Cis-natural antisense transcript

'''Natural antisense transcripts''' (NATs) are a group of RNAs encoded within a cell that have transcript complementarity to other RNA transcripts.<ref name="pmid17409075">{{cite journal|vauthors = Osato N, Suzuki Y, Ikeo K, Gojobori T| title = Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice | journal= Genetics | volume = 176 | issue =12 | pages = 1299–1306 | year = 2007 | pmid = 17409075 | doi = 10.1534/genetics.106.069484|pmc = 1894591 }}</ref> They have been identified in multiple eukaryotes, including humans, mice, yeast and ''Arabidopsis thaliana''.<ref name="pmid9573333">{{cite journal|vauthors = Vanhée-Brossollet C, Vaquero C | title = Do natural antisense transcripts make sense in eukaryotes? | journal = Gene | volume = 211 | issue = 1 | pages = 1–9 | year = 1998 | pmid = 9573333 | doi = 10.1016/S0378-1119(98)00093-6}}</ref> This class of RNAs includes both protein-coding and non-coding RNAs.<ref name="pmid15102435">{{cite journal | vauthors = Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G | title = In search of antisense | journal = Trends Biochem. Sci. | volume = 29 | issue = 2 | pages = 88–94 | year = 2004 | pmid = 15102435 | doi = 10.1016/j.tibs.2003.12.002}}</ref> Current evidence has suggested a variety of regulatory roles for NATs, such as RNA interference (RNAi), alternative splicing, genomic imprinting, and X-chromosome inactivation.<ref name = "pmid16849434">{{cite journal | vauthors = Zhang Y, Liu XS, Liu QR, Wei L | title = Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species | journal = Nucleic Acids Research | volume = 34 | issue = 12 | pages = 3465–3475 | year = 2006 | pmid = 16849434 | doi = 10.1093/nar/gkl473| pmc = 1524920 }}</ref> NATs are broadly grouped into two categories based on whether they act in cis or in trans.<ref name="pmid15356298">{{cite journal| vauthors = Chen J, Sun M, Kent WJ, Huang X, Xie H, Wang W, Zhou G, Shi RZ, Rowley JD | title = Over 20% of human transcripts might form sense–antisense pairs | journal = Nucleic Acids Res | volume = 32 | issue = 16 | pages = 4812–4820 | year = 2004 | pmid = 15356298 | doi = 10.1093/nar/gkh818| pmc = 519112 }}</ref> Trans-NATs are transcribed from a different location than their targets and usually have complementarity to multiple transcripts with some mismatches.<ref name="pmid12665819">{{cite journal | author = Carmichael GG| title = Antisense starts making more sense | journal = Nat Biotechnol | volume = 21 | issue = 4 | pages = 371–372 | year = 2003 | pmid = 12665819 | doi = 10.1038/nbt0403-371| s2cid = 3137487 }}</ref> MicroRNAs (miRNA) are an example of trans-NATs that can target multiple transcripts with a few mismatches.<ref name="pmid12665819"/> '''Cis-natural antisense transcripts''' ('''cis-NATs''') on the other hand are transcribed from the same genomic locus as their target but from the opposite DNA strand and form perfect pairs.<ref name = "pmid15833117">{{cite journal | vauthors = Wang XJ, Gaasterland T, Chua NH | title = Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana | journal = Genome Biol | volume = 6 | issue = 4 | pages =R30 | year = 2005 | pmid = 15833117 | doi = 10.1186/gb-2005-6-4-r30| pmc = 1088958 | doi-access = free }}</ref>

