2 to be included in the processed transcript, including an early stop codon. The resulting mRNA encodes a truncated protein product that is inactive. Females produce the master sex determination protein Sex lethal (Sxl). The Sxl protein is a splicing repressor that binds to an ISS in the RNA of the Tra transcript near the upstream acceptor site, preventing U2AF protein from binding to the polypyrimidine tract. This prevents the use of this junction, shifting the spliceosome binding to the downstream acceptor site. Splicing at this point bypasses the stop codon, which is excised as part of the intron. The resulting mRNA encodes an active Tra protein, which itself is a regulator of alternative splicing of other sex-related genes (see dsx above). [1]

Exon definition: Fas receptor

Alternative splicing of the Fas receptor pre-mRNA Fas alternative splicing.jpg
Alternative splicing of the Fas receptor pre-mRNA

Multiple isoforms of the Fas receptor protein are produced by alternative splicing. Two normally occurring isoforms in humans are produced by an exon-skipping mechanism. An mRNA including exon 6 encodes the membrane-bound form of the Fas receptor, which promotes apoptosis, or programmed cell death. Increased expression of Fas receptor in skin cells chronically exposed to the sun, and absence of expression in skin cancer cells, suggests that this mechanism may be important in elimination of pre-cancerous cells in humans. [29] If exon 6 is skipped, the resulting mRNA encodes a soluble Fas protein that does not promote apoptosis. The inclusion or skipping of the exon depends on two antagonistic proteins, TIA-1 and polypyrimidine tract-binding protein (PTB).

  • The 5' donor site in the intron downstream from exon 6 in the pre-mRNA has a weak agreement with the consensus sequence, and is not bound usually by the U1 snRNP. If U1 does not bind, the exon is skipped (see "a" in accompanying figure).
  • Binding of TIA-1 protein to an intronic splicing enhancer site stabilizes binding of the U1 snRNP. [16] The resulting 5' donor site complex assists in binding of the splicing factor U2AF to the 3' splice site upstream of the exon, through a mechanism that is not yet known (see b). [30]
  • Exon 6 contains a pyrimidine-rich exonic splicing silencer, ure6, where PTB can bind. If PTB binds, it inhibits the effect of the 5' donor complex on the binding of U2AF to the acceptor site, resulting in exon skipping (see c).

This mechanism is an example of exon definition in splicing. A spliceosome assembles on an intron, and the snRNP subunits fold the RNA so that the 5' and 3' ends of the intron are joined. However, recently studied examples such as this one show that there are also interactions between the ends of the exon. In this particular case, these exon definition interactions are necessary to allow the binding of core splicing factors prior to assembly of the spliceosomes on the two flanking introns. [30]

Repressor-activator competition: HIV-1 tat exon 2

Alternative splicing of HIV-1 tat exon 2 Tat exon2 splicing.jpg
Alternative splicing of HIV-1 tat exon 2

HIV, the retrovirus that causes AIDS in humans, produces a single primary RNA transcript, which is alternatively spliced in multiple ways to produce over 40 different mRNAs. [31] Equilibrium among differentially spliced transcripts provides multiple mRNAs encoding different products that are required for viral multiplication. [32] One of the differentially spliced transcripts contains the tat gene, in which exon 2 is a cassette exon that may be skipped or included. The inclusion of tat exon 2 in the RNA is regulated by competition between the splicing repressor hnRNP A1 and the SR protein SC35. Within exon 2 an exonic splicing silencer sequence (ESS) and an exonic splicing enhancer sequence (ESE) overlap. If A1 repressor protein binds to the ESS, it initiates cooperative binding of multiple A1 molecules, extending into the 5' donor site upstream of exon 2 and preventing the binding of the core splicing factor U2AF35 to the polypyrimidine tract. If SC35 binds to the ESE, it prevents A1 binding and maintains the 5' donor site in an accessible state for assembly of the spliceosome. Competition between the activator and repressor ensures that both mRNA types (with and without exon 2) are produced. [31]

Adaptive significance

Genuine alternative splicing occurs in both protein-coding genes and non-coding genes to produce multiple products (proteins or non-coding RNAs). External information is needed in order to decide which product is made, given a DNA sequence and the initial transcript. Since the methods of regulation are inherited, this provides novel ways for mutations to affect gene expression. [33]

Alternative splicing may provide evolutionary flexibility. A single point mutation may cause a given exon to be occasionally excluded or included from a transcript during splicing, allowing production of a new protein isoform without loss of the original protein. [1] Studies have identified intrinsically disordered regions (see Intrinsically unstructured proteins) as enriched in the non-constitutive exons [34] suggesting that protein isoforms may display functional diversity due to the alteration of functional modules within these regions. Such functional diversity achieved by isoforms is reflected by their expression patterns and can be predicted by machine learning approaches. [35] [36] Comparative studies indicate that alternative splicing preceded multicellularity in evolution, and suggest that this mechanism might have been co-opted to assist in the development of multicellular organisms. [37]

Research based on the Human Genome Project and other genome sequencing has shown that humans have only about 30% more genes than the roundworm Caenorhabditis elegans , and only about twice as many as the fly Drosophila melanogaster . This finding led to speculation that the perceived greater complexity of humans, or vertebrates generally, might be due to higher rates of alternative splicing in humans than are found in invertebrates. [38] [39] However, a study on samples of 100,000 expressed sequence tags (EST) each from human, mouse, rat, cow, fly (D. melanogaster), worm (C. elegans), and the plant Arabidopsis thaliana found no large differences in frequency of alternatively spliced genes among humans and any of the other animals tested. [40] Another study, however, proposed that these results were an artifact of the different numbers of ESTs available for the various organisms. When they compared alternative splicing frequencies in random subsets of genes from each organism, the authors concluded that vertebrates do have higher rates of alternative splicing than invertebrates. [41]

