Single cell epigenomic and transcriptomic analysis uncovers potential transcription factors regulating mitotic/meiotic switch

Abstract

In order to reveal the complex mechanism governing the mitotic/meiotic switch in female germ cells at epigenomic and genomic levels, we examined the chromatin accessibility (scATAC-seq) and the transcriptional dynamics (scRNA-seq) in germ cells of mouse embryonic ovary between E11.5 to 13.5 at single-cell resolution. Adopting a strict transcription factors (TFs) screening framework that makes it easier to understand the single-cell chromatin signature and a TF interaction algorithm that integrates the transcript levels, chromatin accessibility, and motif scores, we identified 14 TFs potentially regulating the mitotic/meiotic switch, including TCFL5, E2F1, E2F2, E2F6, E2F8, BATF3, SP1, FOS, FOXN3, VEZF1, GBX2, CEBPG, JUND, and TFDP1. Focusing on TCFL5, we constructed Tcfl5+/− mice which showed significantly reduced fertility and found that decreasing TCFL5 expression in cultured E12.5 ovaries by RNAi impaired meiotic progression from leptotene to zygotene. Bioinformatics analysis of published results of the embryonic germ cell transcriptome and the finding that in these cells central meiotic genes (Stra8, Tcfl5, Sycp3, and E2f2) possess open chromatin status already at the mitotic stage together with other features of TCFL5 (potential capability to interact with core TFs and activate meiotic genes, its progressive activation after preleptotene, binding sites in the promoter region of E2f2 and Sycp3), indicated extensive amplification of transcriptional programs associated to mitotic/meiotic switch with an important contribution of TCFL5. We conclude that the identified TFs, are involved in various stages of the mitotic/meiotic switch in female germ cells, TCFL5 primarily in meiotic progression. Further investigation on these factors might give a significant contribution to unravel the molecular mechanisms of this fundamental process of oogenesis and provide clues about pathologies in women such as primary ovarian insufficiency (POI) due at least in part to meiotic defects.

Single-nucleus multiomics reveals the gene-regulatory networks underlying sex determination of murine primordial germ cells

“…TCFL5 binds to the promoters of meiotic genes such as Sycp1 (synapsis) and Stag3 (cohesion) during spermatogenesis in the mouse 79 . Tcfl5 is indispensable for the completion of meiosis and spermatid maturation 79 , and meiosis of female germ cells 81 . Our multiomics data also demonstrate strong Tfap2c expression and motif enrichment in XX PGCs beginning at E12.5 and continuing through E13.5.…”

Follicular development and ovary aging: single-cell studies

“…Several TFs, including Msx1, Msx2, Gata2, Cdx2, Bmyc, and Sox4, specifically were expressed at the preleptotene stage, implying their possible roles in meiosis initiation of mouse [44]. An identical occasion that STRA8 (stimulated by retinoic acid 8) (preleptotene-leptotene) and subsequent TCFL5 (transcription factor like 5) (leptotene-zygotene) independently orchestrate in female mice meiosis was hypothesized [52]. The majority of oogonia undergo meiosis to become oocytes.…”

“…Furthermore, Ge et al effectively displayed germ cell meiotic initiation through the application of scRNA-seq on 19 387 cells derived from E11.5–E14.5 mouse gonadal ridges and ovaries [47]. A complex network, including KIT, Wingless-Type MMTV Integration Site Family (WNT), BMP, and TGF β signaling pathways, centered on the beginning of meiosis in mice [52]. With the transition from mitosis to meiosis in FGCs, there are dramatic changes in gene expression, with the downregulation of pluripotency marker genes [54] and a substantial overexpression of oocyte marker genes in mouse and human [44, 55, 56].…”

“…REC8 (REC8 meiotic recombination protein) may also be involved in the transition from mitosis to meiosis. Fourteen transcription factors including TCFL5, E2F1, E2F2, and E2F6 were identified as possibly implicated in the mitosis-to-meiosis transition in mice [52].…”

“…Zhang et al also observed that more than 85% of genes increased at the leptotene stage were already strongly expressed before the commencement of meiosis. In addition, Stra8, Tcfl5, Sycp3, and E2f5 genes are already in an open chromatin state during the mitotic phase [52]. Consequently, further research is required to investigate the exact processes of the mitotic-to-meiotic transition.…”