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Genome-wide maps of chromatin state in E12.5 forebrain tissues

ABSTRACT: Genome-wide maps of chromatin state in E12.5 forebrain tissues

PROVIDER: PRJNA716529 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18053900.fastq.gz	Fastqsanger.gz
	SRR18053901_1.fastq.gz	Fastqsanger.gz
	SRR18053901_2.fastq.gz	Fastqsanger.gz
	SRR18053902_1.fastq.gz	Fastqsanger.gz
	SRR18053902_2.fastq.gz	Fastqsanger.gz

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Genome-wide maps of chromatin state in E12.5 forebrain tissues

Project description:The histone methyltransferase complex PRC2 is a crucial chromatin modifier and controls key steps in developmental transitions and cell fate choices. Mutations in PRC2 core subunits are found in Weaver syndrome with craniofacial defects, intellectual disabilities, and often macrocephaly, but its pathogenicity and molecular mechanism are unknown. Here, we examined the role of PRC2/Eed in neural stem/progenitor cells (NSPCs) during cortical neurogenesis We found that Eed is highly expressed in embryonic cerebral cortex and specific deletion of Eed in forebrain reduced the number of upper layer neurons but not deeper layer neurons and ultimately contributed to abnormal cortical development. In addition, our results revealed that PRC2/Eed regulated Hedgehog signaling pathway through activation of Gli3 not dependent on H3K27me3 but H3K27ac. What?s more, Increased Gli3 in NSPCs could reduce Gli1 expression and contribute to the defects of cortical neurogenesis caused by Eed deletion. Finally, Hedgehog signaling activation with small molecule SAG or genetic inactivation of Ptch1 could partially rescue the cortical neurogenesis defects in vivo after Eed depletion. In general, we identified a novel PRC2/Eed-Gli3-Gli1 regulatory axis that is critical for normal cortical neurogenesis. Our findings define a critical function for PRC2/Eed in cortical development and shed light on the genetic basis of intellectual disabilities of neural developmental disorders caused by PRC2/Eed mutation.

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RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - TMT MS RAPIDASH of E12.5 mouse limbs, forebrain, and liver

Project description:Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts. This dataset refers to relative quantification of RAPs enriched by RAPIDASH from E12.5 mouse limbs, forebrain, and liver, as elaborated in Figure 4B.

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Project description:The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile. Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimnb tissues using the Illumina HiSeq 2000.

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