Single-Cell DNA Methylation Analysis of Chicken Lampbrush Chromosomes

Abstract

DNA methylation is an essential epigenetic regulation mechanism implicated in transcription and replication control, developmental reprogramming, retroelements silencing and other genomic processes. During mammalian development, a specific DNA methylation pattern should be established in germ cells to allow embryonic development. Less is known about germ cell DNA methylation in other species. To close this gap, we performed a single-cell methylome analysis of chicken diplotene oocytes. We comprehensively characterized methylation patterns in these cells, obtained methylation-based chicken genome segmentation and identified oocyte-specific methylated gene promoters. Our data show that despite the formation of specific transcriptionally hyperactive genome architecture in chicken diplotene oocytes, methylation patterns in these cells closely resemble genomic distribution observed in somatic tissues.

The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes

“…We have shown that transcription on the majority of normal lateral loops on avian lampbrush chromosomes is initiated at the promoters of active genes; transcription start sites often correspond to CpG islands. This is consistent with previous findings on hypomethylation of the majority of promoters and CpG islands in single-cell methylome data of the chicken diplotene oocytes (Nurislamov et al . 2022).…”

“…g. MHM1 region is not hypermethylated in chicken lampbrush stage oocytes. Single-nucleus DNA methylation profile of chicken lampbrush chromosomes was obtained from (Nurislamov et al 2022). For simplicity, only genes in the MHM1 locus are shown.…”

Lampbrush chromosome studies in the post‐genomic era

“…For example, studies on chicken diplotene oocytes recently showed that genome‐wide DNA methylation pattern is very similar to the somatic cells during mitotic prophase, with hypomethylated CpG islands and hypermethylated intergenic regions. [ 22 ] Only a handful of loci showed oocyte‐specific methylation levels. Consequently, transcription hyperactivation and structural chromatin reorganization occur by methylation‐independent mechanisms.…”

“…To further advance our understanding of lampbrush chromatin organization into functional domains, we consider a comprehensive study of the DNA methylation profile, nucleosome positioning, pattern of epigenetic modifications, and distribution of chromatin contact domains using advanced whole‐genomic approaches, such as single‐cell high‐throughput chromosome conformation capture (Hi‐C) [ 30 ] and bisulfite sequencing, [ 22 ] after careful optimization of the experimental conditions (Box 2). These techniques will allow to create a genome‐wide map of lampbrush chromatin domains with different sets of epigenetic modifications and to suggest mechanisms of chromomeres separation from each other.…”

“…The study of DNA methylation is probably the most straightforward since current methods of single-cell genome-wide bisulfite sequencing can be directly applied to the DNA isolated from individual oocytes. [22]…”