Project description:We report the application of enyzme-based 4C-Seq technique for exploring Pou5f1 enhancer interactome in mouse ES cells. We explored the interactome of Pou5f1 upstream enhancer in mouse ES cells by using an enzyme digestion based 4C-Seq protocol. The interactome is involved in gene active regulation.
Project description:We report the application of 4C-Seq technique for exploring POU5F1 enhancer interactome in mouse embryonic stem cells. A statistical model was built to identify enriched interacting regions from raw 4C data. The biological replicate data were compared to identify reproducible interacting regions. The interacting sites in the reproducible regions are enriched with active histone marks as well as transcription factors Oct4, Klf4, Esrrb, Tcfcp2i1 and Zfx that are critical for reprogramming and pluripotency. Generation of Illumina HiSeq2000 sequencing data using 4C-Seq protocol
Project description:We report the application of 4C-Seq technique for exploring POU5F1 enhancer interactome in mouse embryonic stem cells. A statistical model was built to identify enriched interacting regions from raw 4C data. The biological replicate data were compared to identify reproducible interacting regions. The interacting sites in the reproducible regions are enriched with active histone marks as well as transcription factors Oct4, Klf4, Esrrb, Tcfcp2i1 and Zfx that are critical for reprogramming and pluripotency.
Project description:The development and function of stem and progenitor cells that produce blood cells are vital in physiology. GATA2 mutations cause immunodeficiency, myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). GATA-2 physiological activities necessitate that it be strictly regulated and cell type-specific enhancers fulfill this role. The +9.5 intronic enhancer harbors multiple conserved cis-elements, and germline mutations of these cis-elements are pathogenic in humans. Since mechanisms underlying how GATA2 enhancer disease mutations impact hematopoiesis and pathology are unclear, we generated mouse models of the enhancer mutations. While a multi-motif mutant was embryonic lethal, a single-nucleotide Ets motif mutant was viable and steady-state hematopoiesis was normal. However, the Ets motif mutation abrogated stem/progenitor cell regeneration following stress. These results reveal a new mechanism in human genetics in which a disease mutation inactivates enhancer regenerative activity, while sparing developmental activity. Mutational sensitization to stress that instigates hematopoietic failure constitutes a paradigm for GATA-2-dependent pathogenesis.
Project description:A transcriptome study in mouse hematopoietic stem cells was performed using a sensitive SAGE method, in an attempt to detect medium and low abundant transcripts expressed in these cells. Among a total of 31,380 unique transcript, 17,326 (55%) known genes were detected, 14,054 (45%) low-copy transcripts that have no matches to currently known genes. 3,899 (23%) were alternatively spliced transcripts of the known genes and 3,754 (22%) represent anti-sense transcripts from known genes.
