Polyadenylation

Last updated

Typical structure of a mature eukaryotic mRNA MRNA structure.svg
Typical structure of a mature eukaryotic mRNA

Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. In many bacteria, the poly(A) tail promotes degradation of the mRNA. It, therefore, forms part of the larger process of gene expression.

Contents

The process of polyadenylation begins as the transcription of a gene terminates. The 3′-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the RNA's 3′ end. In some genes these proteins add a poly(A) tail at one of several possible sites. Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing. [1]

The poly(A) tail is important for the nuclear export, translation and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded. [2] However, in a few cell types, mRNAs with short poly(A) tails are stored for later activation by re-polyadenylation in the cytosol. [3] In contrast, when polyadenylation occurs in bacteria, it promotes RNA degradation. [4] This is also sometimes the case for eukaryotic non-coding RNAs. [5] [6]

mRNA molecules in both prokaryotes and eukaryotes have polyadenylated 3′-ends, with the prokaryotic poly(A) tails generally shorter and fewer mRNA molecules polyadenylated. [7]

Background on RNA

Chemical structure of RNA. The sequence of bases differs between RNA molecules. RNA chemical structure adenine.JPG
Chemical structure of RNA. The sequence of bases differs between RNA molecules.

RNAs are a type of large biological molecules, whose individual building blocks are called nucleotides. The name poly(A) tail (for polyadenylic acid tail) [8] reflects the way RNA nucleotides are abbreviated, with a letter for the base the nucleotide contains (A for adenine, C for cytosine, G for guanine and U for uracil). RNAs are produced (transcribed) from a DNA template. By convention, RNA sequences are written in a 5′ to 3′ direction. The 5′ end is the part of the RNA molecule that is transcribed first, and the 3′ end is transcribed last. The 3′ end is also where the poly(A) tail is found on polyadenylated RNAs. [1] [9]

Messenger RNA (mRNA) is RNA that has a coding region that acts as a template for protein synthesis (translation). The rest of the mRNA, the untranslated regions, tune how active the mRNA is. [10] There are also many RNAs that are not translated, called non-coding RNAs. Like the untranslated regions, many of these non-coding RNAs have regulatory roles. [11]

Nuclear polyadenylation

Function

In nuclear polyadenylation, a poly(A) tail is added to an RNA at the end of transcription. On mRNAs, the poly(A) tail protects the mRNA molecule from enzymatic degradation in the cytoplasm and aids in transcription termination, export of the mRNA from the nucleus, and translation. [2] Almost all eukaryotic mRNAs are polyadenylated, [12] with the exception of animal replication-dependent histone mRNAs. [13] These are the only mRNAs in eukaryotes that lack a poly(A) tail, ending instead in a stem-loop structure followed by a purine-rich sequence, termed histone downstream element, that directs where the RNA is cut so that the 3′ end of the histone mRNA is formed. [14]

Many eukaryotic non-coding RNAs are always polyadenylated at the end of transcription. There are small RNAs where the poly(A) tail is seen only in intermediary forms and not in the mature RNA as the ends are removed during processing, the notable ones being microRNAs. [15] [16] But, for many long noncoding RNAs  – a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist, which mediates X chromosome inactivation  – a poly(A) tail is part of the mature RNA. [17]

Mechanism

Proteins involved: [12] [18]

CPSF: cleavage/polyadenylation specificity factor
CstF: cleavage stimulation factor
PAP: polyadenylate polymerase
PABII: polyadenylate binding protein 2
CFI: cleavage factor I
CFII: cleavage factor II

The processive polyadenylation complex in the nucleus of eukaryotes works on products of RNA polymerase II, such as precursor mRNA. Here, a multi-protein complex (see components on the right) [18] cleaves the 3′-most part of a newly produced RNA and polyadenylates the end produced by this cleavage. The cleavage is catalysed by the enzyme CPSF [13] [18] and occurs 10–30 nucleotides downstream of its binding site. [19] This site often has the polyadenylation signal sequence AAUAAA on the RNA, but variants of it that bind more weakly to CPSF exist. [18] [20] Two other proteins add specificity to the binding to an RNA: CstF and CFI. CstF binds to a GU-rich region further downstream of CPSF's site. [21] CFI recognises a third site on the RNA (a set of UGUAA sequences in mammals [22] [23] [24] ) and can recruit CPSF even if the AAUAAA sequence is missing. [25] [26] The polyadenylation signal – the sequence motif recognised by the RNA cleavage complex – varies between groups of eukaryotes. Most human polyadenylation sites contain the AAUAAA sequence, [21] but this sequence is less common in plants and fungi. [27]

The RNA is typically cleaved before transcription termination, as CstF also binds to RNA polymerase II. [28] Through a poorly understood mechanism (as of 2002), it signals for RNA polymerase II to slip off of the transcript. [29] Cleavage also involves the protein CFII, though it is unknown how. [30] The cleavage site associated with a polyadenylation signal can vary up to some 50 nucleotides. [31]

When the RNA is cleaved, polyadenylation starts, catalysed by polyadenylate polymerase. Polyadenylate polymerase builds the poly(A) tail by adding adenosine monophosphate units from adenosine triphosphate to the RNA, cleaving off pyrophosphate. [32] Another protein, PAB2, binds to the new, short poly(A) tail and increases the affinity of polyadenylate polymerase for the RNA. When the poly(A) tail is approximately 250 nucleotides long the enzyme can no longer bind to CPSF and polyadenylation stops, thus determining the length of the poly(A) tail. [33] [34] CPSF is in contact with RNA polymerase II, allowing it to signal the polymerase to terminate transcription. [35] [36] When RNA polymerase II reaches a "termination sequence" (⁵'TTTATT3' on the DNA template and ⁵'AAUAAA3' on the primary transcript), the end of transcription is signaled. [37] The polyadenylation machinery is also physically linked to the spliceosome, a complex that removes introns from RNAs. [26]

Downstream effects

The poly(A) tail acts as the binding site for poly(A)-binding protein. Poly(A)-binding protein promotes export from the nucleus and translation, and inhibits degradation. [38] This protein binds to the poly(A) tail prior to mRNA export from the nucleus and in yeast also recruits poly(A) nuclease, an enzyme that shortens the poly(A) tail and allows the export of the mRNA. Poly(A)-binding protein is exported to the cytoplasm with the RNA. mRNAs that are not exported are degraded by the exosome. [39] [40] Poly(A)-binding protein also can bind to, and thus recruit, several proteins that affect translation, [39] one of these is initiation factor-4G, which in turn recruits the 40S ribosomal subunit. [41] However, a poly(A) tail is not required for the translation of all mRNAs. [42] Further, poly(A) tailing (oligo-adenylation) can determine the fate of RNA molecules that are usually not poly(A)-tailed (such as (small) non-coding (sn)RNAs etc.) and thereby induce their RNA decay. [43]