Disease

Changes in the RNA processing machinery may lead to mis-splicing of multiple transcripts, while single-nucleotide alterations in splice sites or cis-acting splicing regulatory sites may lead to differences in splicing of a single gene, and thus in the mRNA produced from a mutant gene's transcripts. A study in 2005 involving probabilistic analyses indicated that greater than 60% of human disease-causing mutations affect splicing rather than directly affecting coding sequences. [42] A more recent study indicates that one-third of all hereditary diseases are likely to have a splicing component. [20] Regardless of exact percentage, a number of splicing-related diseases do exist. [43] As described below, a prominent example of splicing-related diseases is cancer.

Abnormally spliced mRNAs are also found in a high proportion of cancerous cells. [44] [45] [46] Combined RNA-Seq and proteomics analyses have revealed striking differential expression of splice isoforms of key proteins in important cancer pathways. [47] It is not always clear whether such aberrant patterns of splicing contribute to the cancerous growth, or are merely consequence of cellular abnormalities associated with cancer. For certain types of cancer, like in colorectal and prostate, the number of splicing errors per cancer has been shown to vary greatly between individual cancers, a phenomenon referred to as transcriptome instability. [48] [49] Transcriptome instability has further been shown to correlate grealty with reduced expression level of splicing factor genes. Mutation of DNMT3A has been demonstrated to contribute to hematologic malignancies, and that DNMT3A -mutated cell lines exhibit transcriptome instability as compared to their isogenic wildtype counterparts. [50]

In fact, there is actually a reduction of alternative splicing in cancerous cells compared to normal ones, and the types of splicing differ; for instance, cancerous cells show higher levels of intron retention than normal cells, but lower levels of exon skipping. [51] Some of the differences in splicing in cancerous cells may be due to the high frequency of somatic mutations in splicing factor genes, [46] and some may result from changes in phosphorylation of trans-acting splicing factors. [33] Others may be produced by changes in the relative amounts of splicing factors produced; for instance, breast cancer cells have been shown to have increased levels of the splicing factor SF2/ASF. [52] One study found that a relatively small percentage (383 out of over 26000) of alternative splicing variants were significantly higher in frequency in tumor cells than normal cells, suggesting that there is a limited set of genes which, when mis-spliced, contribute to tumor development. [53] It is believed however that the deleterious effects of mis-spliced transcripts are usually safeguarded and eliminated by a cellular posttranscriptional quality control mechanism termed nonsense-mediated mRNA decay [NMD]. [54]

One example of a specific splicing variant associated with cancers is in one of the human DNMT genes. Three DNMT genes encode enzymes that add methyl groups to DNA, a modification that often has regulatory effects. Several abnormally spliced DNMT3B mRNAs are found in tumors and cancer cell lines. In two separate studies, expression of two of these abnormally spliced mRNAs in mammalian cells caused changes in the DNA methylation patterns in those cells. Cells with one of the abnormal mRNAs also grew twice as fast as control cells, indicating a direct contribution to tumor development by this product. [33]

Another example is the Ron ( MST1R ) proto-oncogene. An important property of cancerous cells is their ability to move and invade normal tissue. Production of an abnormally spliced transcript of Ron has been found to be associated with increased levels of the SF2/ASF in breast cancer cells. The abnormal isoform of the Ron protein encoded by this mRNA leads to cell motility. [52]

Overexpression of a truncated splice variant of the FOSB gene – ΔFosB – in a specific population of neurons in the nucleus accumbens has been identified as the causal mechanism involved in the induction and maintenance of an addiction to drugs and natural rewards. [55] [56] [57] [58]

Recent provocative studies point to a key function of chromatin structure and histone modifications in alternative splicing regulation. These insights suggest that epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced. [59]

Genome-scale (transcriptome-wide) analysis

Transcriptome-wide analysis of alternative splicing is typically performed by high-throughput RNA-sequencing. Most commonly, by short-read sequencing, such as by Illumina instrumentation. But even more informative, by long-read sequencing, such as by Nanopore or PacBio instrumentation. Transcriptome-wide analyses can for example be used to measure the amount of deviating alternative splicing, such as in a cancer cohort. [60]

Deep sequencing technologies have been used to conduct genome-wide analyses of both unprocessed and processed mRNAs; thus providing insights into alternative splicing. For example, results from use of deep sequencing indicate that, in humans, an estimated 95% of transcripts from multiexon genes undergo alternative splicing, with a number of pre-mRNA transcripts spliced in a tissue-specific manner. [2] Functional genomics and computational approaches based on multiple instance learning have also been developed to integrate RNA-seq data to predict functions for alternatively spliced isoforms. [36] Deep sequencing has also aided in the in vivo detection of the transient lariats that are released during splicing, the determination of branch site sequences, and the large-scale mapping of branchpoints in human pre-mRNA transcripts. [61]

