Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Abstract

BackgroundTranscription start sites (TSSs) with pronounced and phased nucleosome arrays downstream and nucleosome-depleted regions upstream of TSSs are observed in various species.ResultsWe have characterized sequence variation and expression properties of this set of TSSs (which we call “Nucleocyclic TSSs”) using germline and somatic cells of three medaka (Oryzias latipes) inbred isolates from different locations. We found nucleocyclic TSSs in medaka to be associated with higher gene expression and characterized by a clear boundary in sequence composition with potentially-nucleosome-destabilizing A/T-enrichment upstream (p < 10−60) and nucleosome- accommodating C/G-enrichment downstream (p < 10−40) that was highly conserved from an ancestor. A substantial genetic distance between the strains facilitated the in-depth analysis of patterns of fixed mutations, revealing a localization-specific equilibrium between the rates of distinct mutation categories that would serve to maintain the conserved sequence anisotropy around TSSs. Downstream of nucleocyclic TSSs, C to T, T to C, and other mutation rates on the sense strand increased around first nucleosome dyads and decreased around first linkers, which contrasted with genomewide mutational patterns around nucleosomes (p < 5 %). C to T rates are higher than G to A rates around nucleosome associated with germline nucleocyclic TSS sites (p < 5 %), potentially due to the asymmetric effect of transcription-coupled repair.ConclusionsOur results demonstrate an atypical evolutionary process surrounding nucleocyclic TSSs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2198-5) contains supplementary material, which is available to authorized users.

Centromere evolution and CpG methylation during vertebrate speciation

“…Inserted DNA fragments in each genome may affect gene regulation during speciation. In the Hd-rR and HNI genomes, we first identified TSSs supported by 5’SAGE tags 19 , 54 that had 1–10-kbp mid-sized insertions within 100 bp from the TSSs in one of the genomes, and we then detected 101 differentially expressed TSSs between Hd-rR and HNI. Specifically, from each strain, we generated two RNA-seq biological replicates from early embryos (blastulae), and we sequenced and processed these four data sets using DESeq2 55 to detect the 101 TSSs that had insertions in their upstream regions (Supplementary Fig.…”

Comparative Analysis of Genome and Epigenome in Closely Related Medaka Species Identifies Conserved Sequence Preferences for DNA Hypomethylated Domains

“…We examined how each type of HMDs (common or species-specific) is reflected in gene transcription of the two species, by conducting a comparison of RNA-seq data. We newly obtained about 62.5 M reads from HNI blastula cells, and for Hd-rR, we utilized our previous RNA-seq data from d-rR (Nakatani et al, 2015), a closed colony line from which the Hd-rR inbred line had been established. After mapping them to the Hd-rR genome, genes were isolated and classified according to those having common HMDs or speciesspecific HMDs in their promoter regions or in gene bodies.…”