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Effect of nuclear pore complex (NPC) blockage by WGA treatment on zygotic genome activation (ZGA) during zebrafish early development

ABSTRACT: Effect of nuclear pore complex (NPC) blockage by WGA treatment on zygotic genome activation (ZGA) during zebrafish early development

PROVIDER: PRJNA878480 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21487520.fastq.gz	Fastqsanger.gz
	SRR21487521.fastq.gz	Fastqsanger.gz
	SRR21487522.fastq.gz	Fastqsanger.gz

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Effect of nuclear pore complex (NPC) blockage by WGA treatment on zygotic genome activation (ZGA) during zebrafish early development

Project description:To investigate the function of nuclear pore complex (NPC) in the regulation of zygotic genome activation (ZGA), we microinjected medium dosage of WGA in zebrafish embryos at 1-cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA-seq of control or WGA treated embryo at comparable developmental time point (4.3 hours post fertilization (hpf) ) or develomental stage (dome).

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Project description:Nuclear pore complexes (NPCs) are giant cylindrical structures embedded into the nuclear envelope and mediate nucleocytoplasmic exchange. NPC longevity has been linked to aging but since they appear to rarely turn over, the underlying mechanisms remain understudied. Here, we show that upon nitrogen starvation and genetic interference with NPC architecture, Nups are rapidly degraded in budding yeast. We demonstrate that NPC turnover involves 25 vacuolar proteases and the core autophagic machinery. Autophagic degradation is mediated by the cytoplasmically exposed Nup159 that serves as intrinsic cargo receptor and directly binds to the autophagic marker protein Atg8. The inducible manner of this mechanism might explain why NPCs are long-lived under specific conditions

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Project description:Nuclear organization has emerged as a critical player in the control of genomic processes, including transcription. In this context, nuclear pore complexes (NPCs) have increasingly recognized interactions with the genome, as exemplified in yeast, where they bind inducible genes and damaged genomic regions, positively impacting their fate. To investigate the pathways fostering chromatin association with NPCs, we have combined genome-wide approaches with live imaging of individually-tagged model loci. Strikingly, ChIP-seq analyses of NPC-bound genes revealed a strong correlation between pore association and the propensity to accumulate co-transcriptional R-loops, which are genotoxic structures forming through hybridization of nascent RNAs with their DNA templates. Manipulating cis- or trans-acting regulators of hybrid formation further demonstrated that R-loop accumulation per se, rather than high transcription or R-loop-associated genetic instability, is the primary trigger for relocation to NPCs. Mechanistically, R-loop-dependent repositioning involves the recognition of displaced ssDNA moieties by the ssDNA-binding protein RPA, and SUMO-dependent interactions between RPA and NPC-associated factors. Preventing R-loop-dependent NPC localization leads to lethality, while permanent NPC tethering of a model hybrid-prone sequence attenuates R-loop-dependent genetic instability. Remarkably, this novel relocation pathway involves similar molecular factors as those required for the association of stalled replication forks or eroded telomeres with NPCs, suggesting the existence of convergent mechanisms for sensing transcriptional and genotoxic stresses.

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