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Series GSE144396 Query DataSets for GSE144396
Status Public on May 13, 2021
Title The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary CpG-islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 possesses an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. Absence of SAMD1 impairs ES cell differentiation processes, leading to miss-regulation of key biological pathways. Together, our work establishes SAMD1 as a novel chromatin regulator acting at unmethylated CGIs.
Overall design ChIP-Seq of SAMD1 (2x), L3MBTL3 (2x), KDM1A (2x), H3K4me2 (2x), H3K4me3 (2x), H3K27ac (1x), H3K27me3 (1x) in WT and SAMD1 knockout cells. RNA-Seq of WT and SAMD1 knockout cells (4x). RNA-Seq after 7 days of undirected differentiation (3x). RNA-Seq after KDM1A and L3MBTL3 KO (3x).
Contributor(s) Stielow B, Nist A, Liefke R
Citation(s) 33980486, 36810619
Submission date Jan 28, 2020
Last update date Mar 15, 2023
Contact name Robert Liefke
Organization name Philipps University of Marburg
Department Institute of Molecular Biology and Tumor Research (IMT)
Street address Hans-Meerwein-Str. 2
City Marburg
State/province Hessen
ZIP/Postal code 35043
Country Germany
Platforms (2)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (55)
GSM4287309 SAMD1_WT_repl1
GSM4287310 SAMD1_SAMD1KO_repl1
GSM4287311 SAMD1_WT_repl2
BioProject PRJNA603553
SRA SRP245629

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
GSE144396_DeSeq2-Differentiation-SAMD1KOvsWT.txt.gz 621.0 Kb (ftp)(http) TXT
GSE144396_DeSeq2-KDM1AKOvsWT.txt.gz 947.1 Kb (ftp)(http) TXT
GSE144396_DeSeq2-L3MBTL3KOvsWT.txt.gz 957.1 Kb (ftp)(http) TXT
GSE144396_NormalizedCounts-Differentiation.txt.gz 1.1 Mb (ftp)(http) TXT
GSE144396_NormalizedCounts-WT-KDM1AKO-L3MBTL3KO.txt.gz 833.3 Kb (ftp)(http) TXT
GSE144396_RAW.tar 6.8 Gb (http)(custom) TAR (of BW)
GSE144396_RNA-Seq_DeSeq2.txt.gz 1.1 Mb (ftp)(http) TXT
GSE144396_RNA-Seq_NormalizedCounts.txt.gz 1.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
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