Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide ChIP sequencing of NUCKS

ABSTRACT: NUCKS has a DNA binding domain at C-terminal region. We found that NUCKS has important roles in regulating glucose homeostasis. To get an unbiased handle on the plausible mechanism(s) of NUCKS action, we performed a genome-wide Chromatin Immunoprecipitation (ChIP)-sequencing for NUCKS in primary hepatocytes. We successfully mapped 25mln reads to the mm9 genome and detected NUCKS binding at 10203 sites, 60% of which were located in the proximity of a Transcription Start Sites (TSS). The peaks of NUCKS occupancy were often broad with some around 1Kb, suggesting that multiple NUCKS molecules could bind cooperatively to the same genomic loci. This study provides information of NUCKS binding sites in Mus musculus genome. Examination of NUCKS binding in mouse primary hepatocytes by Chromatin immunoprecipitation followed by deep sequencing.

ORGANISM(S): Mus musculus

SUBMITTER: Diana Low

PROVIDER: E-GEOD-58100 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Healthy placental development is essential for reproductive success; failure of the feto-maternal interface results in preeclampsia and intrauterine growth retardation. We found that grainyhead-like 2 (GRHL2), a CP2-type transcription factor, is highly expressed in chorionic trophoblast cells, including basal chorionic trophoblast (BCT) cells located at the chorioallantoic interface in murine placentas. Placentas from Grhl2-deficient mouse embryos displayed defects in BCT cell polarity and basement membrane integrity at the chorioallantoic interface, as well as a severe disruption of labyrinth branchingmorphogenesis.Selective Grhl2 inactivation only in epiblastderived cells rescued all placental defects but phenocopied intraembryonic defects observed in global Grhl2 deficiency, implying the importance of Grhl2 activity in trophectoderm-derived cells. ChIPseq identified 5282 GRHL2 binding sites in placental tissue. By integrating these data with placental gene expression profiles, we identified direct and indirect Grhl2 targets and found a marked enrichment of GRHL2 binding adjacent to genes downregulated in Grhl2−/− placentas, which encoded known regulators of placental development and epithelial morphogenesis. These genes included that encoding the serine protease inhibitor Kunitz type 1 (Spint1), which regulates BCT cell integrity and labyrinth formation. In human placenta, we found that human orthologs of murine GRHL2 and its targets displayed co-regulation and were expressed in trophoblast cells in a similar domain as in mouse placenta. Our data indicate that a conserved Grhl2-coordinated gene network controls trophoblast branching morphogenesis, thereby facilitating development of the site of feto-maternal exchange. This might have implications for syndromes related to placental dysfunction. In vivo genome-wide examination of binding sites of the transcription factor GRHL2 by ChIP-seq using wild-type murine E17.5 placenta tissue. Two samples in total: one GRHL2 ChIP sample and one IgG ChIP sample using wild-type placentas tissue as antibody control.

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Genome-wide ChIP sequencing of NUCKS

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