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Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [RNA-Seq]

ABSTRACT: Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [RNA-Seq]

PROVIDER: PRJNA545973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9186340.fastq.gz	Fastqsanger.gz
	SRR9186350.fastq.gz	Fastqsanger.gz
	SRR9186360.fastq.gz	Fastqsanger.gz
	SRR9186370.fastq.gz	Fastqsanger.gz
	SRR9186380.fastq.gz	Fastqsanger.gz

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Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility

Project description:Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility

| PRJNA545972 | ENA

Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [ChIP-Seq]

Project description:Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [ChIP-Seq]

| PRJNA545971 | ENA

Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [ChIP-Seq]

Project description:Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD are unknown. Histone H2B mono-ubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40 and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment=6.01, p=1.67x10-03), some of whom had abnormal laterality associated with cilia dysfunction. In Xenopus, knockdown of rnf20 and rnf40 results in abnormal heart looping, defective development of left-right asymmetry and impaired cilia motility. Rnf20, Rnf40 and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level in Xenopus embryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and non-ciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factor Rfx3. Rnf20 knockdown results in decreased levels of rfx3 mRNA in Xenopus, and exogenous rfx3 can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at the Rfx3 locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.

2019-06-04 | GSE132115 | GEO

Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility [RNA-Seq]

2019-06-04 | GSE132116 | GEO

GlcNAcylation of histone H2B facilitates its monoubiquitination

Project description:This SuperSeries is composed of the following subset Series: GSE33049: GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data] GSE33050: GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data] Refer to individual Series

2011-10-26 | E-GEOD-33051 | biostudies-arrayexpress

Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility.

Project description:Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD is unknown. Histone H2B monoubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40, and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment 6.01, P = 1.67 × 10-03), some of whom had abnormal laterality associated with ciliary dysfunction. In Xenopus, knockdown of rnf20 and rnf40 results in abnormal heart looping, defective development of left-right (LR) asymmetry, and impaired cilia motility. Rnf20, Rnf40, and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level in Xenopus embryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and nonciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factor Rfx3 Rnf20 knockdown results in decreased levels of rfx3 mRNA in Xenopus, and exogenous rfx3 can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at the Rfx3 locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.

| S-EPMC6628794 | biostudies-literature

GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data]

Project description:We report that histone GlcNAcylation of H2B S112 is a vital histone modification which facilitates histone monoubiquitination (ub). In a genome-wide analysis, H2B S112 GlcNAcylation sites were observed widely distributed over entire chromosomes including transcribed gene loci, together with co-localization of H2B S112 GlcNAcylation and K120 ub. Examination of H2B S112 GlcNAc and H2B K120 ub in HeLa S3 cells

2011-10-27 | E-GEOD-33049 | biostudies-arrayexpress

GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data]

2011-10-27 | GSE33049 | GEO

Co-dependency of H2B monoubiquitination and nucleosome re-assembly on Chd1

Project description:Monoubiquitination of histone H2B on lysine 123 (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively. Many of the factors such as Rad6/Bre1, the Paf1 complex, and the Bur1/Bur2 complex were identified to be required for proper histone H3K4 and H3K79 trimethylation, and were shown to function by regulating H2BK123ub levels. Here, we have identified Chd1 as a factor that is required for proper maintenance of H2B monoubiquitination levels, but not for H3K4 and H3K79 trimethylation. Loss of Chd1 results in a substantial loss of H2BK123ub levels with little to no effect on the genome-wide pattern of H3K4 and H3K79 trimethylation. Our data shows that nucleosomal occupancy is reduced in gene bodies in both CHD1 null and K123A backgrounds. We have also demonstrated that Chd1’s function in maintaining H2BK123ub levels is conserved from yeast to human. Our study provides evidence that only small levels of H2BK123ub are necessary for full levels of H3K4 and H3K79 trimethylation in vivo, and points to a role for Chd1 in positively regulating gene expression through promoting nucleosome re-assembly coupled with H2B monoubiquitination. Examination of two histone modifications in wild-type and Chd1 null yeast strains using ChIP-seq. Expression profiling in wild-type and Chd1 null yeast strains using RNA-seq.

2012-05-01 | E-GEOD-36334 | biostudies-arrayexpress

Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-04 | GSE132117 | GEO