== Orientation == thumb|Figure 1: Orientations of cis-NATs within the genome

Cis-NATs have a variety of orientations and differing lengths of overlap between pairs.<ref name = "pmid15833117"/> There have been five identified orientations for cis-NATs to date.<ref>{{cite journal | title= Overlapping Antisense Transcription in the Human Genome | journal = Comparative and Functional Genomics | volume = 3 | issue = 3| pages=244–253 | year=2002 | pmid = 18628857| doi = 10.1002/cfg.173| author= Fahey, M.E. | author2= Moore, T.F. Higgins, D.G. | pmc= 2447278 }}</ref> The most common orientation is head-to-head, where the 5' ends of both transcripts align together.<ref name="pmid15102435"/> This orientation would result in the greatest knockdown of gene expression if transcriptional collision is the reason for transcript inhibition.<ref name="pmid17409075"/> There are however some studies that have suggested that tail-to-tail orientations are the most common NAT pairs.<ref name="pmid17409075"/> Others such as tail to tail, overlapping, nearby head-to- head, and nearby tail-to-tail are less frequently encountered.<ref name="pmid17409075"/> Completely overlapping NATs involve the antisense gene being located completely over top of each other.<ref name="pmid15102435"/> Nearby head-to-head and tail-to-tail orientations are physically discrete from each other but are located very close to each other.<ref name="pmid17409075"/> Current evidence suggests that there is an overrepresentation of NAT pairs in genes that have catalytic activity.<ref name="pmid15102435"/> There may be something about these genes in particular that makes them more prone to this type of regulation.

== Identification approach == Identification of NATs in whole genomes is possible due to the large collection of sequence data available from multiple organisms. ''In silico'' methods for detecting NATs suffer from several shortcomings depending on the source of sequence information.<ref name = "pmid15833117"/> Studies that use mRNA have sequences whose orientations are known, but the amount of mRNA sequence information available is small.<ref name="pmid15102435"/> Predicted gene models using algorithms trained to look for genes gives an increased coverage of the genome at the cost of confidence in the identified gene.<ref name = "pmid15833117"/> Another resource is the extensive expressed sequence tag (EST) libraries but these small sequences must first be assigned an orientation before useful information can be extracted from them.<ref name="pmid15102435"/> Some studies have utilized special sequence information in the ESTs such as the poly(A) signal, poly(A) tail, and splicing sites to both filter the ESTs and to give them the correct transcriptional orientation.<ref name="pmid17409075"/> Combinations of the different sequence sources attempts to maximize coverage as well as maintain integrity in the data.

Pairs of NATs are identified when they form overlapping clusters. There is variability in the cut-off values used in different studies but generally ~20 nucleotides of sequence overlap is considered the minimum for transcripts to be considered and overlapping cluster.<ref name="pmid17409075"/> Also, transcripts must map to only one other mRNA molecule in order for it to be considered a NAT pair.<ref name="pmid17409075"/><ref name = "pmid15833117"/> Currently there are a variety of web and software resources that can be used to look for antisense pairs. The NATsdb or Natural Antisense Transcript database is a rich tool for searching for antisense pairs from multiple organisms.

== Mechanisms == thumb|Transcription collision model for expression inhibition Molecular mechanisms behind the regulatory role of cis-NATs are not currently well understood.<ref name="pmid15102435"/> Three models have been proposed to explain the regulatory effects that cis-NATs have on gene expression. The first model attributes that base pairing between the cis-NAT and its complementary transcript result in a knockdown of mRNA expression.<ref name="pmid16377568">{{cite journal|vauthors = Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK | title = Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis | journal = Cell | volume = 123 | issue = 7 | pages = 1279–1291 | year = 2005 | pmid = 16377568 | doi = 10.1016/j.cell.2005.11.035|pmc = 3137516 }}</ref> The assumption of this model is that there will be a precise alignment of at least 6 base pairs between the cis-NAT pair to make double stranded RNA.<ref name="pmid17409075"/> Epigenetic modifications like DNA methylation and post-translational modification of core histones form the basis of the second model.<ref name="pmid17409075"/> Although it is not yet clearly understood, it is thought that the reverse transcript guides methylation complexes and/or histone-modifying complexes to the promoter regions of the sense transcript and cause an inhibition of expression from the gene.<ref name="pmid17409075"/> Currently it is not known what attributes of cis-NATs are crucial for the epigenetic model of regulation.<ref name="pmid17409075"/> The final proposed model that has gained favour due to recent experimental evidence is the transcriptional collision model. During the process of transcription of cis-NATs, the transcriptional complexes assemble in the promoter regions of the gene. RNA polymerases will then begin transcribing the gene at the transcription initiation site laying down nucleotides in a 5' to 3' direction.<ref name="pmid12665819"/> In the areas of overlap between the cis-NATs the RNA polymerases will collide and stop at the crash site.<ref name="pmid17409075"/> Transcription is inhibited because RNA polymerases prematurely stop and their incomplete transcripts get degraded.<ref name="pmid15647831">{{cite journal| vauthors = Røsok O, Sioud M | title = Systematic search for natural antisense transcripts in eukaryotes (review) | journal = Int J Mol Med | volume = 15 | issue = 2 | pages = 197–203 | year = 2005 | pmid = 15647831 | doi = 10.3892/ijmm.15.2.197}}</ref>

