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Series GSE69162 Query DataSets for GSE69162
Status Public on Jul 18, 2017
Title MLL4 prepares the enhancer landscape for FoxP3 induction via chromatin looping
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary MLL4 is an essential subunit of the H3K4 methylation complexes. We report that Mll4 deficiency compromised Treg development and resulted in substantial decreases in H3K4me1 and chromatin interaction at putative enhancers, a remarkable portion of which were not direct targets of MLL4 but were interacting with Mll4-bound sites. The decrease in H3K4me1 and chromatin interaction at the MLL4-unbound enhancers correlated with MLL4 binding at distant interacting regions. Deletion of an upstream MLL4 binding site reduced H3K4me1 at the FoxP3 regulatory elements looped to the MLL4 binding site and compromised both tTreg and iTreg differentiation. We show that MLL4 catalyses H3K4 methylation at distant unbound enhancers via chromatin looping, thus providing a new mechanism of regulating T cell enhancer landscape and impacting Treg differentiation.
Overall design ChIP-Seq profile of MLL4 binding in mouse Naive CD4+ T cells. ChIP-Seq of histone modification H3K4me1, H3K27me3, H3K27ac, RNA-Seq of gene expression, Hi-C of chromatin conformation capturing in control Naive CD4 T cells and Mll4 KO cells. Chip-Seq of H3K4me1 in control cells and Naive CD4+ T cells in which a MLL4-bound regulatory region upstream to the foxp3 gene were KO by the Crispr technique.
Contributor(s) Placek K, Hu G, Cui K, Zhang D, Ding Y, Lee J, Jang Y, Wang C, Konkel JE, Song J, Liu C, Ge K, Chen W, Zhao K
Citation(s) 28759003
Submission date May 22, 2015
Last update date Jun 01, 2022
Contact name Gangqing Hu
Organization name West Virginia University
Department MicroBiology, Immunology, and Cell Biology
Lab 2072A, HSC North, Floor 2
Street address 64 Medical Center Drive
City Morgantown
State/province West Virginia
ZIP/Postal code 26506-9177
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (27)
GSM1694154 MLL4_r1
GSM1694155 Input
GSM1694156 MLL4_r2
BioProject PRJNA284682
SRA SRP058625

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

Supplementary file Size Download File type/resource
GSE69162_GA4747-1-ATCACG-naivd-CD4-MLL4flflCreNeg-H3K27ac-m1_0_0_noDup-GA4748-2-CGATGT-naive-CD4-MLL4flflCrePos-H3K27ac-m1_0_0_noDup-W200-G400-E10.scoreisland.sicerdiff.txt.gz 1.3 Mb (ftp)(http) TXT
GSE69162_GA4747-1-ATCACG-naive-CD4-MLL4flflCre-H3K27ac-200-500-mouse_Gateway_SuperEnhancers.bed.gz 7.6 Kb (ftp)(http) BED
GSE69162_GA4874-rpkm.txt.gz 484.0 Kb (ftp)(http) TXT
GSE69162_GA4876-rpkm.txt.gz 486.2 Kb (ftp)(http) TXT
GSE69162_GA5043-rpkm.txt.gz 477.5 Kb (ftp)(http) TXT
GSE69162_GA5044-rpkm.txt.gz 477.6 Kb (ftp)(http) TXT
GSE69162_GA5963-TGACCA-ChIPSeq-mouse-MLL3ppMLL4FF-Naiv-CD4-MLL4.sam_noDup-W200-G400-islands-summary-E1000FDR0.001.txt.gz 477.1 Kb (ftp)(http) TXT
GSE69162_GA5963-TGACCA-ChIPSeq-mouse-MLL3ppMLL4FF-Naiv-CD4-MLL4_sam_noDup-W200-G400-islands-summary-E100000FDR0.05.txt.gz 1.5 Mb (ftp)(http) TXT
GSE69162_GA6843-TTAGGC-ChIPSeq-mouse-WT-MLL4-1-kz775kz746_noDup-W200-G400-E1000.scoreisland.txt.gz 371.2 Kb (ftp)(http) TXT
GSE69162_GA6861GA6867_GA7201GA7202_me1Cnt.edger3.txt.gz 2.0 Mb (ftp)(http) TXT
GSE69162_GA6866-GCCAAT-ChIP-seq-mouse-WT-H3K27me3.sam_noDup-GA6872-CTTGTA-ChIP-seq-mouse-MLL4-KO-H3K27me3.sam_noDup-W200-G400-E10.scoreisland.sicerdiff.txt.gz 1.5 Mb (ftp)(http) TXT
GSE69162_GA6875_CD4T_HiC.bin1Kmin1Kmax2M.III.txt.gz 248.1 Mb (ftp)(http) TXT
GSE69162_GA6876_CD4T_HiC.bin1Kmin1Kmax2M.III.txt.gz 229.2 Mb (ftp)(http) TXT
GSE69162_GA7211-GGCTAC-ChIP-seq-mouse-Naive-WT-H3K27me3_noDup-GA7212-CTTGTA-ChIP-seq-mouse-Naive-MLL4-KO-H3K27me3_noDup-W200-G400-E10.scoreisland.sicerdiff.txt.gz 1.7 Mb (ftp)(http) TXT
GSE69162_GA7713_r799l6_HiC.bin1Kmin5Kmax2M.III.txt.gz 42.6 Mb (ftp)(http) TXT
GSE69162_GA7714_r799l6_HiC.bin1Kmin5Kmax2M.III.txt.gz 30.6 Mb (ftp)(http) TXT
GSE69162_KZ852_GA7713_NNNNNN_L3456_R1.fastq.bedpe.iii.txt.gz 134.2 Mb (ftp)(http) TXT
GSE69162_RAW.tar 380.0 Kb (http)(custom) TAR (of TXT)
GSE69162_mll4_ko_pool_GA7715r799r818r909.bedpe.iii.txt.gz 152.1 Mb (ftp)(http) TXT
GSE69162_mll4_wt_pool_GA7714r799r818r909.bedpe.iii.txt.gz 256.3 Mb (ftp)(http) TXT
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