Chromatin accessibility landscapes during onset of salmon maturation v1
Authors: R Mohamed Amin , Naval-Sanchez Marina , Menzies Moira , Evans Bradley , King Harry , Reverter Antonio , Kijas James 
Published: October 2020

Background: Despite sexual development being ubiquitous to vertebrates, the epigenetic mechanisms controlling this fundamental transition remain largely undocumented in many organisms. Our previous own work showed that despite DNA methylations played a key role upregulating a defined set of genes during the maturation process, methylation alone does not control genome-wide patterns of gene expression. This prompted us to to characterise the epigenomic features during onset of maturation at the chromatin level. Results: We performed ATAC-seq (assay for transposase-accessible chromatin sequencing) to produce genome-wide maps of chromatin accessibility changes. ATAC-seq was performed for multiple tissues and peak enrichment around transcription start sites used as the key quality control metric (TSS). Following data pruning, we took 12 liver libraries (3 replicates across all 4 timepoints) and a total of 699 million uniquely mapped paired-end reads forward into joint analysis with RNA-seq and WGBS data. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4 (n=148). The direction of change was approximately balanced between DARs with increased and decreased accessibility, broadly matching the balance between up and down regulated global gene expression changes observed for liver. We next asked if the early changes in chromatin state persisted throughout the time course using hierarchical clustering. The majority of DARs (n=1036; 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points. Similarly, regions that gained accessibility at T2 (n=696; 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes, as opposed to pulsatile epigenomic changes that snapped back after a small number of days or weeks. We observed high correlation between chromatin state changes and altered gene expression for the single tissue with ATAC-seq data (liver). The correlation was highest for differentially accessible regions immediately adjacent to coding genes, implicating cis-regulatory elements (CREs). To examine the biological consequence of chromatin state changes, we focused on CREs given their established role on transcriptional regulation via transcription factors (TFs) binding. We focussed on the subset of CREs that underwent a change in accessibility during the time course to evaluate i) the expression behaviour of their closet gene; ii) the biological function of those genes, and iii) any enrichment for transcription factor binding sites (motifs). We found a small subset of CREs (n = 65) underwent increased accessibility early in the time course and the majority (n = 46; 79%’Χ2p < 8.028-08) upregulated their nearest gene in a tightly coordinated manner. It also appears CREs more tightly controlled the downregulation of genes compared to DARs located in gene bodies, downstream regions or within intergenic regions. The gene set associated with coordinated up regulation exhibited significant GO enrichment related to lipid metabolism and energy metabolism (AAcyl-CoA biosynthesis). Acyl-CoA are coenzymes involved in energy synthesis, consistent with the expectation of liver function through an energetically costly transition such as maturation. Conclusions: The results clearly demonstrated chromatin state changes played a dominant role in directing global changes in gene expression and strongly suggest that chromatin state changes at CREs directly control gene expression in liver and upregulate energy metabolism genes via changes in TF activity.