Deadenylation

In eukaryotic somatic cells, the poly(A) tails of most mRNAs in the cytoplasm gradually get shorter, and mRNAs with shorter poly(A) tail are translated less and degraded sooner. [44] However, it can take many hours before an mRNA is degraded. [45] This deadenylation and degradation process can be accelerated by microRNAs complementary to the 3′ untranslated region of an mRNA. [46] In immature egg cells, mRNAs with shortened poly(A) tails are not degraded, but are instead stored and translationally inactive. These short tailed mRNAs are activated by cytoplasmic polyadenylation after fertilisation, during egg activation. [47]

In animals, poly(A) ribonuclease (PARN) can bind to the 5′ cap and remove nucleotides from the poly(A) tail. The level of access to the 5′ cap and poly(A) tail is important in controlling how soon the mRNA is degraded. PARN deadenylates less if the RNA is bound by the initiation factors 4E (at the 5′ cap) and 4G (at the poly(A) tail), which is why translation reduces deadenylation. The rate of deadenylation may also be regulated by RNA-binding proteins. Additionally, RNA triple helix structures and RNA motifs such as the poly(A) tail 3’ end binding pocket retard deadenylation process and inhibit poly(A) tail removal. [48] Once the poly(A) tail is removed, the decapping complex removes the 5′ cap, leading to a degradation of the RNA. Several other proteins are involved in deadenylation in budding yeast and human cells, most notably the CCR4-Not complex. [49]

Cytoplasmic polyadenylation

There is polyadenylation in the cytosol of some animal cell types, namely in the germline, during early embryogenesis and in post-synaptic sites of nerve cells. This lengthens the poly(A) tail of an mRNA with a shortened poly(A) tail, so that the mRNA will be translated. [44] [50] These shortened poly(A) tails are often less than 20 nucleotides, and are lengthened to around 80–150 nucleotides. [3]

In the early mouse embryo, cytoplasmic polyadenylation of maternal RNAs from the egg cell allows the cell to survive and grow even though transcription does not start until the middle of the 2-cell stage (4-cell stage in human). [51] [52] In the brain, cytoplasmic polyadenylation is active during learning and could play a role in long-term potentiation, which is the strengthening of the signal transmission from a nerve cell to another in response to nerve impulses and is important for learning and memory formation. [3] [53]

Cytoplasmic polyadenylation requires the RNA-binding proteins CPSF and CPEB, and can involve other RNA-binding proteins like Pumilio. [54] Depending on the cell type, the polymerase can be the same type of polyadenylate polymerase (PAP) that is used in the nuclear process, or the cytoplasmic polymerase GLD-2. [55]

Results of using different polyadenylation sites on the same gene Alternative polyadenylation.svg
Results of using different polyadenylation sites on the same gene

Alternative polyadenylation

Many protein-coding genes have more than one polyadenylation site, so a gene can code for several mRNAs that differ in their 3′ end. [27] [56] [57] The 3’ region of a transcript contains many polyadenylation signals (PAS). When more proximal (closer towards 5’ end) PAS sites are utilized, this shortens the length of the 3’ untranslated region (3' UTR) of a transcript. [58] Studies in both humans and flies have shown tissue specific APA. With neuronal tissues preferring distal PAS usage, leading to longer 3’ UTRs and testis tissues preferring proximal PAS leading to shorter 3’ UTRs. [59] [60] Studies have shown there is a correlation between a gene's conservation level and its tendency to do alternative polyadenylation, with highly conserved genes exhibiting more APA. Similarly, highly expressed genes follow this same pattern. [61] Ribo-sequencing data (sequencing of only mRNAs inside ribosomes) has shown that mRNA isoforms with shorter 3’ UTRs are more likely to be translated. [58]

Since alternative polyadenylation changes the length of the 3' UTR, [62] it can also change which binding sites are available for microRNAs in the 3′ UTR. [19] [63] MicroRNAs tend to repress translation and promote degradation of the mRNAs they bind to, although there are examples of microRNAs that stabilise transcripts. [64] [65] Alternative polyadenylation can also shorten the coding region, thus making the mRNA code for a different protein, [66] [67] but this is much less common than just shortening the 3′ untranslated region. [27]

The choice of poly(A) site can be influenced by extracellular stimuli and depends on the expression of the proteins that take part in polyadenylation. [68] [69] For example, the expression of CstF-64, a subunit of cleavage stimulatory factor (CstF), increases in macrophages in response to lipopolysaccharides (a group of bacterial compounds that trigger an immune response). This results in the selection of weak poly(A) sites and thus shorter transcripts. This removes regulatory elements in the 3′ untranslated regions of mRNAs for defense-related products like lysozyme and TNF-α. These mRNAs then have longer half-lives and produce more of these proteins. [68] RNA-binding proteins other than those in the polyadenylation machinery can also affect whether a polyadenylation site is used, [70] [71] [72] [73] as can DNA methylation near the polyadenylation signal. [74] In addition, numerous other components involved in transcription, splicing or other mechanisms regulating RNA biology can affect APA. [75]

Tagging for degradation in eukaryotes

For many non-coding RNAs, including tRNA, rRNA, snRNA, and snoRNA, polyadenylation is a way of marking the RNA for degradation, at least in yeast. [76] This polyadenylation is done in the nucleus by the TRAMP complex, which maintains a tail that is around 4 nucleotides long to the 3′ end. [77] [78] The RNA is then degraded by the exosome. [79] Poly(A) tails have also been found on human rRNA fragments, both the form of homopolymeric (A only) and heterpolymeric (mostly A) tails. [80]

In prokaryotes and organelles

Polyadenylation in bacteria helps polynucleotide phosphorylase degrade past secondary structure Bacterial PNPase and polyadenylation.svg
Polyadenylation in bacteria helps polynucleotide phosphorylase degrade past secondary structure

In many bacteria, both mRNAs and non-coding RNAs can be polyadenylated. This poly(A) tail promotes degradation by the degradosome, which contains two RNA-degrading enzymes: polynucleotide phosphorylase and RNase E. Polynucleotide phosphorylase binds to the 3′ end of RNAs and the 3′ extension provided by the poly(A) tail allows it to bind to the RNAs whose secondary structure would otherwise block the 3′ end. Successive rounds of polyadenylation and degradation of the 3′ end by polynucleotide phosphorylase allows the degradosome to overcome these secondary structures. The poly(A) tail can also recruit RNases that cut the RNA in two. [81] These bacterial poly(A) tails are about 30 nucleotides long. [82]

In as different groups as animals and trypanosomes, the mitochondria contain both stabilising and destabilising poly(A) tails. Destabilising polyadenylation targets both mRNA and noncoding RNAs. The poly(A) tails are 43 nucleotides long on average. The stabilising ones start at the stop codon, and without them the stop codon (UAA) is not complete as the genome only encodes the U or UA part. Plant mitochondria have only destabilising polyadenylation. Mitochondrial polyadenylation has never been observed in either budding or fission yeast. [83] [84]

