Browsing by Subject "ChIP-seq"

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    Genome-wide Analysis Using ChIP-seq Reveals Novel Downstream Targets of Stat3
    (Office of the Vice Chancellor for Research, 2015-04-17) Corry, Kylie A.; Li, Jiliang
    Many cells are involved in the orchestra that is bone homeostasis--particularly osteoclasts and osteoblasts who mediate remodeling of bones. This creates a balance that must be kept in check, otherwise pathologies arise. The JAK-Stat signaling pathway is crucial to maintaining this balance. It has long been known that the transcription factor Stat3 has more profound effects on bone homeostasis than other members of the Stat family of proteins. Recently, a genetic condition called Job’s Syndrome has been specifically linked to point mutations in the STAT3 gene. These patients present with severe bone abnormalities including prominent foreheads, broad nasal bridges, and abnormal eye spacing. Therefore, our lab has extensively studied conditional knockouts of Stat3 in all three types of bones cells in mice and observed severe deficiencies in numerous parameters of normal bone phenotypes. Stat3 seems to play a principal role in the signaling that takes place upon mechanical loading of bone tissues and calling cells into action where they are needed. Furthermore, STAT3 has been found to be up-regulated in the early-response gene cluster following mechanical loading. Our current approach to studying Stat3’s effects on bone include employing available ChIP-seq data in order to elucidate the genome-wide binding patterns of Stat3. From the peak distribution, we can begin to uncover novel downstream effectors of Stat3 signaling that are responsible for the observed phenotypes in our mouse knockout model. A preliminary look at the ChIP-seq data reveals Wnt and Nrf2 signaling to be under the control of Stat3. In our further research we endeavor to experimentally confirm the ChIP-seq data for Stat3 with RNA-seq experiments in the hopes of finding potential therapeutic targets for bone pathologies.
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    Genome-Wide Expression Profiling and Phenotypic Analysis of Downstream Targets Identify the Fox Transcription Factor Jumeau as a Master Regulator of Cardiac Progenitor Cell Division
    (MDPI, 2024-12-01) Hasan, M. Rezaul; Kump, Andrew J.; Stepaniak, Evelyn C.; Panta, Manoj; Shashidhar, Kuncha; Katariya, Rajnandani; Sabbir, Mofazzal K.; Schwab, Kristopher R.; Inlow, Mark H.; Chen, Ye; Ahmad, Shaad M.; Medicine, School of Medicine
    Forkhead box (Fox) transcription factors (TFs) mediate multiple conserved cardiogenic processes in both mammals and Drosophila. Our prior work identified the roles of two Drosophila Fox genes, jumeau (jumu) and Checkpoint suppressor 1-like (CHES-1-like), in cardiac progenitor cell specification and division, and in the proper positioning of cardiac cell subtypes. Fox TF binding sites are also significantly enriched in the enhancers of genes expressed in the heart, suggesting that these genes may play a core regulatory role in one or more of these cardiogenic processes. We identified downstream targets of Jumu by comparing transcriptional expression profiles of flow cytometry-sorted mesodermal cells from wild-type embryos and embryos completely lacking the jumu gene and found that genes with functional annotation and ontological features suggesting roles in cell division were overrepresented among Jumu targets. Phenotypic analysis of a subset of these targets identified 21 jumu-regulated genes that mediate cardiac progenitor cell division, one of which, Retinal Homeobox (Rx), was characterized in more detail. Finally, the observation that many of these 21 genes and/or their orthologs exhibit genetic or physical interactions among themselves indicates that Jumu is a master regulator acting as a hub of a cardiac progenitor cell division-mediating network.
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    Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression
    (BMC, 2022-02-14) Nardelli, Sheila C.; Silmon de Monerri, Natalie C.; Vanagas, Laura; Wang, Xiaonan; Tampaki, Zoi; Sullivan, William J., Jr.; Angel, Sergio O.; Kim, Kami; Pharmacology and Toxicology, School of Medicine
    Background: Toxoplasma gondii is a protozoan parasite that differentiates from acute tachyzoite stages to latent bradyzoite forms in response to environmental cues that modify the epigenome. We studied the distribution of the histone variants CenH3, H3.3, H2A.X, H2A.Z and H2B.Z, by genome-wide chromatin immunoprecipitation to understand the role of variant histones in developmental transitions of T. gondii parasites. Results: H3.3 and H2A.X were detected in telomere and telomere associated sequences, whereas H3.3, H2A.X and CenH3 were enriched in centromeres. Histones H2A.Z and H2B.Z colocalize with the transcriptional activation mark H3K4me3 in promoter regions surrounding the nucleosome-free region upstream of the transcription start site. The H2B.Z/H2A.Z histone pair also localizes to the gene bodies of genes that are silent but poised for activation, including bradyzoite stage-specific genes. The majority of H2A.X and H2A.Z/H2B.Z loci do not overlap, consistent with variant histones demarcating specific functional regions of chromatin. The extent of enrichment of H2A.Z/H2B.Z (and H3.3 and H2A.X) within the entire gene (5'UTR and gene body) reflects the timing of gene expression during the cell cycle, suggesting that dynamic turnover of H2B.Z/H2A.Z occurs during the tachyzoite cell cycle. Thus, the distribution of the variant histone H2A.Z/H2B.Z dimer defines active and developmentally silenced regions of the T. gondii epigenome including genes that are poised for expression. Conclusions: Histone variants mark functional regions of parasite genomes with the dynamic placement of the H2A.Z/H2B.Z dimer implicated as an evolutionarily conserved regulator of parasite and eukaryotic differentiation.