Accession

PRJCA004722

Title

HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

Relevance

Model organism

Data types

Epigenomics
Transcriptome or Gene expression

Organisms

Mus musculus

Description

Histone variants have been implicated in regulating chromatin dynamics and genome functions. Previously, we have shown that histone variant H3.3 actively marks enhancers and cooperates with H2A.Z at promoters to prime the genes into a poised state in mouse embryonic stem cells (mESCs). However, how these two important histone variants collaboratively function in this process still remains elusive. In this study, we showed that depletion of different components of HIRA complex, specific chaperone of H3.3, results in significant decrease of H2A.Z enrichment around TSS regions. In addition, CUT&Tag data and co-immunoprecipitation assay revealed genomic colocalization and biochemical interaction between HIRA complex and SRCAP complex in mESCs, respectively. Furthermore, analyses of genome-wide micrococcal nuclease sequencing and tRA-induced transcriptome demonstrated that HIRA complex contributed to preset a defined chromatin feature around TSS region for poising gene transcription in a H3.3-dependent manner. In summary, our results provide a novel molecular mechanism by which HIRA complex determines the transcriptional potential through collaborating with SRCAP to deposit H2A.Z onto the promoters of the poised genes during mESC differentiation.

Sample scope

Monoisolate

Release date

2022-09-22

Publication

PubMed ID	Article title	Journal name	DOI	Year
34893908	HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs	Nucleic Acids Research	10.1093/nar/gkab1221	2022

Grants

Agency	program	Grant ID	Grant title
National Natural Science Foundation of China (NSFC)		31801062
Ministry of Science and Technology of the People's Republic of China (MOST)		2017YFA0504200
Ministry of Science and Technology of the People's Republic of China (MOST)		2018YFE0203302
National Natural Science Foundation of China (NSFC)		31521002
National Natural Science Foundation of China (NSFC)		31991161
National Natural Science Foundation of China (NSFC)		31630041
Chinese Academy of Sciences (CAS)		QYZDY-SSW-SMC020
Beijing Municipal Science and Technology Commission		Z201100005320013
HHMI		55008737

Submitter

Liwei Zhang (lwzhanghz@ibp.ac.cn)

Organization

Institute of Biophysics, Chinese Academy of Sciences

Submission date

2021-03-16

Project Data

Resource name	Description
BioSample (73) show	-
SAMC477399	rep1 of ATAC-seq of R1 cells with H2a.z knock down
SAMC477398	rep2 of ATAC-seq of R1 cells with H3.3a/b knock out
SAMC477397	rep1 of ATAC-seq of R1 cells with H3.3a/b knock out
SAMC477396	rep2 of ATAC-seq of R1 cells with Ubn1/2 dot mutation
SAMC477395	rep1 of ATAC-seq of R1 cells with Ubn1/2 dot mutation
SAMC477394	rep2 of ATAC-seq of R1 cells with Ubn2 knock out and Ubn1 knock down
SAMC477393	rep1 of ATAC-seq of R1 cells with Ubn2 knock out and Ubn1 knock down
SAMC477392	rep2 of ATAC-seq of R1 cells with Hira knock out
SAMC477391	rep1 of ATAC-seq of R1 cells with Hira knock out
SAMC477390	rep2 of ATAC-seq of R1 cells
SAMC477389	rep1 of ATAC-seq of R1 cells
SAMC477388	rep2 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira full length
SAMC477387	rep1 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira full length
SAMC477386	rep2 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira truncation delta B domain
SAMC477385	rep1 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira truncation delta B domain
SAMC477384	rep2 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira truncation 1-476
SAMC477383	rep1 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira truncation 1-476
SAMC477382	rep2 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira truncation 1-420
SAMC477381	rep1 of H2A.Z ChIP-seq of R1 cells with Hira knock out and transfected vector containing Hira truncation 1-420
SAMC477380	rep2 of H2A.Z ChIP-seq of R1 cells with Hira knock out and empty vector transfected
SAMC477379	rep1 of H2A.Z ChIP-seq of R1 cells with Hira knock out and empty vector transfected
SAMC477378	rep2 of H2A.Z ChIP-seq of R1 cells with empty vector transfected
SAMC477377	rep1 of H2A.Z ChIP-seq of R1 cells with empty vector transfected
SAMC437306	siH2A.Z.rep2
SAMC437305	siH2A.Z.rep1
SAMC437304	ShSRCAP.rep2
SAMC437303	ShSRCAP.rep1
SAMC437302	siNT.rep2
SAMC437301	siNT.rep1
SAMC346649	MNase-R1
SAMC346648	MNase-H3.3-KO
SAMC346647	MNase-siH2AZ
SAMC346646	MNase-UBN-DM
SAMC346645	MNase-HIRA-KO
SAMC346644	MNase-UBN-KO
SAMC346643	RNA-seq_UBN-KO-8h
SAMC346642	RNA-seq_UBN-KO-2h
SAMC346641	RNA-seq_UBN-KO-24h
SAMC346640	RNA-seq_UBN-KO-0h
SAMC346639	RNA-seq_siH2A.Z-8h
SAMC346638	RNA-seq_siH2A.Z-2h
SAMC346637	RNA-seq_siH2A.Z-24h
SAMC346636	RNA-seq_siH2A.Z-0h
SAMC346635	RNA-seq_H3.3-KO-tRA-8h
SAMC346634	RNA-seq_H3.3-KO-tRA-2h
SAMC346633	RNA-seq_H3.3-KO-tRA-24h
SAMC346632	RNA-seq_H3.3-KO-tRA-0h
SAMC346631	RNA-seq_R1-8h
SAMC346630	RNA-seq_R1-2h
SAMC346629	RNA-seq_R1-24h
SAMC346628	RNA-seq_R1-0h
SAMC346627	RNA-seq_HIRA-KO-8h
SAMC346626	RNA-seq_HIRA-KO-2h
SAMC346625	RNA-seq_HIRA-KO-24h
SAMC346624	RNA-seq_HIRA-KO-0h
SAMC346623	RNA-seq_UBN-DM-8h
SAMC346622	RNA-seq_UBN-DM-2h
SAMC346621	RNA-seq_UBN-DM-24h
SAMC346620	RNA-seq_UBN-DM-0h
SAMC346619	R1-CUT&Tag-input
SAMC346618	UBN-KO_SRCAP
SAMC346617	UBN-DM_SRCAP
SAMC346616	HIRA-KO_SRCAP
SAMC346615	H3.3-KO_SRCAP
SAMC346614	R1-SRCAP
SAMC346613	R1-HIRA
SAMC346612	R1-ChIP-input
SAMC346611	UBN-KO_H2A.Z
SAMC346610	UBN-DM_H2A.Z
SAMC346609	ShSRCAP_H2A.Z
SAMC346608	HIRA-KO_H2A.Z
SAMC346607	H3.3-KO_H2A.Z
SAMC346606	R1-H2A.Z
GSA (3)	-
CRA005318	H2A.Z deposition after the rescue of HIRA fragments and chromatin accessibility with HIRA deletion in mouse ESC
CRA004638	The genome wide role of SRCAP in Histone variant H3.3 deposition in mouse
CRA004042	HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs