Quantitative measurements of chromatin modification dynamics during zygotic genome activation

Abstract

Histone posttranslational modifications (PTMs) are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We describe an approach that images fluorescent antibody fragments to quantify PTM enrichment and active transcription at defined loci during zygotic genome activation in living zebrafish embryos. The technique reveals a drastic increase in histone H3 Lys27 acetylation (H3K27ac) before genome activation both at a specific locus and globally.

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

“…Future studies will be required to explore in more detail how Pou5f3, Sox19b and Nanog prime genes for activity. One potential mechanism is that these transcription factors mediate the establishment of H3K27ac at regulatory elements [56,59]. PSN as well as H3K27ac are essential for zygotic genome activation [15,19,59], and the highest H3K27ac enrichment occurs at PSNprimed loci (this study).…”

“…We find that the mir-430 cluster, which is transcribed two orders of magnitude higher than any other region, undergoes a dramatic loss in accessibility when elongation of RNA polymerase II is blocked. The miR-430 cluster is one of the first to be transcribed and initially, all transcribing RNA polymerase II localizes to the two alleles of the miR-430 cluster [19][20][21]56], which might facilitate the formation of RNA-pol II 'trains' capable of evicting nucleosomes, as shown in vitro [33].…”

“…Our finding that regulatory elements can be accessible prior to transcription of associated genes is in agreement with the establishment of other "active" chromatin features prior to gene expression. At zebrafish promoters, for example, the histone modifications H3K4me3 [57,58] and H3K27ac [56,59], a hypomethylated state ( [25,[60][61][62], and well-positioned nucleosomes [63] can be established prior to the time their associated genes become expressed. Similar observations have been made in other species.…”

Chemical Genetics Screen Identifies Epigenetic Mechanisms Involved in Dopaminergic and Noradrenergic Neurogenesis in Zebrafish

“…In this study, we did not experimentally validate, whether the identified HDAC and Bromodomain inhibitors alter histone acetylation or recognition in zebrafish larvae. However, for most of these compounds, the specificity and activity on histone acetylation or acetylated histone recognition, respectively, have recently been reported for larval and adult zebrafish tissues (Pfefferli et al, 2014;Vleeshouwer-Neumann et al, 2015;Pinho et al, 2016;Chan et al, 2019;Sato et al, 2019). An increase in the levels of histone acetylation has been reported in zebrafish tissues after treatment with the HDAC inhibitors Entinostat, Mocetinostat and Vorinostat.…”

“…The Bet-Bromodomain inhibitors block Bet-family proteins binding to acetylated histones, and thus might inhibit active transcription (Jang et al, 2005;Loven et al, 2013). Recently, JQ1 has been reported to block active transcription and RNAP2 recruitment during zygotic genome activation in zebrafish embryos [43.8 µM at blastula stage (Chan et al, 2019); 10 µM at Blastula stage (Sato et al, 2019)]. Furthermore, live cell imaging in zebrafish embryos revealed that JQ1 efficiently abolished the binding of a bromodomain containing reporter construct to Fab-based live endogenous labeled H3K27ac sites (Sato et al, 2019).…”