MIAT | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Aliases | MIAT , C22orf35, GOMAFU, LINC00066, NCRNA00066, RNCR2, lncRNA-myocardial infarction associated transcript (non-protein coding), myocardial infarction associated transcript | ||||||||||||||||||||||||||||||||||||||||||||||||||
External IDs | OMIM: 611082; GeneCards: MIAT; OMA:MIAT - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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MIAT (myocardial infarction-associated transcript), also known as RNCR2 (retinal non-coding RNA 2) or Gomafu, is a long non-coding RNA. Single nucleotide polymorphisms (SNPs) in MIAT are associated with a risk of myocardial infarction. [3] It is expressed in neurons, and located in the nucleus. [4] It plays a role in the regulation of retinal cell fate specification. [5] Crea and collaborators have shown that MIAT is highly up-regulated in aggressive prostate cancer samples, [6] raising the possibility that this gene plays a role in cancer progression. [7]
The MIAT gene is located on Chromosome 22 and is 30,051 bases in length. [8] MIAT's other name, gomafu, is a word in Japanese that means “spotted pattern”. [9] The reason it is named as so is because Gomafu is distributed in the nucleoplasm in a spotted pattern. [9] Moreover, its orientation is a plus strand. [8]
It is also found that MIAT has five exons and is likely to be a functional RNA, since MIAT hasn’t been shown to encode any translational product. [8] Furthermore, the gene encodes a spliced, long non-coding RNA. [8]
The gene is found not only in humans, but also in mice and rats. [9] Orthologs are present in syntenic positions of frog and chicken. [10] It is also found that all gomafu RNA contain tandem repeats of UACUAAC that binds to SPF1, which is a splicing factor. [9]
MIAT was originally discovered as long intergenic noncoding RNAs quite enriched in specific neurons in mouse retina and later more widely expressed in the nervous system and cultured neurons, where it specifies cell identity. [9] Moreover, the gomafu RNA is also quite insoluble [9] and is enriched in PolyA +. Also, there are putative polyadenylation signals (ATTAAA) found at the 3’ end of this gene. The presence of a PolyA tail and multiple exons and introns fulfills the feature of mRNAs transcribed by RNA polymerase II. The stability of the gene is not significantly different from β-actin mRNA. [9]
Myocardial infarction is more commonly known as a heart attack. It is the irreversible death of the heart muscle due to prolonged obstruction of blood supply to the organ. Case-controlled large scale studies utilizing Single Nucleotide Polymorphisms(SNPs) throughout the genome demonstrated that altered expression at 6 SNPs in the MIAT gene might confer genetic susceptibility to myocardial infarctions. MIAT has been demonstrated to encode a nonfunctional RNA. Although the exact function of MIAT is still unclear, knowledge of some of the genetic factors that contribute to the pathogenesis of myocardial infarction can lend itself to better diagnosis, prevention, and treatment. Despite all that has been discovered about MIAT, a causal link between MIAT and myocardial infarctions has not yet been demonstrated. [8]
Additionally, one study demonstrated that expression levels of MIAT are shown to change in peripheral blood cells of patients with acute myocardial infarction. In particular, researchers studied the association between levels of lncRNAs and inflammation markers in patients who have suffered a myocardial infarction. MIAT levels were found to be positively associated with lymphocytes and negatively associated with neutrophils and platelets. In another portion of this study, researchers looked at the association between cardiovascular risk factors and levels of lncRNAs. Smoking was a cardiovascular risk factor that was found to be positively associated with MIAT. Several researchers have reported that levels of lncRNAs are regulated in the cardiac tissue following a heart attack, but it is not known for sure whether it is the myocardial infarction that affects the levels of lncRNAs in peripheral blood cells. [6] MIAT has various genotypes of SNPs and it is possible that only one of them relates to heart disease. [11]
The long non-coding RNA(lncRNA) MIAT is located in the same chromosomal region which is linked to Schizophrenia (SZ) 22Q12.1. [12]
MIAT is upregulated in the nucleus accumbens of cocaine and heroin users. [13] [14] The nucleus accumbens is a region involved in behavior and addiction, [15] suggesting that dysregulation of MIAT can influence behavior.