More historically, alternatively spliced transcripts have been found by comparing EST sequences, but this requires sequencing of very large numbers of ESTs. Most EST libraries come from a very limited number of tissues, so tissue-specific splice variants are likely to be missed in any case. High-throughput approaches to investigate splicing have, however, been developed, such as: DNA microarray-based analyses, RNA-binding assays, and deep sequencing. These methods can be used to screen for polymorphisms or mutations in or around splicing elements that affect protein binding. When combined with splicing assays, including in vivo reporter gene assays, the functional effects of polymorphisms or mutations on the splicing of pre-mRNA transcripts can then be analyzed. [20] [23] [62]

In microarray analysis, arrays of DNA fragments representing individual exons (e.g. Affymetrix exon microarray) or exon/exon boundaries (e.g. arrays from ExonHit or Jivan) have been used. The array is then probed with labeled cDNA from tissues of interest. The probe cDNAs bind to DNA from the exons that are included in mRNAs in their tissue of origin, or to DNA from the boundary where two exons have been joined. This can reveal the presence of particular alternatively spliced mRNAs. [63]

CLIP (Cross-linking and immunoprecipitation) uses UV radiation to link proteins to RNA molecules in a tissue during splicing. A trans-acting splicing regulatory protein of interest is then precipitated using specific antibodies. When the RNA attached to that protein is isolated and cloned, it reveals the target sequences for that protein. [64] Another method for identifying RNA-binding proteins and mapping their binding to pre-mRNA transcripts is "Microarray Evaluation of Genomic Aptamers by shift (MEGAshift)".net [65] This method involves an adaptation of the "Systematic Evolution of Ligands by Exponential Enrichment (SELEX)" method [66] together with a microarray-based readout. Use of the MEGAshift method has provided insights into the regulation of alternative splicing by allowing for the identification of sequences in pre-mRNA transcripts surrounding alternatively spliced exons that mediate binding to different splicing factors, such as ASF/SF2 and PTB. [67] This approach has also been used to aid in determining the relationship between RNA secondary structure and the binding of splicing factors. [22]

Use of reporter assays makes it possible to find the splicing proteins involved in a specific alternative splicing event by constructing reporter genes that will express one of two different fluorescent proteins depending on the splicing reaction that occurs. This method has been used to isolate mutants affecting splicing and thus to identify novel splicing regulatory proteins inactivated in those mutants. [64]

Recent advancements in protein structure prediction have facilitated the development of new tools for genome annotation and alternative splicing anlaysis. For instance, isoform.io, a platform guided by protein structure predictions, has evaluated hundreds of thousands of isoforms of human protein-coding genes assembled from numerous RNA sequencing experiments across a variety of human tissues. This comprehensive analysis has led to the identification of numerous isoforms with more confidently predicted structure and potentially superior function compared to canonical isoforms in the latest human gene database. By integrating structural predictions with expression and evolutionary evidence, this approach has demonstrated the potential of protein structure prediction as a tool for refining the annotation of the human genome. [68]

Databases

There is a collection of alternative splicing databases. [69] [70] [71] These databases are useful for finding genes having pre-mRNAs undergoing alternative splicing and alternative splicing events or to study the functional impact of alternative splicing.

See also

Related Research Articles

An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word intron is derived from the term intragenic region, i.e., a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons.

<span class="mw-page-title-main">RNA splicing</span> Process in molecular biology

RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing all the introns and splicing back together exons. For nuclear-encoded genes, splicing occurs in the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually needed to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing occurs in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). There exist self-splicing introns, that is, ribozymes that can catalyze their own excision from their parent RNA molecule. The process of transcription, splicing and translation is called gene expression, the central dogma of molecular biology.

<span class="mw-page-title-main">Spliceosome</span> Molecular machine that removes intron RNA from the primary transcript

A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specific proteins to form a small nuclear ribonucleoprotein complex, which in turn combines with other snRNPs to form a large ribonucleoprotein complex called a spliceosome. The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript. This process is generally referred to as splicing. An analogy is a film editor, who selectively cuts out irrelevant or incorrect material from the initial film and sends the cleaned-up version to the director for the final cut.

<span class="mw-page-title-main">Protein isoform</span> Forms of a protein produced from different genes

A protein isoform, or "protein variant", is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences. While many perform the same or similar biological roles, some isoforms have unique functions. A set of protein isoforms may be formed from alternative splicings, variable promoter usage, or other post-transcriptional modifications of a single gene; post-translational modifications are generally not considered. Through RNA splicing mechanisms, mRNA has the ability to select different protein-coding segments (exons) of a gene, or even different parts of exons from RNA to form different mRNA sequences. Each unique sequence produces a specific form of a protein.

Trans-splicing is a special form of RNA processing where exons from two different primary RNA transcripts are joined end to end and ligated. It is usually found in eukaryotes and mediated by the spliceosome, although some bacteria and archaea also have "half-genes" for tRNAs.

<span class="mw-page-title-main">SR protein</span>

SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are "S" and "R" respectively. SR proteins are ~200-600 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.

<span class="mw-page-title-main">Primary transcript</span> RNA produced by transcription

A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.

RNA-binding proteins are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein complexes. RBPs contain various structural motifs, such as RNA recognition motif (RRM), dsRNA binding domain, zinc finger and others. They are cytoplasmic and nuclear proteins. However, since most mature RNA is exported from the nucleus relatively quickly, most RBPs in the nucleus exist as complexes of protein and pre-mRNA called heterogeneous ribonucleoprotein particles (hnRNPs). RBPs have crucial roles in various cellular processes such as: cellular function, transport and localization. They especially play a major role in post-transcriptional control of RNAs, such as: splicing, polyadenylation, mRNA stabilization, mRNA localization and translation. Eukaryotic cells express diverse RBPs with unique RNA-binding activity and protein–protein interaction. According to the Eukaryotic RBP Database (EuRBPDB), there are 2961 genes encoding RBPs in humans. During evolution, the diversity of RBPs greatly increased with the increase in the number of introns. Diversity enabled eukaryotic cells to utilize RNA exons in various arrangements, giving rise to a unique RNP (ribonucleoprotein) for each RNA. Although RBPs have a crucial role in post-transcriptional regulation in gene expression, relatively few RBPs have been studied systematically.It has now become clear that RNA–RBP interactions play important roles in many biological processes among organisms.