While many bacteria and mitochondria have polyadenylate polymerases, they also have another type of polyadenylation, performed by polynucleotide phosphorylase itself. This enzyme is found in bacteria, [85] mitochondria, [86] plastids [87] and as a constituent of the archaeal exosome (in those archaea that have an exosome). [88] It can synthesise a 3′ extension where the vast majority of the bases are adenines. Like in bacteria, polyadenylation by polynucleotide phosphorylase promotes degradation of the RNA in plastids [89] and likely also archaea. [83]

Evolution

Although polyadenylation is seen in almost all organisms, it is not universal. [7] [90] However, the wide distribution of this modification and the fact that it is present in organisms from all three domains of life implies that the last universal common ancestor of all living organisms, it is presumed, had some form of polyadenylation system. [82] A few organisms do not polyadenylate mRNA, which implies that they have lost their polyadenylation machineries during evolution. Although no examples of eukaryotes that lack polyadenylation are known, mRNAs from the bacterium Mycoplasma gallisepticum and the salt-tolerant archaean Haloferax volcanii lack this modification. [91] [92]

The most ancient polyadenylating enzyme is polynucleotide phosphorylase. This enzyme is part of both the bacterial degradosome and the archaeal exosome, [93] two closely related complexes that recycle RNA into nucleotides. This enzyme degrades RNA by attacking the bond between the 3′-most nucleotides with a phosphate, breaking off a diphosphate nucleotide. This reaction is reversible, and so the enzyme can also extend RNA with more nucleotides. The heteropolymeric tail added by polynucleotide phosphorylase is very rich in adenine. The choice of adenine is most likely the result of higher ADP concentrations than other nucleotides as a result of using ATP as an energy currency, making it more likely to be incorporated in this tail in early lifeforms. It has been suggested that the involvement of adenine-rich tails in RNA degradation prompted the later evolution of polyadenylate polymerases (the enzymes that produce poly(A) tails with no other nucleotides in them). [94]

Polyadenylate polymerases are not as ancient. They have separately evolved in both bacteria and eukaryotes from CCA-adding enzyme, which is the enzyme that completes the 3′ ends of tRNAs. Its catalytic domain is homologous to that of other polymerases. [79] It is presumed that the horizontal transfer of bacterial CCA-adding enzyme to eukaryotes allowed the archaeal-like CCA-adding enzyme to switch function to a poly(A) polymerase. [82] Some lineages, like archaea and cyanobacteria, never evolved a polyadenylate polymerase. [94]

Polyadenylate tails are observed in several RNA viruses, including Influenza A, [95] Coronavirus, [96] Alfalfa mosaic virus, [97] and Duck Hepatitis A. [98] Some viruses, such as HIV-1 and Poliovirus, inhibit the cell's poly-A binding protein (PABPC1) in order to emphasize their own genes' expression over the host cell's. [99]

History

Poly(A)polymerase was first identified in 1960 as an enzymatic activity in extracts made from cell nuclei that could polymerise ATP, but not ADP, into polyadenine. [100] [101] Although identified in many types of cells, this activity had no known function until 1971, when poly(A) sequences were found in mRNAs. [102] [103] The only function of these sequences was thought at first to be protection of the 3′ end of the RNA from nucleases, but later the specific roles of polyadenylation in nuclear export and translation were identified. The polymerases responsible for polyadenylation were first purified and characterized in the 1960s and 1970s, but the large number of accessory proteins that control this process were discovered only in the early 1990s. [102]

See also

Related Research Articles

<span class="mw-page-title-main">Messenger RNA</span> RNA that is read by the ribosome to produce a protein

In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.

<span class="mw-page-title-main">Three prime untranslated region</span> Sequence at the 3 end of messenger RNA that does not code for product

In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. The 3′-UTR often contains regulatory regions that post-transcriptionally influence gene expression.

In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.

In molecular biology, the five-prime cap is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation of stable and mature messenger RNA able to undergo translation during protein synthesis. Mitochondrial mRNA and chloroplastic mRNA are not capped.

<span class="mw-page-title-main">Exonuclease</span> Class of enzymes; type of nuclease

Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is the endonuclease, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA: 5′ to 3′ exonuclease (Xrn1), which is a dependent decapping protein; 3′ to 5′ exonuclease, an independent protein; and poly(A)-specific 3′ to 5′ exonuclease.

<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.

Cleavage and polyadenylation specificity factor (CPSF) is involved in the cleavage of the 3' signaling region from a newly synthesized pre-messenger RNA (pre-mRNA) molecule in the process of gene transcription. In eukaryotes, messenger RNA precursors (pre-mRNA) are transcribed in the nucleus from DNA by the enzyme, RNA polymerase II. The pre-mRNA must undergo post-transcriptional modifications, forming mature RNA (mRNA), before they can be transported into the cytoplasm for translation into proteins. The post-transcriptional modifications are: the addition of a 5' m7G cap, splicing of intronic sequences, and 3' cleavage and polyadenylation.

<span class="mw-page-title-main">Exosome complex</span> Protein complex that degrades RNA

The exosome complex is a multi-protein intracellular complex capable of degrading various types of RNA molecules. Exosome complexes are found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.

<span class="mw-page-title-main">Eukaryotic transcription</span> Transcription is heterocatalytic function of DNA

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes comes in three variations, each translating a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.

<span class="mw-page-title-main">Polynucleotide phosphorylase</span> Class of enzymes

Polynucleotide Phosphorylase (PNPase) is a bifunctional enzyme with a phosphorolytic 3' to 5' exoribonuclease activity and a 3'-terminal oligonucleotide polymerase activity. That is, it dismantles the RNA chain starting at the 3' end and working toward the 5' end. It also synthesizes long, highly heteropolymeric tails in vivo. It accounts for all of the observed residual polyadenylation in strains of Escherichia coli missing the normal polyadenylation enzyme. Discovered by Marianne Grunberg-Manago working in Severo Ochoa's lab in 1955, the RNA-polymerization activity of PNPase was initially believed to be responsible for DNA-dependent synthesis of messenger RNA, a notion that was disproven by the late 1950s.

<span class="mw-page-title-main">Poly(A)-binding protein</span> RNA binding protein

Poly(A)-binding protein is an RNA-binding protein which triggers the binding of eukaryotic initiation factor 4 complex (eIF4G) directly to the poly(A) tail of mRNA which is 200-250 nucleotides long. The poly(A) tail is located on the 3' end of mRNA and was discovered by Mary Edmonds, who also characterized the poly-A polymerase enzyme that generates the poly(a) tail. The binding protein is also involved in mRNA precursors by helping polyadenylate polymerase add the poly(A) nucleotide tail to the pre-mRNA before translation. The nuclear isoform selectively binds to around 50 nucleotides and stimulates the activity of polyadenylate polymerase by increasing its affinity towards RNA. Poly(A)-binding protein is also present during stages of mRNA metabolism including nonsense-mediated decay and nucleocytoplasmic trafficking. The poly(A)-binding protein may also protect the tail from degradation and regulate mRNA production. Without these two proteins in-tandem, then the poly(A) tail would not be added and the RNA would degrade quickly.