It is well accepted that alternative splicing has a role in SZ pathology. [16] MIAT is associated with alternative splicing through its interaction with splicing factor 1(SF1) [10] and with genes DISC1 and ERBB4. [17] MIAT binds directly to the splicing regulator quaking homolog (QKI) and serine/arginine-rich splicing factor 1 (SRSF1). [18] QKI gene expression is decreased in specific brain regions in SZ [19] [20] and it has been proposed to be involved in SZ. [21] [22]
Post -mortem SZ brains have upregulated expression of both DISC1 and ERBB4. [18] Overexpression of MIAT in human-induced pluripotent stem cell (HiPSC)-derived neurons shows a significant decrease in expression of both DISC1 and ERBB4 and their alternative spliced variants. [18] This is opposite to the upregulated expression seen in SZ patient brains. [18] ASO mediated knockdown of MIAT in (HiPSC)-derived neurons increase the expression of both DISC1 and ERBB4 splice variants, but not their unspliced transcripts. [18] This is almost exactly matching the aberrant splicing pattern seen in post-mortem SZ patient’s brains. [18] These results suggests that loss of function mutations or decreased expression of MIAT is involved in driving aberrant cortical splicing patterns observed in SZ post-mortem brains. [18]
MIAT up-regulation and down-regulation has been linked to various types of cancer and other pathologies.
In a study of glioblastoma multiforme, increased expression of MIAT was linked to increased survival rates. [23] In addition, the glioma cells were found to how significantly down-regulated MIAT. [23] The role of MIAT in lymphocytic leukemia is very different from that of glioblastoma. In certain aggressive cell lines of chronic lymphocytic leukemias, MIAT is upregulated and depends on the presence of a transcriptional regulator, OCT4. [24] OCT4 serves a positive regulator of MIAT transcription and as of now is the only known regulator. However, analysis of relative concentrations of MIAT and OCT4 have indicated that other regulatory factors are in play. [24]
Beyond its role in cancer, MIAT misexpression has also been linked to neurovascular dysfunction. [25]
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.
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR.
Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.
Disrupted in schizophrenia 1 is a protein that in humans is encoded by the DISC1 gene. In coordination with a wide array of interacting partners, DISC1 has been shown to participate in the regulation of cell proliferation, differentiation, migration, neuronal axon and dendrite outgrowth, mitochondrial transport, fission and/or fusion, and cell-to-cell adhesion. Several studies have shown that unregulated expression or altered protein structure of DISC1 may predispose individuals to the development of schizophrenia, clinical depression, bipolar disorder, and other psychiatric conditions. The cellular functions that are disrupted by permutations in DISC1, which lead to the development of these disorders, have yet to be clearly defined and are the subject of current ongoing research. Although, recent genetic studies of large schizophrenia cohorts have failed to implicate DISC1 as a risk gene at the gene level, the DISC1 interactome gene set was associated with schizophrenia, showing evidence from genome-wide association studies of the role of DISC1 and interacting partners in schizophrenia susceptibility.
Receptor tyrosine-protein kinase erbB-4 is an enzyme that in humans is encoded by the ERBB4 gene. Alternatively spliced variants that encode different protein isoforms have been described; however, not all variants have been fully characterized.
Quaking homolog, KH domain RNA binding (mouse), also known as QKI, is a protein which in humans is encoded by the QKI gene.
Long non-coding RNAs are a type of RNA, generally defined as transcripts more than 200 nucleotides that are not translated into protein. This arbitrary limit distinguishes long ncRNAs from small non-coding RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. Given that some lncRNAs have been reported to have the potential to encode small proteins or micro-peptides, the latest definition of lncRNA is a class of RNA molecules of over 200 nucleotides that have no or limited coding capacity. Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of lncRNA which do not overlap protein-coding genes.
MEG3 is a maternally expressed, imprinted long non-coding RNA gene. At least 12 different isoforms of MEG3 are generated by alternative splicing. Expression of MEG3 is lost in cancer cells. It acts as a growth suppressor in tumour cells, and activates p53. A pituitary transcript variant has been associated with inhibited cell proliferation. Studies in mouse and sheep suggest that an upstream intergenic differentially methylated region (IG-DMR) regulates imprinting of the region. The expression profile in mouse of the co-regulated Meg3 and Dlk1 genes suggests a causative role in the pathologies found in uniparental disomy animals, characterized by defects in skeletal muscle maturation, bone formation, placenta size and organization and prenatal lethality. The sheep homolog is associated with the callipyge mutation which in heterozygous individuals affects a muscle-specific long-range control element located in the DLK1-GTL2 intergenic region and results in the callipyge muscular hypertrophy. The non-Mendelian inheritance pattern, known as polar overdominance, likely results from the combination of the cis-effect on the expression levels of genes in the DLK1-GTL2 imprinted domain, and trans interaction between the products of reciprocally imprinted genes. MEG3 is thought to play a role in the development of Alzheimer's disease by triggering necroptosis.