<span class="mw-page-title-main">Post-transcriptional modification</span> RNA processing within a biological cell

Transcriptional modification or co-transcriptional modification is a set of biological processes common to most eukaryotic cells by which an RNA primary transcript is chemically altered following transcription from a gene to produce a mature, functional RNA molecule that can then leave the nucleus and perform any of a variety of different functions in the cell. There are many types of post-transcriptional modifications achieved through a diverse class of molecular mechanisms.

<span class="mw-page-title-main">Splice site mutation</span> Mutation at a location where intron splicing takes place

A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of abnormal proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be included. Introns are supposed to be removed, while the exons are expressed.

In molecular biology, an exonic splicing enhancer (ESE) is a DNA sequence motif consisting of 6 bases within an exon that directs, or enhances, accurate splicing of heterogeneous nuclear RNA (hnRNA) or pre-mRNA into messenger RNA (mRNA).

An exonic splicing silencer (ESS) is a short region of an exon and is a cis-regulatory element. A set of 103 hexanucleotides known as FAS-hex3 has been shown to be abundant in ESS regions. ESSs inhibit or silence splicing of the pre-mRNA and contribute to constitutive and alternate splicing. To elicit the silencing effect, ESSs recruit proteins that will negatively affect the core splicing machinery.

<span class="mw-page-title-main">RBM10</span> Protein-coding gene in the species Homo sapiens

RNA-binding motif 10 is a protein that is encoded by the RBM10 gene. This gene maps on the X chromosome at Xp11.23 in humans. RBM10 is a regulator of alternative splicing. Alternative splicing is a process associated with gene expression to produce multiple protein isoforms from a single gene, thereby creating functional diversity and cellular complexity. RBM10 influences the expression of many genes, participating in various cellular processes and pathways such as cell proliferation and apoptosis. Its mutations are associated with various human diseases such as TARP syndrome, an X-linked congenital disorder in males resulting in pre‐ or postnatal lethality, and various cancers in adults.

<span class="mw-page-title-main">RBM9</span> Protein-coding gene in the species Homo sapiens

RNA binding motif protein 9 (RBM9), also known as Rbfox2, is a protein which in humans is encoded by the RBM9 gene.

<span class="mw-page-title-main">RBFOX1</span> Protein-coding gene in the species Homo sapiens

Fox-1 homolog A, also known as ataxin 2-binding protein 1 (A2BP1) or hexaribonucleotide-binding protein 1 (HRNBP1) or RNA binding protein, fox-1 homolog (Rbfox1), is a protein that in humans is encoded by the RBFOX1 gene.

<span class="mw-page-title-main">BLCAP</span> Protein-coding gene in the species Homo sapiens

Bladder cancer-associated protein is a protein that in humans is encoded by the BLCAP gene.

De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome.

<span class="mw-page-title-main">Circular RNA</span> Type of RNA found in cells

In molecular biology, circular RNA is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop. In circular RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together. This feature confers numerous properties to circular RNA, many of which have only recently been identified.

<span class="mw-page-title-main">Minigene</span>

A minigene is a minimal gene fragment that includes an exon and the control regions necessary for the gene to express itself in the same way as a wild type gene fragment. This is a minigene in its most basic sense. More complex minigenes can be constructed containing multiple exons and intron(s). Minigenes provide a valuable tool for researchers evaluating splicing patterns both in vivo and in vitro biochemically assessed experiments. Specifically, minigenes are used as splice reporter vectors and act as a probe to determine which factors are important in splicing outcomes. They can be constructed to test the way both cis-regulatory elements and trans-regulatory elements affect gene expression.

Exitrons are produced through alternative splicing and have characteristics of both introns and exons, but are described as retained introns. Even though they are considered introns, which are typically cut out of pre mRNA sequences, there are significant problems that arise when exitrons are spliced out of these strands, with the most obvious result being altered protein structures and functions. They were first discovered in plants, but have recently been found in metazoan species as well.