The cytoplasmic polyadenylation element (CPE) is a sequence element found in the 3' untranslated region of messenger RNA. While several sequence elements are known to regulate cytoplasmic polyadenylation, CPE is the best characterized. The most common CPE sequence is UUUUAU, though there are other variations. Binding of CPE binding protein to this region promotes the extension of the existing polyadenine tail and, in general, activation of the mRNA for protein translation. This elongation occurs after the mRNA has been exported from the nucleus to the cytoplasm. A longer poly(A) tail attracts more cytoplasmic polyadenine binding proteins (PABPs) which interact with several other cytoplasmic proteins that encourage the mRNA and the ribosome to associate. The lengthening of the poly(A) tail thus has a role in increasing translational efficiency of the mRNA. The polyadenine tails are extended from approximately 40 bases to 150 bases.

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

TRAMP complex is a multiprotein, heterotrimeric complex having distributive polyadenylation activity and identifies wide varieties of RNAs produced by polymerases. It was originally discovered in Saccharomycescerevisiae by LaCava et al., Vanacova et al. and Wyers et al. in 2005.

The degradosome is a multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase.

<span class="mw-page-title-main">PABPC1</span> Protein-coding gene in the species Homo sapiens

Polyadenylate-binding protein 1 is a protein that in humans is encoded by the PABPC1 gene. The protein PABP1 binds mRNA and facilitates a variety of functions such as transport into and out of the nucleus, degradation, translation, and stability. There are two separate PABP1 proteins, one which is located in the nucleus (PABPN1) and the other which is found in the cytoplasm (PABPC1). The location of PABP1 affects the role of that protein and its function with RNA.

<span class="mw-page-title-main">Polynucleotide adenylyltransferase</span> Class of enzymes

In enzymology, a polynucleotide adenylyltransferase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Poly(A)-specific ribonuclease</span> Protein-coding gene in the species Homo sapiens

Poly(A)-specific ribonuclease (PARN), also known as polyadenylate-specific ribonuclease or deadenylating nuclease (DAN), is an enzyme that in humans is encoded by the PARN gene.

<span class="mw-page-title-main">PAPOLA</span> Protein-coding gene in humans

Poly(A) polymerase alpha is an enzyme that in humans is encoded by the PAPOLA gene.

Post-transcriptional regulation is the control of gene expression at the RNA level. It occurs once the RNA polymerase has been attached to the gene's promoter and is synthesizing the nucleotide sequence. Therefore, as the name indicates, it occurs between the transcription phase and the translation phase of gene expression. These controls are critical for the regulation of many genes across human tissues. It also plays a big role in cell physiology, being implicated in pathologies such as cancer and neurodegenerative diseases.

<span class="mw-page-title-main">GLD-2</span> Protein-coding gene in the species Homo sapiens

GLD-2 is a cytoplasmic poly(A) polymerase (cytoPAPs) which adds successive AMP monomers to the 3’ end of specific RNAs, forming a poly(A) tail, which is a process known as polyadenylation.

