Coding region: Difference between revisions

Revision as of 16:55, 6 August 2020

Revision as of 10:12, 16 September 2020

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{{short description|Portion of gene's sequence which codes for protein}}

{{more citations needed|date=August 2018}}

The '''coding region''' of a [[gene]], also known as the '''CDS''' (from ''coding sequence''), is the portion of a gene's [[DNA]] or [[RNA]] that codes for [[protein]].<ref name=":12">{{cite web|url=http://genome.wellcome.ac.uk/doc_WTD020755.html|title=Gene Structure|last=Twyman|first=Richard|date=1 August 2003|publisher=The Wellcome Trust|url-status=dead|archive-url=https://web.archive.org/web/20070328214808/http://genome.wellcome.ac.uk/doc_WTD020755.html|archive-date=28 March 2007|access-date=6 April 2003}}</ref> Studying the length, composition, regulation, splicing, structures, and functions of coding regions compared to non-coding regions over different species and time periods can provide a significant amount of important information regarding gene organization and evolution of [[prokaryote]]s and [[eukaryote]]s.<ref>{{Cite journal | vauthors = Höglund M, Säll T, Röhme D |date=February 1990|title=On the origin of coding sequences from random open reading frames|journal=Journal of Molecular Evolution|volume=30|issue=2|pages=104–108|doi=10.1007/bf02099936|issn=0022-2844|bibcode=1990JMolE..30..104H|s2cid=5978109}}</ref> This can further assist in mapping the [[Human Genome Project|human genome]] and developing gene therapy.<ref>{{cite journal | vauthors = Sakharkar MK, Chow VT, Kangueane P | title = Distributions of exons and introns in the human genome | journal = In Silico Biology | volume = 4 | issue = 4 | pages = 387–93 | date = 2004 | pmid = 15217358 }}</ref>

== Definition ==

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== History ==

In 1978, [[Walter Gilbert]] published "Why Genes in Pieces" which first began to explore the idea that the gene is a mosaic—that each full [[nucleic acid]] strand is not coded continuously but is interrupted by "silent" non-coding regions. This was the first indication that there needed to be a distinction between the parts of the genome that code for protein, now called coding regions, and those that do not.<ref>{{cite journal | vauthors = Gilbert W | title = Why genes in pieces? | journal = Nature | volume = 271 | issue = 5645 | pages = 501 | date = February 1978 | pmid = 622185 | doi = 10.1038/271501a0 | bibcode = 1978Natur.271..501G | s2cid = 4216649 }}</ref>

== Composition ==

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== Coding Sequence Detection ==

While identification of [[open reading frames]] within a DNA sequence is straightforward, identifying coding sequences is not, because the cell translates only a subset of all open reading frames to proteins.<ref>{{cite journal | vauthors = Furuno M, Kasukawa T, Saito R, Adachi J, Suzuki H, Baldarelli R, Hayashizaki Y, Okazaki Y | display-authors = 6 | title = CDS annotation in full-length cDNA sequence | journal = Genome Research | volume = 13 | issue = 6B | pages = 1478–87 | date = June 2003 | pmid = 12819146 | pmc = 403693 | doi = 10.1101/gr.1060303 | url = http://genome.cshlp.org/content/13/6b/1478.full.pdf+html | publisher = Cold Spring Harbor Laboratory Press }}</ref> Currently CDS prediction uses sampling and sequencing of mRNA from cells, although there is still the problem of determining which parts of a given mRNA are actually translated to protein. CDS prediction is a subset of [[gene prediction]], the latter also including prediction of DNA sequences that code not only for protein but also for other functional elements such as RNA genes and regulatory sequences.

In both [[prokaryote]]s and [[eukaryote]]s, [[Overlapping gene|gene overlapping]] occurs relatively often in both DNA and RNA viruses as an evolutionary advantage to reduce genome size while retaining the ability to produce various proteins from the available coding regions.<ref>{{cite journal | vauthors = Rogozin IB, Spiridonov AN, Sorokin AV, Wolf YI, Jordan IK, Tatusov RL, Koonin EV | title = Purifying and directional selection in overlapping prokaryotic genes | language = English | journal = Trends in Genetics | volume = 18 | issue = 5 | pages = 228–32 | date = May 2002 | pmid = 12047938 | doi = 10.1016/S0168-9525(02)02649-5 | url = https://www.cell.com/trends/genetics/abstract/S0168-9525(02)02649-5 }}</ref><ref>{{cite journal | vauthors = Chirico N, Vianelli A, Belshaw R | title = Why genes overlap in viruses | journal = Proceedings. Biological Sciences | volume = 277 | issue = 1701 | pages = 3809–17 | date = December 2010 | pmid = 20610432 | pmc = 2992710 | doi = 10.1098/rspb.2010.1052 }}</ref> For both DNA and RNA, [[Sequence alignment#Pairwise alignment|pairwise alignments]] can detect overlapping coding regions, including short [[open reading frame]]s in viruses, but would require a known coding strand to compare the potential overlapping coding strand with.<ref>{{cite journal | vauthors = Firth AE, Brown CM | title = Detecting overlapping coding sequences with pairwise alignments | journal = Bioinformatics | volume = 21 | issue = 3 | pages = 282–92 | date = February 2005 | pmid = 15347574 | doi = 10.1093/bioinformatics/bti007 | url = https://academic.oup.com/bioinformatics/article/21/3/282/237775 | doi-access = free }}</ref> An alternative method using single genome sequences would not require multiple genome sequences to execute comparisons but would require at least 50 nucleotides overlapping in order to be sensitive.<ref>{{cite journal | vauthors = Schlub TE, Buchmann JP, Holmes EC | title = A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences | journal = Molecular Biology and Evolution | volume = 35 | issue = 10 | pages = 2572–2581 | date = October 2018 | pmid = 30099499 | pmc = 6188560 | doi = 10.1093/molbev/msy155 | editor-first = Harmit | editor-last = Malik }}</ref>