References

  1. 1 2 3 4 5 6 7 8 Black DL (2003). "Mechanisms of alternative pre-messenger RNA splicing" (PDF). Annual Review of Biochemistry. 72 (1): 291–336. doi:10.1146/annurev.biochem.72.121801.161720. PMID   12626338. S2CID   23576288.
  2. 1 2 3 Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (December 2008). "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing". Nature Genetics. 40 (12): 1413–5. doi:10.1038/ng.259. PMID   18978789. S2CID   9228930.
  3. ↑ Bhuiyan SA, Ly S, Phan M, Huntington B, Hogan E, Liu CC, Liu J, Pavlidis P (2018). "Systematic evaluation of isoform function in literature reports of alternative splicing". BMC Genomics. 19 (1): 637. doi: 10.1186/s12864-018-5013-2 . PMC   6114036 . PMID   30153812. S2CID   52113302.
  4. ↑ Tress ML, Abascal F, Valencia A (2017). "Alternative splicing may not be the key to proteome complexity". Trends in Biochemical Sciences. 42 (2): 98–110. doi:10.1016/j.tibs.2016.08.008. PMC   6526280 . PMID   27712956.
  5. ↑ Chow LT, Gelinas RE, Broker TR, Roberts RJ (September 1977). "An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA". Cell. 12 (1): 1–8. doi:10.1016/0092-8674(77)90180-5. PMID   902310. S2CID   2099968.
  6. ↑ Berget SM, Moore C, Sharp PA (August 1977). "Spliced segments at the 5' terminus of adenovirus 2 late mRNA". Proceedings of the National Academy of Sciences of the United States of America. 74 (8): 3171–5. Bibcode:1977PNAS...74.3171B. doi: 10.1073/pnas.74.8.3171 . PMC   431482 . PMID   269380.
  7. 1 2 3 Leff SE, Rosenfeld MG, Evans RM (1986). "Complex transcriptional units: diversity in gene expression by alternative RNA processing". Annual Review of Biochemistry. 55 (1): 1091–117. doi:10.1146/annurev.bi.55.070186.005303. PMID   3017190.
  8. ↑ Chow LT, Broker TR (October 1978). "The spliced structures of adenovirus 2 fiber message and the other late mRNAs". Cell. 15 (2): 497–510. doi:10.1016/0092-8674(78)90019-3. PMID   719751. S2CID   44642349.
  9. ↑ Nevins JR, Darnell JE (December 1978). "Steps in the processing of Ad2 mRNA: poly(A)+ nuclear sequences are conserved and poly(A) addition precedes splicing". Cell. 15 (4): 1477–93. doi:10.1016/0092-8674(78)90071-5. PMID   729004. S2CID   39704416.
  10. ↑ Rosenfeld MG, Amara SG, Roos BA, Ong ES, Evans RM (March 1981). "Altered expression of the calcitonin gene associated with RNA polymorphism". Nature. 290 (5801): 63–5. Bibcode:1981Natur.290...63R. doi:10.1038/290063a0. PMID   7207587. S2CID   4318349.
  11. ↑ Rosenfeld MG, Lin CR, Amara SG, Stolarsky L, Roos BA, Ong ES, Evans RM (March 1982). "Calcitonin mRNA polymorphism: peptide switching associated with alternative RNA splicing events". Proceedings of the National Academy of Sciences of the United States of America. 79 (6): 1717–21. Bibcode:1982PNAS...79.1717R. doi: 10.1073/pnas.79.6.1717 . PMC   346051 . PMID   6952224.
  12. ↑ Maki R, Roeder W, Traunecker A, Sidman C, Wabl M, Raschke W, Tonegawa S (May 1981). "The role of DNA rearrangement and alternative RNA processing in the expression of immunoglobulin delta genes". Cell. 24 (2): 353–65. doi:10.1016/0092-8674(81)90325-1. PMID   6786756. S2CID   13208589.
  13. ↑ Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, et al. (June 2000). "Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity". Cell. 101 (6): 671–84. doi: 10.1016/S0092-8674(00)80878-8 . PMID   10892653. S2CID   13829976.
  14. 1 2 Westergren Jakobsson A, Segerman B, Wallerman O, Lind SB, Zhao H, Rubin CJ, et al. (November 2020). "The Human Adenovirus Type 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs". Journal of Virology. 95 (4). doi:10.1128/JVI.01869-20. PMC   7851563 . PMID   33239457.
  15. 1 2 3 4 5 Sammeth M, Foissac S, Guigó R (August 2008). Brent MR (ed.). "A general definition and nomenclature for alternative splicing events". PLOS Computational Biology. 4 (8): e1000147. Bibcode:2008PLSCB...4E0147S. doi: 10.1371/journal.pcbi.1000147 . PMC   2467475 . PMID   18688268.
  16. 1 2 3 4 5 6 7 8 Matlin AJ, Clark F, Smith CW (May 2005). "Understanding alternative splicing: towards a cellular code". Nature Reviews. Molecular Cell Biology. 6 (5): 386–98. doi:10.1038/nrm1645. PMID   15956978. S2CID   14883495.
  17. ↑ Ner-Gaon, Hadas; Halachmi, Ronit; Savaldi-Goldstein, Sigal; Rubin, Eitan; Ophir, Ron; Fluhr, Robert (2004). "Intron retention is a major phenomenon in alternative splicing in Arabidopsis". The Plant Journal. 39 (6): 877–885. doi: 10.1111/j.1365-313X.2004.02172.x . ISSN   1365-313X. PMID   15341630.
  18. ↑ Gao K, Masuda A, Matsuura T, Ohno K (April 2008). "Human branch point consensus sequence is yUnAy". Nucleic Acids Research. 36 (7): 2257–67. doi:10.1093/nar/gkn073. PMC   2367711 . PMID   18285363.
  19. ↑ Clark D (2005). Molecular biology. Amsterdam: Elsevier Academic Press. ISBN   978-0-12-175551-5.
  20. 1 2 3 Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG (July 2011). "Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes". Proceedings of the National Academy of Sciences of the United States of America. 108 (27): 11093–8. Bibcode:2011PNAS..10811093H. doi: 10.1073/pnas.1101135108 . PMC   3131313 . PMID   21685335.