References

  1. 1 2 Proudfoot NJ, Furger A, Dye MJ (February 2002). "Integrating mRNA processing with transcription". Cell. 108 (4): 501–12. doi: 10.1016/S0092-8674(02)00617-7 . PMID   11909521. S2CID   478260.
  2. 1 2 Guhaniyogi J, Brewer G (March 2001). "Regulation of mRNA stability in mammalian cells". Gene. 265 (1–2): 11–23. doi:10.1016/S0378-1119(01)00350-X. PMC   3340483 . PMID   11255003.
  3. 1 2 3 Richter JD (June 1999). "Cytoplasmic polyadenylation in development and beyond". Microbiology and Molecular Biology Reviews. 63 (2): 446–56. doi:10.1128/MMBR.63.2.446-456.1999. PMC   98972 . PMID   10357857.
  4. ↑ Steege DA (August 2000). "Emerging features of mRNA decay in bacteria". RNA. 6 (8): 1079–90. doi:10.1017/S1355838200001023. PMC   1369983 . PMID   10943888.
  5. ↑ Zhuang Y, Zhang H, Lin S (June 2013). "Polyadenylation of 18S rRNA in algae(1)". Journal of Phycology. 49 (3): 570–9. Bibcode:2013JPcgy..49..570Z. doi:10.1111/jpy.12068. PMID   27007045. S2CID   19863143.
  6. ↑ Anderson JT (August 2005). "RNA turnover: unexpected consequences of being tailed". Current Biology. 15 (16): R635-8. Bibcode:2005CBio...15.R635A. doi: 10.1016/j.cub.2005.08.002 . PMID   16111937. S2CID   19003617.
  7. 1 2 Sarkar N (June 1997). "Polyadenylation of mRNA in prokaryotes". Annual Review of Biochemistry. 66 (1): 173–97. doi:10.1146/annurev.biochem.66.1.173. PMID   9242905.
  8. ↑ Stevens A (1963). "Ribonucleic Acids-Biosynthesis and Degradation". Annual Review of Biochemistry. 32: 15–42. doi:10.1146/annurev.bi.32.070163.000311. PMID   14140701.
  9. ↑ Lehninger AL, Nelson DL, Cox MM, eds. (1993). Principles of biochemistry (2nd ed.). New York: Worth. ISBN   978-0-87901-500-8.[ page needed ]
  10. ↑ Abaza I, Gebauer F (March 2008). "Trading translation with RNA-binding proteins". RNA. 14 (3): 404–9. doi:10.1261/rna.848208. PMC   2248257 . PMID   18212021.
  11. ↑ Mattick JS, Makunin IV (April 2006). "Non-coding RNA". Human Molecular Genetics. 15 Spec No 1 (90001): R17-29. doi: 10.1093/hmg/ddl046 . PMID   16651366.
  12. 1 2 Hunt AG, Xu R, Addepalli B, Rao S, Forbes KP, Meeks LR, Xing D, Mo M, Zhao H, Bandyopadhyay A, Dampanaboina L, Marion A, Von Lanken C, Li QQ (May 2008). "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling". BMC Genomics. 9: 220. doi: 10.1186/1471-2164-9-220 . PMC   2391170 . PMID   18479511.
  13. 1 2 Dávila López M, Samuelsson T (January 2008). "Early evolution of histone mRNA 3′ end processing". RNA. 14 (1): 1–10. doi:10.1261/rna.782308. PMC   2151031 . PMID   17998288.
  14. ↑ Marzluff WF, Gongidi P, Woods KR, Jin J, Maltais LJ (November 2002). "The human and mouse replication-dependent histone genes". Genomics. 80 (5): 487–98. doi:10.1016/S0888-7543(02)96850-3. PMID   12408966.
  15. ↑ Saini HK, Griffiths-Jones S, Enright AJ (November 2007). "Genomic analysis of human microRNA transcripts". Proceedings of the National Academy of Sciences of the United States of America. 104 (45): 17719–24. Bibcode:2007PNAS..10417719S. doi: 10.1073/pnas.0703890104 . PMC   2077053 . PMID   17965236.
  16. ↑ Yoshikawa M, Peragine A, Park MY, Poethig RS (September 2005). "A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis". Genes & Development. 19 (18): 2164–75. doi:10.1101/gad.1352605. PMC   1221887 . PMID   16131612.
  17. ↑ Amaral PP, Mattick JS (August 2008). "Noncoding RNA in development". Mammalian Genome. 19 (7–8): 454–92. doi:10.1007/s00335-008-9136-7. PMID   18839252. S2CID   206956408.
  18. 1 2 3 4 Bienroth S, Keller W, Wahle E (February 1993). "Assembly of a processive messenger RNA polyadenylation complex". The EMBO Journal. 12 (2): 585–94. doi:10.1002/j.1460-2075.1993.tb05690.x. PMC   413241 . PMID   8440247.
  19. 1 2 Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey JR, MacDonald CC, Graber JH (2006). "Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis". Nucleic Acids Research. 35 (1): 234–46. doi:10.1093/nar/gkl919. PMC   1802579 . PMID   17158511.
  20. ↑ Lutz CS (October 2008). "Alternative polyadenylation: a twist on mRNA 3′ end formation". ACS Chemical Biology. 3 (10): 609–17. doi:10.1021/cb800138w. PMID   18817380.
  21. 1 2 Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D (July 2000). "Patterns of variant polyadenylation signal usage in human genes". Genome Research. 10 (7): 1001–10. doi:10.1101/gr.10.7.1001. PMC   310884 . PMID   10899149.
  22. ↑ Brown KM, Gilmartin GM (December 2003). "A mechanism for the regulation of pre-mRNA 3′ processing by human cleavage factor Im". Molecular Cell. 12 (6): 1467–76. doi: 10.1016/S1097-2765(03)00453-2 . PMID   14690600.
  23. ↑ Yang Q, Gilmartin GM, Doublié S (June 2010). "Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3′ processing". Proceedings of the National Academy of Sciences of the United States of America. 107 (22): 10062–7. Bibcode:2010PNAS..10710062Y. doi: 10.1073/pnas.1000848107 . PMC   2890493 . PMID   20479262.
  24. ↑ Yang Q, Coseno M, Gilmartin GM, Doublié S (March 2011). "Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping". Structure. 19 (3): 368–77. doi:10.1016/j.str.2010.12.021. PMC   3056899 . PMID   21295486.
  25. ↑ Venkataraman K, Brown KM, Gilmartin GM (June 2005). "Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition". Genes & Development. 19 (11): 1315–27. doi:10.1101/gad.1298605. PMC   1142555 . PMID   15937220.
  26. 1 2 Millevoi S, Loulergue C, Dettwiler S, Karaa SZ, Keller W, Antoniou M, Vagner S (October 2006). "An interaction between U2AF 65 and CF I(m) links the splicing and 3′ end processing machineries". The EMBO Journal. 25 (20): 4854–64. doi:10.1038/sj.emboj.7601331. PMC   1618107 . PMID   17024186.
  27. 1 2 3 Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ (May 2008). "Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation". Nucleic Acids Research. 36 (9): 3150–61. doi:10.1093/nar/gkn158. PMC   2396415 . PMID   18411206.
  28. ↑ Glover-Cutter K, Kim S, Espinosa J, Bentley DL (January 2008). "RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes". Nature Structural & Molecular Biology. 15 (1): 71–8. doi:10.1038/nsmb1352. PMC   2836588 . PMID   18157150.
  29. ↑ Molecular Biology of the Cell, Chapter 6, "From DNA to RNA". 4th edition. Alberts B, Johnson A, Lewis J, et al. New York: Garland Science; 2002.
