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Series GSE139975 Query DataSets for GSE139975
Status Public on May 31, 2021
Title In vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Between birth and adulthood cardiomyocytes (CMs) undergo dramatic changes in size, ultrastructure, metabolism, and gene expression, in a process collectively referred to as CM maturation. The transcriptional network that coordinates CM maturation is poorly understood, creating a bottleneck for cardiac regenerative medicine. Forward genetic screens are a powerful, unbiased method to gain novel insights into transcriptional networks, yet this approach has rarely been used in vivo in mammals because of high resource demands. Here we utilized somatic mutagenesis to perform the first reported in vivo CRISPR genetic screen within a mammalian heart. We discovered and validated several novel transcriptional regulators of CM maturation. Among them were RNF20 and RNF40, which form a complex that monoubiquitinates H2B on lysine 120. Mechanistic studies indicated that this epigenetic mark controls dynamic changes in gene expression required for CM maturation. These insights into CM maturation will inform efforts in cardiac regenerative medicine. More broadly, our approach will enable unbiased forward genetics across mammalian organ systems.
Overall design A CRISPR guide RNA library was recovered from Myh7YFP+ cardiomyocytes, sequenced, and gRNA enrichment calculated. Gene expression was assessed in P6 GATA4/6 knockout cardiomyocytes by RNA-sequencing. Gene expression was assessed in P28 RNF20/40 depleted cardiomyocytes by RNA-sequencing. H2Bub1 ChIP-sequencing was conducted on P1 and P28 cardiomyocytes. H3K4me3 and H3K36me3 ChIP-sequencing was conducted on P7 wildtype and Rnf20 cardiomyocyte-specific KO ventricles.
Contributor(s) VanDusen NJ, Pu WT
Citation(s) 34290256
Submission date Nov 05, 2019
Last update date Aug 18, 2021
Contact name Nathan J VanDusen
Organization name Boston Children's Hospital
Department Cardiology
Lab Pu
Street address 61 Binney St, Enders 1254
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (70)
GSM4150667 Screen-S01-input
GSM4150668 Screen-S02-YFP
GSM4150669 Screen-S03-input
BioProject PRJNA587765
SRA SRP228497

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139975_GATA_RNA-seq.txt.gz 459.0 Kb (ftp)(http) TXT
GSE139975_H2Bub1_ChIP-seq.txt.gz 1.6 Mb (ftp)(http) TXT
GSE139975_H3K36me3_ChIP-seq.txt.gz 1.1 Mb (ftp)(http) TXT
GSE139975_H3K4me3_ChIP-seq.txt.gz 315.0 Kb (ftp)(http) TXT
GSE139975_RAW.tar 4.9 Gb (http)(custom) TAR (of BW)
GSE139975_RNF_RNA-seq.txt.gz 610.1 Kb (ftp)(http) TXT
GSE139975_screen_gRNA.txt.gz 783.3 Kb (ftp)(http) TXT
GSE139975_screen_gene.txt.gz 97.7 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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