  21. ↑ Warf MB, Berglund JA (March 2010). "Role of RNA structure in regulating pre-mRNA splicing". Trends in Biochemical Sciences. 35 (3): 169–78. doi:10.1016/j.tibs.2009.10.004. PMC   2834840 . PMID   19959365.
  22. 1 2 Reid DC, Chang BL, Gunderson SI, Alpert L, Thompson WA, Fairbrother WG (December 2009). "Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence". RNA. 15 (12): 2385–97. doi:10.1261/rna.1821809. PMC   2779669 . PMID   19861426.
  23. 1 2 3 4 Wang Z, Burge CB (May 2008). "Splicing regulation: from a parts list of regulatory elements to an integrated splicing code" (Free full text). RNA. 14 (5): 802–13. doi:10.1261/rna.876308. PMC   2327353 . PMID   18369186.
  24. 1 2 Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, et al. (May 2010). "Deciphering the splicing code". Nature. 465 (7294): 53–9. Bibcode:2010Natur.465...53B. doi:10.1038/nature09000. PMID   20445623. S2CID   2398858.
  25. ↑ Ke S, Zhang XH, Chasin LA (April 2008). "Positive selection acting on splicing motifs reflects compensatory evolution". Genome Research. 18 (4): 533–43. doi:10.1101/gr.070268.107. PMC   2279241 . PMID   18204002.
  26. ↑ Fairbrother WG, Holste D, Burge CB, Sharp PA (September 2004). "Single nucleotide polymorphism-based validation of exonic splicing enhancers". PLOS Biology. 2 (9): E268. doi: 10.1371/journal.pbio.0020268 . PMC   514884 . PMID   15340491.
  27. 1 2 Lynch KW, Maniatis T (August 1996). "Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer". Genes & Development. 10 (16): 2089–101. doi: 10.1101/gad.10.16.2089 . PMID   8769651.
  28. ↑ Graveley BR, Hertel KJ, Maniatis T (June 2001). "The role of U2AF35 and U2AF65 in enhancer-dependent splicing". RNA. 7 (6): 806–18. doi:10.1017/S1355838201010317. PMC   1370132 . PMID   11421359.
  29. ↑ Filipowicz E, Adegboyega P, Sanchez RL, Gatalica Z (February 2002). "Expression of CD95 (Fas) in sun-exposed human skin and cutaneous carcinomas". Cancer. 94 (3): 814–9. doi: 10.1002/cncr.10277 . PMID   11857317. S2CID   23772719.
  30. 1 2 Izquierdo JM, Majós N, Bonnal S, Martínez C, Castelo R, Guigó R, et al. (August 2005). "Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition". Molecular Cell. 19 (4): 475–84. doi: 10.1016/j.molcel.2005.06.015 . PMID   16109372.
  31. 1 2 Zahler AM, Damgaard CK, Kjems J, Caputi M (March 2004). "SC35 and heterogeneous nuclear ribonucleoprotein A/B proteins bind to a juxtaposed exonic splicing enhancer/exonic splicing silencer element to regulate HIV-1 tat exon 2 splicing". The Journal of Biological Chemistry. 279 (11): 10077–84. doi: 10.1074/jbc.M312743200 . PMID   14703516.
  32. ↑ Jacquenet S, Méreau A, Bilodeau PS, Damier L, Stoltzfus CM, Branlant C (November 2001). "A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H". The Journal of Biological Chemistry. 276 (44): 40464–75. doi: 10.1074/jbc.M104070200 . PMID   11526107.
  33. 1 2 3 Fackenthal JD, Godley LA (2008). "Aberrant RNA splicing and its functional consequences in cancer cells" (Free full text). Disease Models & Mechanisms. 1 (1): 37–42. doi:10.1242/dmm.000331. PMC   2561970 . PMID   19048051.
  34. ↑ Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, Oldfield CJ, et al. (May 2006). "Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms". Proceedings of the National Academy of Sciences of the United States of America. 103 (22): 8390–5. Bibcode:2006PNAS..103.8390R. doi: 10.1073/pnas.0507916103 . PMC   1482503 . PMID   16717195.
  35. ↑ Li HD, Menon R, Omenn GS, Guan Y (August 2014). "The emerging era of genomic data integration for analyzing splice isoform function". Trends in Genetics. 30 (8): 340–7. doi:10.1016/j.tig.2014.05.005. PMC   4112133 . PMID   24951248.
  36. 1 2 Eksi R, Li HD, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y (Nov 2013). "Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data". PLOS Computational Biology. 9 (11): e1003314. Bibcode:2013PLSCB...9E3314E. doi: 10.1371/journal.pcbi.1003314 . PMC   3820534 . PMID   24244129.
  37. ↑ Irimia M, Rukov JL, Penny D, Roy SW (October 2007). "Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing". BMC Evolutionary Biology. 7 (1): 188. Bibcode:2007BMCEE...7..188I. doi: 10.1186/1471-2148-7-188 . PMC   2082043 . PMID   17916237.
  38. ↑ Ewing B, Green P (June 2000). "Analysis of expressed sequence tags indicates 35,000 human genes". Nature Genetics. 25 (2): 232–4. doi:10.1038/76115. PMID   10835644. S2CID   19165121.
  39. ↑ Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C, et al. (June 2000). "Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence". Nature Genetics. 25 (2): 235–8. doi:10.1038/76118. PMID   10835645. S2CID   44052050.
  40. ↑ Brett D, Pospisil H, Valcárcel J, Reich J, Bork P (January 2002). "Alternative splicing and genome complexity". Nature Genetics. 30 (1): 29–30. doi:10.1038/ng803. PMID   11743582. S2CID   2724843.