  30. ↑ Stumpf G, Domdey H (November 1996). "Dependence of yeast pre-mRNA 3′-end processing on CFT1: a sequence homolog of the mammalian AAUAAA binding factor". Science. 274 (5292): 1517–20. Bibcode:1996Sci...274.1517S. doi:10.1126/science.274.5292.1517. PMID   8929410. S2CID   34840144.
  31. ↑ Iseli C, Stevenson BJ, de Souza SJ, Samaia HB, Camargo AA, Buetow KH, Strausberg RL, Simpson AJ, Bucher P, Jongeneel CV (July 2002). "Long-range heterogeneity at the 3′ ends of human mRNAs". Genome Research. 12 (7): 1068–74. doi:10.1101/gr.62002. PMC   186619 . PMID   12097343.
  32. ↑ Balbo PB, Bohm A (September 2007). "Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis". Structure. 15 (9): 1117–31. doi:10.1016/j.str.2007.07.010. PMC   2032019 . PMID   17850751.
  33. ↑ Viphakone N, Voisinet-Hakil F, Minvielle-Sebastia L (April 2008). "Molecular dissection of mRNA poly(A) tail length control in yeast". Nucleic Acids Research. 36 (7): 2418–33. doi:10.1093/nar/gkn080. PMC   2367721 . PMID   18304944.
  34. ↑ Wahle E (February 1995). "Poly(A) tail length control is caused by termination of processive synthesis". The Journal of Biological Chemistry. 270 (6): 2800–8. doi: 10.1074/jbc.270.6.2800 . PMID   7852352.
  35. ↑ Dichtl B, Blank D, Sadowski M, Hübner W, Weiser S, Keller W (August 2002). "Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination". The EMBO Journal. 21 (15): 4125–35. doi:10.1093/emboj/cdf390. PMC   126137 . PMID   12145212.
  36. ↑ Nag A, Narsinh K, Martinson HG (July 2007). "The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase". Nature Structural & Molecular Biology. 14 (7): 662–9. doi:10.1038/nsmb1253. PMID   17572685. S2CID   5777074.
  37. ↑ Tefferi A, Wieben ED, Dewald GW, Whiteman DA, Bernard ME, Spelsberg TC (August 2002). "Primer on medical genomics part II: Background principles and methods in molecular genetics". Mayo Clinic Proceedings. 77 (8): 785–808. doi:10.4065/77.8.785. PMID   12173714. S2CID   2237085.
  38. ↑ Coller JM, Gray NK, Wickens MP (October 1998). "mRNA stabilization by poly(A) binding protein is independent of poly(A) and requires translation". Genes & Development. 12 (20): 3226–35. doi:10.1101/gad.12.20.3226. PMC   317214 . PMID   9784497.
  39. 1 2 Siddiqui N, Mangus DA, Chang TC, Palermino JM, Shyu AB, Gehring K (August 2007). "Poly(A) nuclease interacts with the C-terminal domain of polyadenylate-binding protein domain from poly(A)-binding protein". The Journal of Biological Chemistry. 282 (34): 25067–75. doi: 10.1074/jbc.M701256200 . PMID   17595167.
  40. ↑ Vinciguerra P, Stutz F (June 2004). "mRNA export: an assembly line from genes to nuclear pores". Current Opinion in Cell Biology. 16 (3): 285–92. doi:10.1016/j.ceb.2004.03.013. PMID   15145353.
  41. ↑ Gray NK, Coller JM, Dickson KS, Wickens M (September 2000). "Multiple portions of poly(A)-binding protein stimulate translation in vivo". The EMBO Journal. 19 (17): 4723–33. doi:10.1093/emboj/19.17.4723. PMC   302064 . PMID   10970864.
  42. ↑ Meaux S, Van Hoof A (July 2006). "Yeast transcripts cleaved by an internal ribozyme provide new insight into the role of the cap and poly(A) tail in translation and mRNA decay". RNA. 12 (7): 1323–37. doi:10.1261/rna.46306. PMC   1484436 . PMID   16714281.
  43. ↑ Kargapolova Y, Levin M, Lackner K, Danckwardt S (June 2017). "sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs". Nucleic Acids Research. 45 (10): 6074–6086. doi:10.1093/nar/gkx152. PMC   5449641 . PMID   28334977.
  44. 1 2 Meijer HA, Bushell M, Hill K, Gant TW, Willis AE, Jones P, de Moor CH (2007). "A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells". Nucleic Acids Research. 35 (19): e132. doi:10.1093/nar/gkm830. PMC   2095794 . PMID   17933768.
  45. ↑ Lehner B, Sanderson CM (July 2004). "A protein interaction framework for human mRNA degradation". Genome Research. 14 (7): 1315–23. doi:10.1101/gr.2122004. PMC   442147 . PMID   15231747.
  46. ↑ Wu L, Fan J, Belasco JG (March 2006). "MicroRNAs direct rapid deadenylation of mRNA". Proceedings of the National Academy of Sciences of the United States of America. 103 (11): 4034–9. Bibcode:2006PNAS..103.4034W. doi: 10.1073/pnas.0510928103 . PMC   1449641 . PMID   16495412.
  47. ↑ Cui J, Sackton KL, Horner VL, Kumar KE, Wolfner MF (April 2008). "Wispy, the Drosophila homolog of GLD-2, is required during oogenesis and egg activation". Genetics. 178 (4): 2017–29. doi:10.1534/genetics.107.084558. PMC   2323793 . PMID   18430932.
  48. ↑ Torabi, Seyed-Fakhreddin; Vaidya, Anand T.; Tycowski, Kazimierz T.; DeGregorio, Suzanne J.; Wang, Jimin; Shu, Mei-Di; Steitz, Thomas A.; Steitz, Joan A. (2021-02-05). "RNA stabilization by a poly(A) tail 3′-end binding pocket and other modes of poly(A)-RNA interaction". Science. 371 (6529): eabe6523. doi:10.1126/science.abe6523. ISSN   0036-8075. PMC   9491362 . PMID   33414189. S2CID   231195473.
  49. ↑ Wilusz CJ, Wormington M, Peltz SW (April 2001). "The cap-to-tail guide to mRNA turnover". Nature Reviews Molecular Cell Biology. 2 (4): 237–46. doi:10.1038/35067025. PMID   11283721. S2CID   9734550.
  50. ↑ Jung MY, Lorenz L, Richter JD (June 2006). "Translational control by neuroguidin, a eukaryotic initiation factor 4E and CPEB binding protein". Molecular and Cellular Biology. 26 (11): 4277–87. doi:10.1128/MCB.02470-05. PMC   1489097 . PMID   16705177.
  51. ↑ Sakurai T, Sato M, Kimura M (November 2005). "Diverse patterns of poly(A) tail elongation and shortening of murine maternal mRNAs from fully grown oocyte to 2-cell embryo stages". Biochemical and Biophysical Research Communications. 336 (4): 1181–9. doi:10.1016/j.bbrc.2005.08.250. PMID   16169522.
  52. ↑ Taft RA (January 2008). "Virtues and limitations of the preimplantation mouse embryo as a model system". Theriogenology. 69 (1): 10–6. doi:10.1016/j.theriogenology.2007.09.032. PMC   2239213 . PMID   18023855.
  53. ↑ Richter JD (June 2007). "CPEB: a life in translation". Trends in Biochemical Sciences. 32 (6): 279–85. doi:10.1016/j.tibs.2007.04.004. PMID   17481902.
  54. ↑ Piqué M, López JM, Foissac S, Guigó R, Méndez R (February 2008). "A combinatorial code for CPE-mediated translational control". Cell. 132 (3): 434–48. doi: 10.1016/j.cell.2007.12.038 . PMID   18267074. S2CID   16092673.
  55. ↑ Benoit P, Papin C, Kwak JE, Wickens M, Simonelig M (June 2008). "PAP- and GLD-2-type poly(A) polymerases are required sequentially in cytoplasmic polyadenylation and oogenesis in Drosophila". Development. 135 (11): 1969–79. doi: 10.1242/dev.021444 . PMC   9154023 . PMID   18434412.
