Transcription-associated compositional skews in drosophila genes

Bergman, J, Betancourt, AJ ORCID: 0000-0001-9351-1413 and Vogl, C (2018) Transcription-associated compositional skews in drosophila genes Genome Biology and Evolution, 10 (1). pp. 269-275. ISSN 1759-6653, 1759-6653

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Abstract

In many organisms, local deviations from Chargaff’s second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome data set of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expression, comparable in strength to similar correlations between expression levels and genome-wide sequence features. This correlation is relatively stronger for germline, compared with somatic expression, consistent with the process of transcription-associated mutation bias. We also inferred mutation rates from alleles segregating at low frequencies in short introns, and show that, whereas the overall GC content of short introns does not conform to the equilibrium expectation, the level of the observed deviation from the second parity rule is generally consistent with the inferred rates.

Item Type:	Article
Uncontrolled Keywords:	Chargaff's second parity rule, compositional skew, transcription-associated mutation bias, base composition evolution
Depositing User:	Symplectic Admin
Date Deposited:	13 Nov 2017 11:29
Last Modified:	22 Jan 2026 19:46
DOI:	10.1093/gbe/evx200
Open Access URL:	https://academic.oup.com/gbe/article-pdf/10/1/269/...
Related Websites:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3012065
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