Coding region: Difference between revisions

Revision as of 02:47, 22 May 2023

Revision as of 06:46, 9 July 2023

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== Structure and function ==

[[File:Coding Region in DNA.png|thumb|398x398px|'''Transcription''': RNA Polymerase (RNAP) uses a template DNA strand and begins coding at the promoter sequence (green) and ends at the terminator sequence (red) in order to encompass the entire coding region into the pre-mRNA (teal). The pre-mRNA is polymerised 5' to 3' and the template DNA read 3' to 5']] [[File:Transcription label en.jpg|thumb|An electron-micrograph of DNA strands decorated by hundreds of RNAP molecules too small to be resolved. Each RNAP is transcribing an RNA strand, which can be seen branching off from the DNA. "Begin" indicates the 3' end of the DNA, where RNAP initiates transcription; "End" indicates the 5' end, where the longer RNA molecules are completely transcribed.]]

In [[DNA]], the coding region is flanked by the [[Promoter (genetics)|promoter sequence]] on the 5' end of the [[template strand]] and the termination sequence on the 3' end. During [[Transcription (biology)|transcription]], the [[RNA Polymerase|RNA Polymerase (RNAP)]] binds to the promoter sequence and moves along the template strand to the coding region. RNAP then adds RNA [[nucleotide]]s complementary to the coding region in order to form the [[mRNA]], substituting [[uracil]] in place of [[thymine]].<ref name=":2">Overview of transcription. (n.d.). Retrieved from <nowiki>https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/overview-of-transcription</nowiki> .</ref> This continues until the RNAP reaches the termination sequence.<ref name=":2" />

After transcription and maturation, the [[mature mRNA]] formed encompasses multiple parts important for its eventual translation into [[protein]]. The coding region in an mRNA is flanked by the [[Five prime untranslated region|5' untranslated region]] (5'-UTR) and [[Three prime untranslated region|3' untranslated region]] (3'-UTR),<ref name=":12"/> the [[Five-prime cap|5' cap]], and [[Poly a tail|Poly-A tail]]. During [[Translation (biology)|translation]], the [[ribosome]] facilitates the attachment of the [[Transfer RNA|tRNAs]] to the coding region, 3 nucleotides at a time ([[codons]]).<ref>{{Cite web|url=https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/|title=Translation: DNA to mRNA to Protein|last=Clancy|first=Suzanne|date=2008|website=Scitable: By Nature Education}}</ref> The tRNAs transfer their associated [[amino acid]]s to the growing [[polypeptide]] chain, eventually forming the protein defined in the initial DNA coding region.

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=== Mutation types ===

[[File:Different_Types_of_Mutations.png|thumb|381x381px|Examples of the various forms of '''point mutations''' that may exist within coding regions. Such alterations may or may not have phenotypic changes, depending on whether or not they code for different amino acids during translation.<ref>{{Citation|last=Jonsta247|title=English: Example of silent mutation|date=2013-05-10|url=https://commons.wikimedia.org/wiki/File:Different_Types_of_Mutations.png|access-date=2019-11-19}}</ref>]]

There are various forms of mutations that can occur in coding regions. One form is [[silent mutation]]s, in which a change in nucleotides does not result in any change in amino acid after transcription and translation.<ref name=":3">Yang, J. (2016, March 23). What are Genetic Mutation? Retrieved from <nowiki>https://www.singerinstruments.com/resource/what-are-genetic-mutation/</nowiki> .</ref> There also exist [[nonsense mutation]]s, where base alterations in the coding region code for a premature stop codon, producing a shorter final protein. [[Point mutation|Point mutations]], or single base pair changes in the coding region, that code for different amino acids during translation, are called [[missense mutation]]s. Other types of mutations include [[frameshift mutation]]s such as [[Insertion mutation|insertions]] or [[Deletion (genetics)|deletions]].<ref name=":3" />

=== Formation ===

Some forms of mutations are [[Heredity|hereditary]] ([[germline mutation]]s), or passed on from a parent to its offspring.<ref name=":4">What is a gene mutation and how do mutations occur? - Genetics Home Reference - NIH. (n.d.). Retrieved from <nowiki>https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation</nowiki> .</ref> Such mutated coding regions are present in all cells within the organism. Other forms of mutations are acquired ([[somatic mutation]]s) during an organisms lifetime, and may not be constant cell-to-cell.<ref name=":4" /> These changes can be caused by [[mutagen]]s, [[carcinogen]]s, or other environmental agents (ex. [[Ultraviolet|UV]]). Acquired mutations can also be a result of copy-errors during [[DNA replication]] and are not passed down to offspring. Changes in the coding region can also be [[De novo mutation|de novo]] (new); such changes are thought to occur shortly after [[Fertilisation|fertilization]], resulting in a mutation present in the offspring's DNA while being absent in both the sperm and egg cells.<ref name=":4" />

=== Prevention ===

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== Constrained coding regions (CCRs) ==

While it is well known that the genome of one individual can have extensive differences when compared to the genome of another, recent research has found that some coding regions are highly constrained, or resistant to mutation, between individuals of the same species. This is similar to the concept of interspecies constraint in [[Conserved sequence|conserved sequences]]. Researchers termed these highly constrained sequences constrained coding regions (CCRs), and have also discovered that such regions may be involved in high [[purifying selection]]. On average, there is approximately 1 protein-altering mutation every 7 coding bases, but some CCRs can have over 100 bases in sequence with no observed protein-altering mutations, some without even synonymous mutations.<ref name=":0">Havrilla, J. M., Pedersen, B. S., Layer, R. M., & Quinlan, A. R. (2018). A map of constrained coding regions in the human genome. ''Nature Genetics'', 88–95. {{doi: |10.1101/220814}}</ref> These patterns of constraint between genomes may provide clues to the sources of rare [[Developmental disorder|developmental diseases]] or potentially even embryonic lethality. Clinically validated variants and [[de novo mutation]]s in CCRs have been previously linked to disorders such as [[infantile epileptic encephalopathy]], developmental delay and severe heart disease.<ref name=":0" />

== Coding sequence detection ==