ABSTRACT: Profiling of H3K4me1 genome wide occupancy in mESC WT, LSD1 KO, and rescued with WT LSD1 (RO) and with mutant LSD1 (AK) to explore the effects of LSD1 on histone methylation.
Project description:CUT&RUN LoV-U was performed against SMAD4 using two different antibodies in M170117 human melanoma cells under 4 conditions: Control (DMSO), TGFb, MEKi and TGFb + MEKi (Both).
Project description:We aimed to compare CTCF binding patterns, chromatin states and 3D genome structure in the absence and after activation of Wnt signaling in HEK293T cells.
Project description:CUT&RUN was performed for Sox2 on ex-vivo dissected visual thalamic nuclei from P0 mice, revealing context specific activity of Sox2 binding in differentiated neurons.
Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).
Project description:Using CUT&RUN, we systematically measured the genome-wide binding profiles of key transcription factors and cofactors that track the activity of ontogenetically relevant signaling pathways in developing mouse tissues. This produced numerous genome-wide biding tracks for different tissues at two developmental stages in biological duplicate. Submitted files include raw fastq files, bigwig files from merged biological replicates, and peak sets.
Project description:SALL4 builds a complex with histone deacetylases, and is thought to confer its effects epigenetically. Both loss of Sall4 and inhibition of HDAC2 leads to an invasiveness in human melanoma cells. To study co-occupancy of SALL4 and HDAC2, we employed CUT&RUN targeting SALL4 and HDAC2 in human melanoma cells (M010817).
Project description:Other than in the development of the brain, SOX2 is essential for the long-term self-renewal of neural stem cells (NSCs). The mechanisms of how SOX2 maintains the stemness of NSCs is not yet understood. We have identified Fos as a downstream target of SOX2, and therefore used CUT&RUN to investigate where these transcription factors - and the c-FOS partner c-JUN - interact with the genome. By comparing binding patterns of c-FOS, c-JUN and SOX2, we find that they co-occupate the promoter of the SOCS3 locus, which we also have identified as a gene that rescues SOX2 deletion induced senescence when overexpressed in neurospheres grown from Sox2-deleted mouse NSCs. Taken together, our data provide a basis for elucidating a gene regulatory network necessary for the maintenance of self-renewal in post-embryonic neural stem cells.
Project description:To study the epigenetic regulation of intestinal epithelium we focus on the role of chromatin modulators. Lysine-specific histone demethylase 1a (KDM1A, LSD1) is one of the enzymes that can erase the H3K4me1/2 mark. To assess the role of LSD1 in intestinal epithelium we studied wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (KO) (Villin-Cre+; Lsd1f/f) mice. We found that KO mice completely lack Paneth cells, and have altered stem cell characteristics compared to WT littermates. To assess genome-wide ATAC levels in WT and KO small intestines, we isolated intestinal epithelium tissue from wild type mice and LSD1 KO mice. This tissue was digested to single cells and performed ATAC seq as described in the protocols.
Project description:Ppm1d T/+ mice exhibit altered BM composition. The aim is to determine the molecular mechanisms possibly responsible for this alterations in sorted long-term hematopoietic stem cells isolated from bone marrow. Long-term HSCs (LT-HSCs sorted from 12-week-old WT and Ppm1DT/+ mice. The Ppm1dT/+ HSC transcriptome shows enrichment of MYC, mTOR compared to WT.