  41. ↑ Kim E, Magen A, Ast G (2006). "Different levels of alternative splicing among eukaryotes". Nucleic Acids Research. 35 (1): 125–31. doi:10.1093/nar/gkl924. PMC   1802581 . PMID   17158149.
  42. ↑ López-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R (March 2005). "Are splicing mutations the most frequent cause of hereditary disease?". FEBS Letters. 579 (9): 1900–3. doi:10.1016/j.febslet.2005.02.047. PMID   15792793. S2CID   30174458.
  43. ↑ Ward AJ, Cooper TA (January 2010). "The pathobiology of splicing". The Journal of Pathology. 220 (2): 152–63. doi:10.1002/path.2649. PMC   2855871 . PMID   19918805.
  44. ↑ Skotheim RI, Nees M (2007). "Alternative splicing in cancer: noise, functional, or systematic?". The International Journal of Biochemistry & Cell Biology. 39 (7–8): 1432–49. doi:10.1016/j.biocel.2007.02.016. PMID   17416541.
  45. ↑ He C, Zhou F, Zuo Z, Cheng H, Zhou R (2009). Bauer JA (ed.). "A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis". PLOS ONE. 4 (3): e4732. Bibcode:2009PLoSO...4.4732H. doi: 10.1371/journal.pone.0004732 . PMC   2648985 . PMID   19266097.
  46. 1 2 Sveen A, Kilpinen S, Ruusulehto A, Lothe RA, Skotheim RI (May 2016). "Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes". Oncogene. 35 (19): 2413–27. doi: 10.1038/onc.2015.318 . PMID   26300000. S2CID   22943729.
  47. ↑ Omenn GS, Guan Y, Menon R (July 2014). "A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines". Journal of Proteomics. 107: 103–12. doi:10.1016/j.jprot.2014.04.012. PMC   4123867 . PMID   24802673.
  48. ↑ Sveen A, Johannessen B, Teixeira MR, Lothe RA, Skotheim RI (August 2014). "Transcriptome instability as a molecular pan-cancer characteristic of carcinomas". BMC Genomics. 15 (1): 672. doi: 10.1186/1471-2164-15-672 . PMC   3219073 . PMID   25109687.
  49. ↑ Sveen A, Agesen TH, Nesbakken A, Rognum TO, Lothe RA, Skotheim RI (May 2011). "Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival". Genome Medicine. 3 (5): 32. doi: 10.1186/gm248 . PMC   4137096 . PMID   21619627.
  50. ↑ Banaszak LG, Giudice V, Zhao X, Wu Z, Gao S, Hosokawa K, et al. (March 2018). "Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing". Blood Cells, Molecules & Diseases. 69: 10–22. doi:10.1016/j.bcmd.2017.12.002. PMC   6728079 . PMID   29324392.
  51. ↑ Kim E, Goren A, Ast G (January 2008). "Insights into the connection between cancer and alternative splicing". Trends in Genetics. 24 (1): 7–10. doi:10.1016/j.tig.2007.10.001. PMID   18054115.
  52. 1 2 Ghigna C, Giordano S, Shen H, Benvenuto F, Castiglioni F, Comoglio PM, et al. (December 2005). "Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene". Molecular Cell. 20 (6): 881–90. doi: 10.1016/j.molcel.2005.10.026 . PMID   16364913.
  53. ↑ Hui L, Zhang X, Wu X, Lin Z, Wang Q, Li Y, Hu G (April 2004). "Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment". Oncogene. 23 (17): 3013–23. doi: 10.1038/sj.onc.1207362 . PMID   15048092.
  54. ↑ Danckwardt S, Neu-Yilik G, Thermann R, Frede U, Hentze MW, Kulozik AE (March 2002). "Abnormally spliced beta-globin mRNAs: a single point mutation generates transcripts sensitive and insensitive to nonsense-mediated mRNA decay". Blood. 99 (5): 1811–6. doi: 10.1182/blood.V99.5.1811 . PMID   11861299. S2CID   17128174.
  55. ↑ Nestler EJ (December 2013). "Cellular basis of memory for addiction". Dialogues in Clinical Neuroscience. 15 (4): 431–43. doi:10.31887/DCNS.2013.15.4/enestler. PMC   3898681 . PMID   24459410. DESPITE THE IMPORTANCE OF NUMEROUS PSYCHOSOCIAL FACTORS, AT ITS CORE, DRUG ADDICTION INVOLVES A BIOLOGICAL PROCESS: the ability of repeated exposure to a drug of abuse to induce changes in a vulnerable brain that drive the compulsive seeking and taking of drugs, and loss of control over drug use, that define a state of addiction. ... A large body of literature has demonstrated that such ΔFosB induction in D1-type NAc neurons increases an animal's sensitivity to drug as well as natural rewards and promotes drug self-administration, presumably through a process of positive reinforcement
  56. ↑ Ruffle JK (November 2014). "Molecular neurobiology of addiction: what's all the (Δ)FosB about?". The American Journal of Drug and Alcohol Abuse. 40 (6): 428–37. doi:10.3109/00952990.2014.933840. PMID   25083822. S2CID   19157711. ΔFosB is an essential transcription factor implicated in the molecular and behavioral pathways of addiction following repeated drug exposure. The formation of ΔFosB in multiple brain regions, and the molecular pathway leading to the formation of AP-1 complexes is well understood. The establishment of a functional purpose for ΔFosB has allowed further determination as to some of the key aspects of its molecular cascades, involving effectors such as GluR2 (87,88), Cdk5 (93) and NFkB (100). Moreover, many of these molecular changes identified are now directly linked to the structural, physiological and behavioral changes observed following chronic drug exposure (60,95,97,102). New frontiers of research investigating the molecular roles of ΔFosB have been opened by epigenetic studies, and recent advances have illustrated the role of ΔFosB acting on DNA and histones, truly as a molecular switch (34). As a consequence of our improved understanding of ΔFosB in addiction, it is possible to evaluate the addictive potential of current medications (119), as well as use it as a biomarker for assessing the efficacy of therapeutic interventions (121,122,124). Some of these proposed interventions have limitations (125) or are in their infancy (75). However, it is hoped that some of these preliminary findings may lead to innovative treatments, which are much needed in addiction.
