Project description:Hi-C was used to examine long range chromatin interactions in B cell progenitors in the presence and absence of the Erg transcription factor. Specifically, OP9 cultured B220+ B-cell progenitors derived from the bone marrow of Rag1CreT/+;ErgΔ/Δ mice and from Rag1CreT/+ and Rag1Cre+/+;Erg fl/fl control mice were isolated and DNA interactions were profiled by in situ Hi-C.
Project description:Droplet-based single-cell RNA-seq of fibroadipogenic progenitors (FAPs) isolated from whole limb skeletal muscles of 8 month old WT and Dysferllin KO mice.
Project description:In this assay, we aimed to investigate the impacts of ZFP661 on the permeability of CTCF barriers to chromatin interactions. To achieve this, we generated high-resolution Hi-C maps using WT and Zfp661 knockout (KO) mESCs. Our findings demonstrate that ZFP661 suppresses the trapping of cohesin at the CTCF barriers and modulates their permeability.
Project description:mRNAseq and proteomic data set of one week old WT (Chop wt/wt CkmmCre wt/wt Dars2 fl/fl), Chop KO (Chop ko/ko CkmmCre wt/wt Dars2 fl/fl), Dars2 KO (Chop wt/wt CkmmCre tg/wt Dars2 fl/fl) and DKO (Chop ko/ko CkmmCre tg/wt Dars2 fl/fl) mice
Project description:To comprehensively examine differences of gene expression patterns between WT and ATG5 KO HSCs/progenitors, we isolated LSK cells and conducted the microarray analysis.
Project description:To comprehensively investigate differences of gene expression patterns between Spred1 WT and KO HSCs/progenitors, we isolated HSCs/progenitor cells and performed the microarray analysis.
Project description:RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 embryoid bodies (EBs), QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT pancreatic progenitors (PP1), QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1. DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to tightly regulate the methylation landscape remains a central question. Utilizing a knockin DNA methylation reporter, we performed a genome-wide CRISPR/Cas screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate cooperation of QSER1 and TET1 through genetic and biochemical interactions to inhibit DNMT3-mediated de novo methylation and safeguard developmental programs.
Project description:Precise vascular patterning is critical for normal growth and development. The ERG transcription factor drives Delta like ligand 4 (DLL4)/Notch signalling and is thought to act as pivotal regulators of endothelial cell (EC) dynamics and developmental angiogenesis. However, molecular regulation of ERG activity remains obscure. Using a series of EC specific Focal Adhesion Kinase (FAK)-knockout (KO) and point-mutant FAK-knockin mice, we show that loss of ECFAK, its kinase activity or phosphorylation at FAK-Y397, but not FAK-Y861, reduces ERG and DLL4 expression levels together with concomitant aberrations in vascular patterning. Rapid Immunoprecipitation Mass Spectrometry of Endogenous Proteins identified that endothelial nuclear-FAK interacts with the de-ubiquitinase USP9x and the ubiquitin ligase TRIM25 enzymes. Further in silico analysis corroborates that ERG interacts with USP9x and TRIM25. Moreover, ERG levels are reduced in FAKKO ECs via a ubiquitin-mediated post-translational modification programme involving USP9x and TRIM25. Re-expression of ERG in vivo and in vitro rescues the aberrant vessel sprouting defects observed in the absence of ECFAK. Our findings identify ECFAK as a regulator of retinal vascular patterning by controlling ERG protein degradation via TRIM25/USP9x.
Project description:To investigate the role of the transcription factor ERG in hematopoiesis we generated Erg heterozygous knockout and conditional Erg knockout mice. We found that several hematopoietic cell types were decreased in these mice. To define Erg downstream target genes in hematopoietic stem cells, we sorted Lineage-, Sca-1+, c-kit+, CD150+, CD48- cells from Erg +/- mice for gene expression analysis. To define Erg downstream target genes in hematopoietic progenitors, we sorted multipotent progenitors (Lineage-, Sca-1+, c-kit+, CD150-) from Erg -/- mice for gene expression analysis.