Please use this identifier to cite or link to this item: doi:10.22028/D291-30494
Title: SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome
Author(s): Neininger, Kerstin
Marschall, Tobias
Helms, Volkhard
Language: English
Volume: 14
Issue: 4
Publisher/Platform: PLOS
Year of Publication: 2019
DDC notations: 004 Computer science, internet
Publikation type: Journal Article
Abstract: Single-nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans and drive phenotypic variation. Due to evolutionary conservation, SNPs and indels (insertion and deletions) are depleted in functionally important sequence elements. Recently, population-scale sequencing efforts such as the 1000 Genomes Project and the Genome of the Netherlands Project have catalogued large numbers of sequence variants. Here, we present a systematic analysis of the polymorphisms reported by these two projects in different coding and non-coding genomic elements of the human genome (intergenic regions, CpG islands, promoters, 5' UTRs, coding exons, 3' UTRs, introns, and intragenic regions). Furthermore, we were especially interested in the distribution of SNPs and indels in direct vicinity to the transcription start site (TSS) and translation start site (CSS). Thereby, we discovered an enrichment of dinucleotides CpG and CpA and an accumulation of SNPs at base position -1 relative to the TSS that involved primarily CpG and CpA dinucleotides. Genes having a CpG dinucleotide at TSS position -1 were enriched in the functional GO terms "Phosphoprotein", "Alternative splicing", and "Protein binding". Focusing on the CSS, we compared SNP patterns in the flanking regions of canonical and alternative AUG and near-cognate start sites where we considered alternative starts previously identified by experimental ribosome profiling. We observed similar conservation patterns of canonical and alternative translation start sites, which underlines the importance of alternative translation mechanisms for cellular function.
DOI of the first publication: 10.1371/journal.pone.0214816
Link to this record: urn:nbn:de:bsz:291--ds-304943
ISSN: 1932-6203
Date of registration: 30-Mar-2020
Faculty: MI - Fakultät für Mathematik und Informatik
NT - Naturwissenschaftlich- Technische Fakultät
Department: MI - Informatik
NT - Biowissenschaften
Professorship: MI - Prof. Dr. Tobias Marschall
NT - Prof. Dr. Volkhard Helms
Collections:SciDok - Der Wissenschaftsserver der Universität des Saarlandes

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