Transcription bodies regulate gene expression by sequestering CDK9

Abstract

The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells, but it remains unclear if and how they affect gene expression. Here, we disrupted the formation of two prominent transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analyzed the effect on gene expression using enriched SLAM-Seq and live-cell imaging. We found that the disruption of transcription bodies results in the upregulation of genes that already have accessible chromatin and are poised to be transcribed when the two transcription bodies are present. Live-cell imaging suggests that the disruption of these transcription bodies enables poised genes to be transcribed in ectopic transcription bodies. Our results suggest that transcription bodies regulate transcription genome-wide by sequestering components of the transcriptional machinery.

CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts

“…Due to toxicity effect of s4-UTP in combination of RfxCas13d protein, 25mM aliquots were selected as final concentration for Slam-Seq experiment. This reduced levels of s4-UTP could potentially compromise the coverage of label reads compared to optimized conditions in zebrafish embryos 6,18,59 . 25 embryos were collected at 4 hpf and snap-frozen in 500 µl of Trizol in tubes protected from light.…”

“…Nanog, SoxB1 and Pou5f3) or chromatin remodelers controlling ZGA, and the microRNA, miR-430, and codon optimality with a major role in the clearance of the maternal RNA after ZGA 4,[7][8][9][10][11][12][13][14][15] . In addition, translational control of maternal mRNAs and complete nuclear pore complexes maturation are other mechanisms controlling ZGA 5,12,[16][17][18] . Despite these advances, the maternally-instructed post-translational regulatory mechanisms such as protein phosphorylation or ubiquitination modulating MZT are much less understood specially in vertebrates 2,19 and a systematic analysis is needed.…”

Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

“…Similarly, we observe all three classes of Pol II pSer5 organization during the minor wave of genome activation at 2.5 hpf, although there were fewer active sites, which is consistent with lower levels of transcription at this time (fig. S9, A to H) ( 16 , 17 , 46 ). This suggests that each class of Pol II organization represents a generalizable state of Pol II organization broadly used throughout genome activation.…”