Neuregulin 3, also known as NRG3, is a neural-enriched member of the neuregulin protein family which in humans is encoded by the NRG3 gene. The NRGs are a group of signaling proteins part of the superfamily of epidermal growth factor, EGF like polypeptide growth factor. These groups of proteins possess an 'EGF-like domain' that consists of six cysteine residues and three disulfide bridges predicted by the consensus sequence of the cysteine residues.
HOTAIR is a human gene located between HOXC11 and HOXC12 on chromosome 12. It is the first example of an RNA expressed on one chromosome that has been found to influence the transcription of the HOXD cluster posterior genes located on chromosome 2. The sequence and function of HOTAIR are different in humans and mice. Sequence analysis of HOTAIR revealed that it exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. A subsequent study identified HOTAIR has 32 nucleotides long conserved noncoding element (CNE) that has a paralogous copy in HOXD cluster region, suggesting that the HOTAIR conserved sequences predate whole genome duplication events at the root of vertebrate. While the conserved sequence paralogous with HOXD cluster is 32 nucleotide long, the HOTAIR sequence conserved from human to fish is about 200 nucleotide long and is marked by active enhancer features.
Growth arrest-specific 5 is a non-protein coding RNA that in humans is encoded by the GAS5 gene.
MALAT 1 also known as NEAT2 is a large, infrequently spliced non-coding RNA, which is highly conserved amongst mammals and highly expressed in the nucleus. It regulates the expression of metastasis-associated genes. It also positively regulates cell motility via the transcriptional and/or post-transcriptional regulation of motility-related genes. MALAT1 may play a role in temperature-dependent sex determination in the Red-eared slider turtle.
CDKN2B-AS, also known as ANRIL is a long non-coding RNA consisting of 19 exons, spanning 126.3kb in the genome, and its spliced product is a 3834bp RNA. It is located within the p15/CDKN2B-p16/CDKN2A-p14/ARF gene cluster, in the antisense direction. Single nucleotide polymorphisms (SNPs) which alter the expression of CDKN2B-AS are associated with human healthy life expectancy, as well as with multiple diseases, including coronary artery disease, diabetes and many cancers. It binds to chromobox 7 (CBX7) within the polycomb repressive complex 1 and to SUZ12, a component of polycomb repression complex 2 and through these interactions is involved in transcriptional repression.
In molecular biology, disrupted in schizophrenia 2 , also known as DISC2, is a long non-coding RNA molecule. In humans, the DISC2 gene that produces the DISC2 RNA molecule is located on chromosome 1, at the breakpoint associated with the chromosomal translocation found in Schizophrenia. It is antisense to the DISC1 gene and may regulate the expression of DISC1. DISC2 may also contribute to other psychiatric disorders.
HOXA11-AS lncRNA is a long non-coding RNA from the antisense strand in the homeobox A. The HOX gene contains four clusters. The sense strand of the HOXA gene codes for proteins. Alternative names for HOXA11-AS lncRNA are: HOXA-AS5, HOXA11S, HOXA11-AS1, HOXA11AS, or NCRNA00076. This gene is 3,885 nucleotides long and resides at chromosome 7 (7p15.2) and is transcribed from an independent gene promoter. Being a lncRNA, it is longer than 200 nucleotides in length, in contrast to regular non-coding RNAs.
Epigenetics of human development is the study of how epigenetics effects human development.
Solute carrier family 39 member 12 is a protein that in humans is encoded by the SLC39A12 gene.
Brain cytoplasmic 200 long-noncoding RNA is a 200 nucleotide RNA transcript found predominantly in the brain with a primary function of regulating translation by inhibiting its initiation. As a long non-coding RNA, it belongs to a family of RNA transcripts that are not translated into protein (ncRNAs). Of these ncRNAs, lncRNAs are transcripts of 200 nucleotides or longer and are almost three times more prevalent than protein-coding genes. Nevertheless, only a few of the almost 60,000 lncRNAs have been characterized, and little is known about their diverse functions. BC200 is one lncRNA that has given insight into their specific role in translation regulation, and implications in various forms of cancer as well as Alzheimer's disease.
Small nucleolar RNA host gene 1 is a non-protein coding RNA that in humans is encoded by the SNHG1 gene.
A majority of the human genome is made up of non-protein coding DNA. It infers that such sequences are not commonly employed to encode for a protein. However, even though these regions do not code for protein, they have other functions and carry necessary regulatory information.They can be classified based on the size of the ncRNA. Small noncoding RNA is usually categorized as being under 200 bp in length, whereas long noncoding RNA is greater than 200bp. In addition, they can be categorized by their function within the cell; Infrastructural and Regulatory ncRNAs. Infrastructural ncRNAs seem to have a housekeeping role in translation and splicing and include species such as rRNA, tRNA, snRNA.Regulatory ncRNAs are involved in the modification of other RNAs.