  56. ↑ Tian B, Hu J, Zhang H, Lutz CS (2005). "A large-scale analysis of mRNA polyadenylation of human and mouse genes". Nucleic Acids Research. 33 (1): 201–12. doi:10.1093/nar/gki158. PMC   546146 . PMID   15647503.
  57. ↑ Danckwardt S, Hentze MW, Kulozik AE (February 2008). "3′ end mRNA processing: molecular mechanisms and implications for health and disease". The EMBO Journal. 27 (3): 482–98. doi:10.1038/sj.emboj.7601932. PMC   2241648 . PMID   18256699.
  58. 1 2 Tian, Bin; Manley, James L. (2017). "Alternative polyadenylation of mRNA precursors". Nature Reviews. Molecular Cell Biology. 18 (1): 18–30. doi:10.1038/nrm.2016.116. ISSN   1471-0080. PMC   5483950 . PMID   27677860.
  59. ↑ Zhang, Haibo; Lee, Ju Youn; Tian, Bin (2005). "Biased alternative polyadenylation in human tissues". Genome Biology. 6 (12): R100. doi: 10.1186/gb-2005-6-12-r100 . ISSN   1474-760X. PMC   1414089 . PMID   16356263.
  60. ↑ Smibert, Peter; Miura, Pedro; Westholm, Jakub O.; Shenker, Sol; May, Gemma; Duff, Michael O.; Zhang, Dayu; Eads, Brian D.; Carlson, Joe; Brown, James B.; Eisman, Robert C. (2012). "Global patterns of tissue-specific alternative polyadenylation in Drosophila". Cell Reports. 1 (3): 277–289. doi:10.1016/j.celrep.2012.01.001. ISSN   2211-1247. PMC   3368434 . PMID   22685694.
  61. ↑ Lee, Ju Youn; Ji, Zhe; Tian, Bin (2008). "Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes". Nucleic Acids Research. 36 (17): 5581–5590. doi:10.1093/nar/gkn540. ISSN   1362-4962. PMC   2553571 . PMID   18757892.
  62. ↑ Ogorodnikov A, Kargapolova Y, Danckwardt S (June 2016). "Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end". Pflügers Archiv. 468 (6): 993–1012. doi:10.1007/s00424-016-1828-3. PMC   4893057 . PMID   27220521.
  63. ↑ Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB (June 2008). "Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites". Science. 320 (5883): 1643–7. Bibcode:2008Sci...320.1643S. doi:10.1126/science.1155390. PMC   2587246 . PMID   18566288.
  64. ↑ Tili E, Michaille JJ, Calin GA (April 2008). "Expression and function of micro-RNAs in immune cells during normal or disease state". International Journal of Medical Sciences. 5 (2): 73–9. doi:10.7150/ijms.5.73. PMC   2288788 . PMID   18392144.
  65. ↑ Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, Pillai B (November 2008). "MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene". Nucleic Acids Research. 36 (19): 6318–32. doi:10.1093/nar/gkn624. PMC   2577349 . PMID   18835850.
  66. ↑ Alt FW, Bothwell AL, Knapp M, Siden E, Mather E, Koshland M, Baltimore D (June 1980). "Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3′ ends". Cell. 20 (2): 293–301. doi:10.1016/0092-8674(80)90615-7. PMID   6771018. S2CID   7448467.
  67. ↑ Tian B, Pan Z, Lee JY (February 2007). "Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing". Genome Research. 17 (2): 156–65. doi:10.1101/gr.5532707. PMC   1781347 . PMID   17210931.
  68. 1 2 Shell SA, Hesse C, Morris SM, Milcarek C (December 2005). "Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection". The Journal of Biological Chemistry. 280 (48): 39950–61. doi: 10.1074/jbc.M508848200 . PMID   16207706.
  69. ↑ Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Poetsch A, Binder H, Macher-Göppinger S, Probst HC, Tian B, Schaefer M, Lackner KJ, Westermann F, Danckwardt S (December 2018). "Transcriptome 3′ end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma". Nature Communications. 9 (1): 5331. Bibcode:2018NatCo...9.5331O. doi:10.1038/s41467-018-07580-5. PMC   6294251 . PMID   30552333.
  70. ↑ Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB (November 2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–9. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC   2597294 . PMID   18978773.
  71. ↑ Hall-Pogar T, Liang S, Hague LK, Lutz CS (July 2007). "Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3′-UTR". RNA. 13 (7): 1103–15. doi:10.1261/rna.577707. PMC   1894925 . PMID   17507659.
  72. ↑ Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE (June 2007). "Splicing factors stimulate polyadenylation via USEs at non-canonical 3′ end formation signals". The EMBO Journal. 26 (11): 2658–69. doi:10.1038/sj.emboj.7601699. PMC   1888663 . PMID   17464285.
  73. ↑ Danckwardt S, Gantzert AS, Macher-Goeppinger S, Probst HC, Gentzel M, Wilm M, Gröne HJ, Schirmacher P, Hentze MW, Kulozik AE (February 2011). "p38 MAPK controls prothrombin expression by regulated RNA 3′ end processing". Molecular Cell. 41 (3): 298–310. doi: 10.1016/j.molcel.2010.12.032 . PMID   21292162.
  74. ↑ Wood AJ, Schulz R, Woodfine K, Koltowska K, Beechey CV, Peters J, Bourc'his D, Oakey RJ (May 2008). "Regulation of alternative polyadenylation by genomic imprinting". Genes & Development. 22 (9): 1141–6. doi:10.1101/gad.473408. PMC   2335310 . PMID   18451104.
  75. ↑ Marini F, Scherzinger D, Danckwardt S (2021). "TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation". Nucleic Acids Research. 49 (D1): D:243–D253. doi:10.1093/nar/gkaa722. PMC   7778938 . PMID   32976578.
  76. ↑ Reinisch KM, Wolin SL (April 2007). "Emerging themes in non-coding RNA quality control". Current Opinion in Structural Biology. 17 (2): 209–14. doi:10.1016/j.sbi.2007.03.012. PMID   17395456.
  77. ↑ Jia H, Wang X, Liu F, Guenther UP, Srinivasan S, Anderson JT, Jankowsky E (June 2011). "The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex". Cell. 145 (6): 890–901. doi:10.1016/j.cell.2011.05.010. PMC   3115544 . PMID   21663793.
  78. ↑ LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D (June 2005). "RNA degradation by the exosome is promoted by a nuclear polyadenylation complex". Cell. 121 (5): 713–24. doi: 10.1016/j.cell.2005.04.029 . PMID   15935758. S2CID   14898055.
  79. 1 2 Martin G, Keller W (November 2007). "RNA-specific ribonucleotidyl transferases". RNA. 13 (11): 1834–49. doi:10.1261/rna.652807. PMC   2040100 . PMID   17872511.
  80. ↑ Slomovic S, Laufer D, Geiger D, Schuster G (2006). "Polyadenylation of ribosomal RNA in human cells". Nucleic Acids Research. 34 (10): 2966–75. doi:10.1093/nar/gkl357. PMC   1474067 . PMID   16738135.