== Importance == Regulation of many biological processes such as development, metabolism and many others requires a careful co-ordination between many different genes; this is usually referred to as a gene regulatory network. A flurry of interest in gene regulatory networks has been sparked by the advent of sequenced genomes of multiple organisms. The next step is to use this information to figure out how genes work together and not just in isolation. During the processes of mammalian development, there is an inactivation of the extra X-chromosome in females. It has been shown that a NAT pair called Xist and Tsix are involved in the hypermethylation of the chromosome.<ref name="pmid16409644">{{cite journal| vauthors = Li YY, Qin L, Guo ZM, Liu L, Xu H, Hao P, Su J, Shi Y, He WZ, Li YX | title = In silico discovery of human natural antisense transcripts | journal = BMC Bioinformatics | volume = 7| pages = 18 | year = 2006| pmid = 16409644 | doi = 10.1186/1471-2105-7-18| pmc = 1369008 | doi-access = free }}</ref> As much as 20–30% of mammalian genes have been shown to be the targets of miRNAs, which highlights the importance of these molecules as regulators across a wide number of genes.<ref name="pmid11818131">{{cite journal | vauthors = Lehner B, Williams G, Campbell RD, Sanderson CM | title = Antisense transcripts in the human genome| journal = Trends Genet | volume = 18 | issue = 2 | pages = 63–65 | year = 2002 | pmid = 11818131 | doi = 10.1016/S0168-9525(02)02598-2}}</ref> Evolutionary reasons for utilizing RNA for regulation of genes may be that it is less costly and faster than synthesizing proteins not needed by the cell.<ref name="pmid17409075"/> This could have had a selective advantage for early eukaryotes with this type of transcriptional regulation.

== Disease == {{See also|Antisense RNA}} thumb|Figure 3: Aberrant transcription of antisense transcripts can result in inhibition of oncogenes and allow cell to continue past cell cycle check points. Putative new oncogenes and tumor suppressor genes can be found by looking for upregulated antisense transcripts in cancer cells. Antisense transcription might contribute to disease through chromosomal changes that result in the production of aberrant antisense transcripts.<ref name = "pmid16849434"/> A documented case of cis-NATs being involved in human disease comes from an inherited form of α-thalassemia where there is silencing of the hemoglobin α-2 gene through the action of a cis-NAT.<ref name = "pmid16849434"/> It is thought that in malignant cancer cells with activated transposable elements creates a large amount of transcriptional noise.<ref name = "pmid16849434"/> It is likely that aberrant antisense RNA transcripts resulting from this transcriptional noise may cause stochastic methylation of CpG islands associated with oncogenes and tumor suppressor genes.<ref name = "pmid16849434"/> This inhibition would further progress the malignancy of the cells since they lose key regulator genes.<ref name = "pmid16849434"/> By looking at upregulated antisense transcripts in tumor cells, researchers are able to look for more candidate tumor suppressor genes.<ref name = "pmid16849434"/> Also, aberrant cis-NATs have been implicated in neurological diseases such as Parkinson's disease.<ref name = "pmid16849434"/>

== References == {{Reflist}}

Category:Antisense RNA