Open AccessNatural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast
Author(s) -
ClémentZiza Mathieu,
Marsellach Francesc X,
Codlin Sandra,
Papadakis Manos A,
Reinhardt Susanne,
RodríguezLópez María,
Martin Stuart,
Marguerat Samuel,
Schmidt Alexander,
Lee Eunhye,
Workman Christopher T,
Bähler Jürg,
Beyer Andreas
Publication year - 2014
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.20145123
Subject(s) - biology , expression quantitative trait loci , gene , genetics , transcriptome , antisense rna , quantitative trait locus , rna , coding region , computational biology , genetic variation , gene expression , non coding rna , single nucleotide polymorphism , genotype
Our current understanding of how natural genetic variation affects gene expression beyond well‐annotated coding genes is still limited. The use of deep sequencing technologies for the study of expression quantitative trait loci ( eQTL s) has the potential to close this gap. Here, we generated the first recombinant strain library for fission yeast and conducted an RNA ‐seq‐based QTL study of the coding, non‐coding, and antisense transcriptomes. We show that the frequency of distal effects ( trans‐ eQTL s) greatly exceeds the number of local effects ( cis‐ eQTL s) and that non‐coding RNA s are as likely to be affected by eQTL s as protein‐coding RNA s. We identified a genetic variation of swc5 that modifies the levels of 871 RNA s, with effects on both sense and antisense transcription, and show that this effect most likely goes through a compromised deposition of the histone variant H2A.Z. The strains, methods, and datasets generated here provide a rich resource for future studies.