Maternal and zygotic contributions to H3K4me1 chromatin marking during germ layer formation

Kitt D Paraiso; Ira L Blitz; Ken W Y Cho

doi:10.1016/j.ydbio.2024.11.006

Maternal and zygotic contributions to H3K4me1 chromatin marking during germ layer formation

Dev Biol. 2024 Nov 15:518:8-19. doi: 10.1016/j.ydbio.2024.11.006. Online ahead of print.

Authors

Kitt D Paraiso¹, Ira L Blitz², Ken W Y Cho³

Affiliations

¹ Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
² Developmental and Cell Biology, University of California, Irvine, CA, USA.
³ Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA. Electronic address: kwcho@uci.edu.

PMID: 39550025
DOI: 10.1016/j.ydbio.2024.11.006

Abstract

An early step in triploblastic embryo differentiation is the formation of the three germ layers. Maternal pioneer transcription factors (TFs) bind to embryonic enhancers before zygotic genome activation, initiating germ layer specification. While maternal TFs' role in establishing epigenetic marks is known, how early pluripotent cells gain spatially restricted epigenetic identities remains unclear. We show that by the early gastrula stage, H3K4me1-marked regions become distinct in each germ layer, with certain chromatin regions forming high density H3K4me1 marked regions (HDRs). Genes associated with these HDRs are more robustly expressed compared to those associated with low density H3K4me1 marked regions (LDRs) in the genome. This process is driven by the sequential actions of maternal and zygotic factors. Knockdown of key maternal endodermal TFs (Otx1, Vegt and Foxh1) leads to a loss of endodermal H3K4me1 marks in endoderm, with a concurrent emergence of ectodermal and mesodermal marks, indicating a shift in chromatin state. This work highlights the importance of coordinated activities of maternal and zygotic TFs in defining the regionally-resolved and dynamic process of chromatin modification conferred by H3K4me1 in the early Xenopus embryo.

Keywords: Canalization; Epigenetics; Gene expression; Histone modification; Robustness; Super enhancers; Transcription factors; Zygotic genome activation.