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Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain

ABSTRACT: Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain

PROVIDER: PRJNA875434 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR21232763_1.fastq.gz	Fastqsanger.gz
	SRR21232763_2.fastq.gz	Fastqsanger.gz
	SRR21232764_1.fastq.gz	Fastqsanger.gz
	SRR21232764_2.fastq.gz	Fastqsanger.gz

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Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain [RNA-seq]

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Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain [CUT&RUN]

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Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain

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Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain [CUT&RUN]

Project description:Approximately 3 × 105 NPCs sorted for Sox2-eGFP were mixed with 3 × 104 Drosophila S2 cells per reaction. We performed CUT&RUN using the protocol developed by the Henikoff lab (Skene and Henikoff, 2017). In brief, Bio-Mag®Plus Concanavalin-A (Con A) coated beads (Bangs Laboratories BP531) were washed and activated with Binding buffer. Nuclei of NPCs with S2 spike-in were gently prepared (see Subcellular Protein Extraction section). Activated Con A beads and nuclei were then mixed and rotated for 5 min at room temperature. They were then blocked with Digitonin block buffer for 5 min at room temperature. 0.5-1 μg of primary antibody with 0.25 μg Spike-in antibody (Active Motif 61686) diluted in Digitonin block buffer was added to the bead-nuclei mixture and incubated for 3 hours (histone marks) or O/N (the rest) at 4 °C. Beads were washed three times with Digitonin block buffer and incubated with pA-MNase for 1 hour at 4 °C. Beads were washed three times with Wash buffer and incubated in Wash buffer for 10 min on ice. The pA-MNase was activated by incubating the beads with 2 mM CaCl2 for 25 min on ice and quenched by adding the Stop buffer. DNA was released from the beads by incubating them for 30 min at 37 °C and collected by centrifugation at 16,000 x g for 5 min at 4 °C. DNA was then isolated by using a phenol/chloroform extraction method.

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SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development.

Project description: Not available

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Genome-wide maps of SNIP1 in 293T

Project description:We found SNIP1 occupied at promoters and there is an overlap betwween and TET2- and SNIP1-binding events.

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DPF3 and SNIP1 IP-MS in 786-O cells

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The polycomb repressive complex PRC2 regulates proliferation and neurogenesis in the Xenopus retina, and is governed by Wnt/beta-catenin signaling

Project description:The histone methyltransferase complex PRC2 controls key steps in developmental transitions and cell fate choices. However, its roles in vertebrate eye development remain unknown. Here we report that in Xenopus PRC2 regulates the progression of retinal progenitors from proliferation to differentiation. We show that the PRC2 core components are enriched in retinal progenitors and downregulated with differentiation. Knockdown of the PRC2 core component Ezh2 leads to reduced retinal progenitor proliferation in part due to upregulation of the cdk inhibitor p15Ink4b. In addition, while PRC2 knockdown does not alter eye patterning, retinal progenitor gene expression or expression of the neural competence factor Sox2, it does cause suppression of proneural bHLH gene expression, indicating that PRC2 is critical for the initiation of neural differentiation in the retina. Consistent with this, knocking down or blocking PRC2 function constrains the generation of most retinal neural cell types and promotes a Mueller glial cell fate decision. We also show that Wnt/?-catenin signaling acting through the receptor Frizzled 5, but independent of Sox2, regulates expression of key PRC2 subunits in the developing retina. This is consistent with a role for this pathway in coordinating proliferation and the transition to neurogenesis in the Xenopus retina. Our data establishes PRC2 as a regulator of proliferation and differentiation during eye development. Xenopus embryos were injected at the 8-cell stage with 5ng Ezh2 ATG MO or 5ng control MO (scrambled sequence of Ezh2 ATG MO) together with 400 pg mRNA for GFP as a lineage tracer. At stage 27, GFP-positive eyes were isolated by microdissection. Pools of 20-25 eyes were used to prepare total RNA for each sample on the microarray. 4 control and 4 Ezh2 ATG MO samples were hybridized to Agilent 1-color microarrays.

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Phosphorylation of SF3B1 by CDK11 1 orchestrates spliceosome activation via SNIP1 dependent RES complex recruitment

Project description:Splicing Factor 3b Subunit 1 (SF3B1), a core component of the spliceosome, undergoes dynamic phosphorylation and dephosphorylation during the splicing cycle to regulate pre-mRNA splicing. Twenty-eight threonine/proline repeats are phosphorylated by CDK11 during spliceosome activation and remain phosphorylated in the catalytically active spliceosomes. The function of phosphorylated SF3B1 (P-SF3B1), and the identity of spliceosomes stalled by CDK11 inhibition remain unclear. Using quantitative proteomics of chromatin-associated spliceosomes, we identify a previously uncharacterized intermediate complex BOTS964, arrested by CDK11 inhibitor OTS964, that incorporates the nineteen-related (NTR) but not nineteen (NTC) complex. iCLIP-seq revealed that P-SF3B1 engages with the U6 snRNA internal stem-loop (ISL), suggesting a potential role in stabilizing the RNA catalytic core. We further demonstrate that P-SF3B1 is recognized by forkhead-associated (FHA) domain of SNIP1, which promotes recruitment of retention and splicing (RES) complex during spliceosome activation. Acute SNIP1 depletion disrupts RES incorporation, causes widespread splicing defects, and promotes hyperphosphorylation of SF3B1 by CDK11. Mutations in SNIP1 FHA domain, including the neurodevelopmental disorder associated E366G variant, impair P-SF3B1 binding, pre-mRNA splicing, and cell viability. Together, these findings uncover the phosphorylation-dependent CDK11/P-SF3B1/SNIP1 signaling axis that is critical for pre-mRNA splicing and cellular proliferation and provide a mechanistic insight into its dysregulation in disease.

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