Author response: Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Abstract

Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation on chromatin. In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution.

PRC1 Catalytic Activity Is Central to Polycomb System Function

“…The high-throughput data reported in this study have been deposited in GEO under the accession number GEO: GSE132754. Published data used in this study include BioCAP-seq (GEO: GSE43512 (Long et al, 2013)); MAX ChIP-seq (GEO: GSE48175; (Krepelova et al, 2014)); H2AK119ub1, H3K27me3 and RING1B cChIP-seq together with corresponding Inputs in PRC1 CKO ESCs (GEO: GSE119618; (Fursova et al, 2019)); cRNA-seq in Pcgf4 À/À 4;Pcgf2 fl/fl (GEO: GSE119619; (Fursova et al, 2019)); CaptureC in RING1B deg and control cell lines (Rhodes et al, 2019), and 4sU RNA-seq gene expression data for mESCs following RA-induced differentiation (GEO: GSE98756) (Dimitrova et al, 2018). All R and Perl scripts used for data analysis in this study are available upon request.…”

“…Mouse genes in a custom non-redundant set (n = 20633) that was used for differential gene expression analysis were classified into three groups based on the overlap of their gene promoters with non-methylated CpG islands (NMI), as well as RING1B-and SUZ12bound sites. NMIs (n = 27047) were identified using MACS2 peak calling from BioCAP-seq data (Long et al, 2013) as regions which are enriched with non-methylated CpG-rich DNA. All genes with promoters (TSS ± 2500 bp) not overlapping with NMIs were referred to as non-NMI genes (n = 5326).…”

Chromatin Control of Developmental Dynamics and Plasticity

“…DNA methylation is a feature shared by all vertebrates and by many, but not all, non-vertebrate organisms. In vertebrates, up to 90% of all CG dinucleotides, which tend to be interspersed across the genome, are methylated, with the exception of unmethylated islands (Bogdanovi c et al, 2016;Long et al, 2013). These regions are relatively rich in CG dinucleotides, especially in mammals (CpG islands), and often overlap with regulatory sequences (Bogdanovic and Gomez-Skarmeta, 2014).…”