A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

Yavor Hadzhiev,Divyasree Poovathumkadavil,Sarah Bajan,Sascha Conic,Haseeb K Qureshi,Agnieszka Gambus,Làszlò Tora,John S Fossey,Lucy Wheatley,Aleksandra Jasiulewicz,Ferenc Müller,Huy Van Nguyen,Ledean Cooper,György Hutvàgner,Attila Sik,Joseph W Wragg

doi:10.1038/s41467-019-08487-5

Yavor Hadzhiev, Divyasree Poovathumkadavil + Show 14 more

Open Access

https://doi.org/10.1038/s41467-019-08487-5

Copy DOI

Abstract

Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). However, a set of genes escapes global repression and gets activated before MBT. Here we describe the formation and the spatio-temporal dynamics of a pair of distinct transcription compartments, which encompasses the earliest gene expression in zebrafish. 4D imaging of pri-miR430 and zinc-finger-gene activities by a novel, native transcription imaging approach reveals transcriptional sharing of nuclear compartments, which are regulated by homologous chromosome organisation. These compartments carry the majority of nascent-RNAs and active Polymerase II, are chromatin-depleted and represent the main sites of detectable transcription before MBT. Transcription occurs during the S-phase of increasingly permissive cleavage cycles. It is proposed, that the transcription compartment is part of the regulatory architecture of embryonic nuclei and offers a transcriptionally competent environment to facilitate early escape from repression before global genome activation.

Highlights

Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT)
Genome activation is regulated by a threshold nucleo-cytoplasmic (NC) ratio, which is reached at the midblastula transition (MBT)[3] and reflects release from repression by diluted maternal factors, such as histones and replication factors[4,5,6,7], Together with genome activation, simultaneous clearance of maternal RNAs8 at MBT overhauls the embryonic transcriptome[9]
A series of three miR430- targeting morpholino oligonucleotide (MO) (Supplementary Table 1) were generated, which upon microinjection into fertilised eggs led to the detection of two distinct transcription foci in nuclei of zebrafish blastula embryos, by lightsheet imaging (Fig. 1a, b)

Summary

Introduction

Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). The first genes expressed in the zebrafish embryo include microRNAs, which drive the clearance of maternal mRNAs13, as well as transcription factors and chromatin binding proteins, which may play a role in the main wave of genome activation[10] The existence of this first wave of genome activation raises the question of how genes escape the repressive environment before the threshold NC is reached at MBT. It remains unknown how transcription can occur during the short cell cycles consisting only of S and M-phases. MOVIE enabled investigation of the spatio-temporal dynamics of this transcription compartment, which is a characteristic feature of pre-MBT embryos

Methods

Results

Conclusion