  81. ↑ Régnier P, Arraiano CM (March 2000). "Degradation of mRNA in bacteria: emergence of ubiquitous features". BioEssays. 22 (3): 235–44. doi:10.1002/(SICI)1521-1878(200003)22:3<235::AID-BIES5>3.0.CO;2-2. PMID   10684583. S2CID   26109164.
  82. 1 2 3 Anantharaman V, Koonin EV, Aravind L (April 2002). "Comparative genomics and evolution of proteins involved in RNA metabolism". Nucleic Acids Research. 30 (7): 1427–64. doi:10.1093/nar/30.7.1427. PMC   101826 . PMID   11917006.
  83. 1 2 Slomovic S, Portnoy V, Liveanu V, Schuster G (2006). "RNA Polyadenylation in Prokaryotes and Organelles; Different Tails Tell Different Tales". Critical Reviews in Plant Sciences. 25 (1): 65–77. Bibcode:2006CRvPS..25...65S. doi:10.1080/07352680500391337. S2CID   86607431.
  84. ↑ Chang, Jeong Ho; Tong, Liang (2012). "Mitochondrial poly(A) polymerase and polyadenylation". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1819 (9–10): 992–997. doi:10.1016/j.bbagrm.2011.10.012. ISSN   0006-3002. PMC   3307840 . PMID   22172994.
  85. ↑ Chang SA, Cozad M, Mackie GA, Jones GH (January 2008). "Kinetics of polynucleotide phosphorylase: comparison of enzymes from Streptomyces and Escherichia coli and effects of nucleoside diphosphates". Journal of Bacteriology. 190 (1): 98–106. doi:10.1128/JB.00327-07. PMC   2223728 . PMID   17965156.
  86. ↑ Nagaike T, Suzuki T, Ueda T (April 2008). "Polyadenylation in mammalian mitochondria: insights from recent studies". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1779 (4): 266–9. doi:10.1016/j.bbagrm.2008.02.001. PMID   18312863.
  87. ↑ Walter M, Kilian J, Kudla J (December 2002). "PNPase activity determines the efficiency of mRNA 3′-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts". The EMBO Journal. 21 (24): 6905–14. doi:10.1093/emboj/cdf686. PMC   139106 . PMID   12486011.
  88. ↑ Portnoy V, Schuster G (2006). "RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R". Nucleic Acids Research. 34 (20): 5923–31. doi:10.1093/nar/gkl763. PMC   1635327 . PMID   17065466.
  89. ↑ Yehudai-Resheff S, Portnoy V, Yogev S, Adir N, Schuster G (September 2003). "Domain analysis of the chloroplast polynucleotide phosphorylase reveals discrete functions in RNA degradation, polyadenylation, and sequence homology with exosome proteins". The Plant Cell. 15 (9): 2003–19. doi:10.1105/tpc.013326. PMC   181327 . PMID   12953107.
  90. ↑ Slomovic S, Portnoy V, Schuster G (2008). "Chapter 24 Detection and Characterization of Polyadenylated RNA in Eukarya, Bacteria, Archaea, and Organelles". RNA Turnover in Bacteria, Archaea and Organelles. Methods in Enzymology. Vol. 447. pp. 501–20. doi:10.1016/S0076-6879(08)02224-6. ISBN   978-0-12-374377-0. PMID   19161858.
  91. ↑ Portnoy V, Evguenieva-Hackenberg E, Klein F, Walter P, Lorentzen E, Klug G, Schuster G (December 2005). "RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus". EMBO Reports. 6 (12): 1188–93. doi:10.1038/sj.embor.7400571. PMC   1369208 . PMID   16282984.
  92. ↑ Portnoy V, Schuster G (June 2008). "Mycoplasma gallisepticum as the first analyzed bacterium in which RNA is not polyadenylated". FEMS Microbiology Letters. 283 (1): 97–103. doi: 10.1111/j.1574-6968.2008.01157.x . PMID   18399989.
  93. ↑ Evguenieva-Hackenberg E, Roppelt V, Finsterseifer P, Klug G (December 2008). "Rrp4 and Csl4 are needed for efficient degradation but not for polyadenylation of synthetic and natural RNA by the archaeal exosome". Biochemistry. 47 (50): 13158–68. doi:10.1021/bi8012214. PMID   19053279.
  94. 1 2 Slomovic S, Portnoy V, Yehudai-Resheff S, Bronshtein E, Schuster G (April 2008). "Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1779 (4): 247–55. doi:10.1016/j.bbagrm.2007.12.004. PMID   18177749.
  95. ↑ Poon, Leo L. M.; Pritlove, David C.; Fodor, Ervin; Brownlee, George G. (1 April 1999). "Direct Evidence that the Poly(A) Tail of Influenza A Virus mRNA Is Synthesized by Reiterative Copying of a U Track in the Virion RNA Template". Journal of Virology. 73 (4): 3473–3476. doi: 10.1128/JVI.73.4.3473-3476.1999 . PMC   104115 . PMID   10074205.
  96. ↑ Wu, Hung-Yi; Ke, Ting-Yung; Liao, Wei-Yu; Chang, Nai-Yun (2013). "Regulation of Coronaviral Poly(A) Tail Length during Infection". PLOS ONE. 8 (7): e70548. Bibcode:2013PLoSO...870548W. doi: 10.1371/journal.pone.0070548 . PMC   3726627 . PMID   23923003.
  97. ↑ Neeleman, Lyda; Olsthoorn, René C. L.; Linthorst, Huub J. M.; Bol, John F. (4 December 2001). "Translation of a nonpolyadenylated viral RNA is enhanced by binding of viral coat protein or polyadenylation of the RNA". Proceedings of the National Academy of Sciences. 98 (25): 14286–14291. Bibcode:2001PNAS...9814286N. doi: 10.1073/pnas.251542798 . PMC   64674 . PMID   11717411.
  98. ↑ Chen, Jun-Hao; Zhang, Rui-Hua; Lin, Shao-Li; Li, Peng-Fei; Lan, Jing-Jing; Song, Sha-Sha; Gao, Ji-Ming; Wang, Yu; Xie, Zhi-Jing; Li, Fu-Chang; Jiang, Shi-Jin (2018). "The Functional Role of the 3′ Untranslated Region and Poly(A) Tail of Duck Hepatitis a Virus Type 1 in Viral Replication and Regulation of IRES-Mediated Translation". Frontiers in Microbiology. 9: 2250. doi: 10.3389/fmicb.2018.02250 . PMC   6167517 . PMID   30319572.
  99. ↑ "Inhibition of host poly(A)-binding protein by virus ~ ViralZone". viralzone.expasy.org.
  100. ↑ Edmonds, Mary; Abrams, Richard (April 1960). "Polynucleotide Biosynthesis: Formation of a Sequence of Adenylate Units from Adenosine Triphosphate by an Enzyme from Thymus Nuclei". Journal of Biological Chemistry. 235 (4): 1142–1149. doi: 10.1016/S0021-9258(18)69494-3 .
  101. ↑ Colgan DF, Manley JL (November 1997). "Mechanism and regulation of mRNA polyadenylation". Genes & Development. 11 (21): 2755–66. doi: 10.1101/gad.11.21.2755 . PMID   9353246.
  102. 1 2 Edmonds, M (2002). A history of poly A sequences: from formation to factors to function. Progress in Nucleic Acid Research and Molecular Biology. Vol. 71. pp. 285–389. doi:10.1016/S0079-6603(02)71046-5. ISBN   978-0-12-540071-8. PMID   12102557.
  103. ↑ Edmonds, M.; Vaughan, M. H.; Nakazato, H. (1 June 1971). "Polyadenylic Acid Sequences in the Heterogeneous Nuclear RNA and Rapidly-Labeled Polyribosomal RNA of HeLa Cells: Possible Evidence for a Precursor Relationship". Proceedings of the National Academy of Sciences. 68 (6): 1336–1340. Bibcode:1971PNAS...68.1336E. doi: 10.1073/pnas.68.6.1336 . PMC   389184 . PMID   5288383.

Further reading

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.