  57. ↑ Biliński P, Wojtyła A, Kapka-Skrzypczak L, Chwedorowicz R, Cyranka M, Studziński T (2012). "Epigenetic regulation in drug addiction". Annals of Agricultural and Environmental Medicine. 19 (3): 491–6. PMID   23020045. For these reasons, ΔFosB is considered a primary and causative transcription factor in creating new neural connections in the reward centre, prefrontal cortex, and other regions of the limbic system. This is reflected in the increased, stable and long-lasting level of sensitivity to cocaine and other drugs, and tendency to relapse even after long periods of abstinence. These newly constructed networks function very efficiently via new pathways as soon as drugs of abuse are further taken
  58. ↑ Olsen CM (December 2011). "Natural rewards, neuroplasticity, and non-drug addictions". Neuropharmacology. 61 (7): 1109–22. doi:10.1016/j.neuropharm.2011.03.010. PMC   3139704 . PMID   21459101.
  59. ↑ Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (January 2011). "Epigenetics in alternative pre-mRNA splicing". Cell. 144 (1): 16–26. doi:10.1016/j.cell.2010.11.056. PMC   3038581 . PMID   21215366.
  60. ↑ Strømme JM, Johannessen B, Skotheim RI (2023). "Deviating alternative splicing as a molecular subtype of microsatellite stable colorectal cancer". JCO Clinical Cancer Informatics. 7 (7): e2200159. doi: 10.1200/CCI.22.00159 . hdl: 10852/108838 . PMID   36821799.
  61. ↑ Taggart AJ, DeSimone AM, Shih JS, Filloux ME, Fairbrother WG (June 2012). "Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo". Nature Structural & Molecular Biology. 19 (7): 719–21. doi:10.1038/nsmb.2327. PMC   3465671 . PMID   22705790.
  62. ↑ Fairbrother WG, Yeh RF, Sharp PA, Burge CB (August 2002). "Predictive identification of exonic splicing enhancers in human genes". Science. 297 (5583): 1007–13. Bibcode:2002Sci...297.1007F. doi: 10.1126/science.1073774 . PMID   12114529. S2CID   8689111.
  63. ↑ Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, et al. (December 2004). "Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform". Molecular Cell. 16 (6): 929–41. doi: 10.1016/j.molcel.2004.12.004 . PMID   15610736.
  64. 1 2 David CJ, Manley JL (February 2008). "The search for alternative splicing regulators: new approaches offer a path to a splicing code". Genes & Development. 22 (3): 279–85. doi:10.1101/gad.1643108. PMC   2731647 . PMID   18245441.
  65. ↑ Watkins KH, Stewart A, Fairbrother W (December 2009). "A rapid high-throughput method for mapping ribonucleoproteins (RNPs) on human pre-mRNA". Journal of Visualized Experiments. 34 (34): 1622. doi:10.3791/1622. PMC   3152247 . PMID   19956082.
  66. ↑ Tuerk C, Gold L (August 1990). "Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase". Science. 249 (4968): 505–10. Bibcode:1990Sci...249..505T. doi:10.1126/science.2200121. PMID   2200121.
  67. ↑ Chang B, Levin J, Thompson WA, Fairbrother WG (March 2010). "High-throughput binding analysis determines the binding specificity of ASF/SF2 on alternatively spliced human pre-mRNAs". Combinatorial Chemistry & High Throughput Screening. 13 (3): 242–52. doi:10.2174/138620710790980522. PMC   3427726 . PMID   20015017.
  68. ↑ Sommer, Markus J.; Cha, Sooyoung; Varabyou, Ales; Rincon, Natalia; Park, Sukhwan; Minkin, Ilia; Pertea, Mihaela; Steinegger, Martin; Salzberg, Steven L. (2022-12-15). "Structure-guided isoform identification for the human transcriptome". eLife. 11: e82556. doi: 10.7554/eLife.82556 . PMC   9812405 . PMID   36519529.
  69. ↑ Tapial J, Ha KC, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, et al. (October 2017). "An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms". Genome Research. 27 (10): 1759–1768. doi:10.1101/gr.220962.117. PMC   5630039 . PMID   28855263.
  70. ↑ Louadi Z, Yuan K, Gress A, Tsoy O, Kalinina OV, Baumbach J, et al. (January 2021). "DIGGER: exploring the functional role of alternative splicing in protein interactions". Nucleic Acids Research. 49 (D1): D309–D318. doi: 10.1093/nar/gkaa768 . PMC   7778957 . PMID   32976589.
  71. ↑ Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, et al. (January 2013). "APPRIS: annotation of principal and alternative splice isoforms". Nucleic Acids Research. 41 (Database issue): D110-7. doi:10.1093/nar/gks1058. PMC   3531113 . PMID   23161672.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.