Remodelling of H3K4me3 histone tail modifications across life stages in Atlantic salmon

Abstract

Atlantic salmon undergo a series of preparatory adaptation for a life in the sea, referred to as smoltification. Recent studies have focused on the genetic base of this process and revealed genome-wide transcriptional remodeling related to smoltification and seawater-transfer in different tissues, especially in the liver (Harvey, 2019; Gillard et al., 2018). However, we know very little about the mechanisms that drive the dynamics of genome regulation during smoltification. A factor that controls the transcriptional level gene expression is Epigenetics, Epigenetics is a common term for various chemical alterations of the DNA molecule or chemical modifications to the histone tail, which is called histone tail modification. one of the well-studied histone tail modification H3K4me3 is reported to associate with active promoter. In this project, we aim to interpret this histone tail modification remodeling of gene expression during different life-stages of salmon. We generate ChIP-seq data for H3K4me3, profiled the life-stage associated landscape of H3K4me3 in Atlantic salmon liver by using H3K4me specific antibody. 14 fish (4 parr, 6 smolt, and 4 seawater) across three life stages (parr, smolt, and seawater) were sampled. We found H3K4me3 signals in all life stages are enriched in the promoter and 5UTR of gene region. The life stage-specific genes with the H3K4me3 signal reflecting the physiological characteristics of that stage and associated with smolt liver function and development. By linking the H3K4me3-marked genes with life-stage associated dynamic co-expressed gene cluster from previous study (Harvey, 2019), we find the histone code is weakly correlated with differential gene expression. In conclusion, the analyses of H3K4me3-signals and gene expression fits with a model where some genes are regulated through histone tails remodeling during parr-smolt transformation, but that this level of genome regulation does not play the major role in the developmental transition from a parr to a smolt. Unfortunately, we failed to produce high-quality ChIP-seq data from biological replicates. Hence, data analysis based on genome-wide patterns of H3K4me3-signals from pooled replicates, which only allowed us to assess the H3K4me3 signals in a qualitative way.

Atlanterhavslaks gjennomgår en serie forberedende tilpasninger for et liv i havet, kalt smoltifisering. Nyere studier har fokusert på den genetiske basisen i denne prosessen og avdekket omfattende transkripsjonelle endringer relatert til smoltifisering og overgang fra ferskvann til saltvann i forskjellige vev, spesielt i leveren (Harvey, 2019; Gillard et al., 2018). Vi vet imidlertid veldig lite om mekanismene som driver dynamikken i genreguleringen under smoltifisering. En faktor som kontrollerer genekspresjonen på transkripsjonelt nivå er epigenetikk. Epigenetikk er en vanlig betegnelse for forskjellige kjemiske endringer av DNA-molekylet eller kjemiske modifikasjoner av histonhalene. En av de godt studerte histonhalemodifiseringene, H3K4me3, assosierer med aktive promoterer. I dette prosjektet tar vi sikte på å tolke denne histonhalemodifiseringen som remodellering av genuttrykk i løpet av laksens forskjellige livsfaser.