NDLI: Human Coding Synonymous Single Nucleotide Polymorphisms at Ramp Regions of mRNA Translation

Content Provider	PubMed Central
Author	Quan, Li Qu, Hui-qi
Editor	Wei, Zhi
Copyright Year	2013
Abstract	According to the ramp model of mRNA translation, the first 50 codons favor rare codons and have slower speed of translation. This study aims to detect translational selection on coding synonymous single nucleotide polymorphisms (sSNP) to support the ramp theory. We investigated fourfold degenerate site (FFDS) sSNPs with A↔G or C↔T substitutions in human genome for distribution bias of synonymous codons (SC), grouped by CpG or non-CpG sites. Distribution bias of sSNPs between the 3rd ∼50th codons and the 51st ∼ remainder codons at non-CpG sites were observed. In the 3rd ∼50th codons, G→A sSNPs at non-CpG sites are favored than A→G sSNPs [P = 2.89×10−3], and C→T at non-CpG sites are favored than T→C sSNPs [P = 8.50×10−3]. The favored direction of SC usage change is from more frequent SCs to less frequent SCs. The distribution bias is more obvious in synonymous substitutions CG(G→A), AC(C→T), and CT(C→T). The distribution bias of sSNPs in human genome, i.e. frequent SCs to less frequent SCs is favored in the 3rd ∼50th codons, indicates translational selection on sSNPs in the ramp regions of mRNA templates.
Related Links	http://dx.doi.org/10.1371/journal.pone.0059706
Starting Page	59706
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	3
Volume Number	8
Language	English
Publisher	Public Library of Science
Publisher Date	2013-03-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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