DOCSLIB.ORG

Charting Brachyury-Mediated Developmental Pathways During Early Mouse Embryogenesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Charting Brachyury-Mediated Developmental Pathways During Early Mouse Embryogenesis Charting Brachyury-mediated developmental pathways during early mouse embryogenesis Macarena Lolasa,b, Pablo D. T. Valenzuelab, Robert Tjiana,c,1, and Zhe Liud,1 dJunior Fellow Program, aJanelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147; bFundación Ciencia para la Vida, Santiago 7780272, Chile; and cLi Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 Contributed by Robert Tjian, February 11, 2014 (sent for review January 14, 2014) To gain insights into coordinated lineage-specification and mor- cells play diverse and indispensable roles in early mouse phogenetic processes during early embryogenesis, here we report development. a systematic identification of transcriptional programs mediated In mouse ES cell-based differentiation systems, Brachyury is by a key developmental regulator—Brachyury. High-resolution widely used as a mesoendoderm marker, and Brachyury-positive chromosomal localization mapping of Brachyury by ChIP sequenc- cells were able to differentiate into mesodermal and definitive ing and ChIP-exonuclease revealed distinct sequence signatures endodermal lineages, such as cardiomyocytes and hepatocytes enriched in Brachyury-bound enhancers. A combination of genome- (8–10). In a previous study, we found that depletion of a core wide in vitro and in vivo perturbation analysis and cross-species promoter factor, the TATA binding protein-associated factor 3, evolutionary comparison unveiled a detailed Brachyury-depen- in ES cells leads to significant up-regulation of Brachyury and dent gene-regulatory network that directly links the function of mesoderm lineages during ES cell differentiation (11). Here, we Brachyury to diverse developmental pathways and cellular house- systematically characterized the molecular function of Brachyury keeping programs. We also show that Brachyury functions pri- during ES cell differentiation by genomic, single-cell imaging, marily as a transcriptional activator genome-wide and that an and biochemical approaches. We then contrasted our results unexpected gene-regulatory feedback loop consisting of Brachyury, with published zebrafish and Xenopus Brachyury binding site Foxa2, and Sox17 directs proper stem-cell lineage commitment mapping data (12, 13) to compare evolutionarily convergent or BIOLOGY during streak formation. Target gene and mRNA-sequencing cor- divergent pathways. We further extended these studies to examine DEVELOPMENTAL relation analysis of the Tc mouse model supports a crucial role of the direct impact of Brachyury loss of function during early de- Brachyury in up-regulating multiple key hematopoietic and muscle- velopment with the Tc mouse model. Together, our data provide fate regulators. Our results thus chart a comprehensive map of a systematic and comprehensive view of Brachyury-mediated the Brachyury-mediated gene-regulatory network and how it regulation and also reveal unique mechanistic insights into how influences in vivo developmental homeostasis and coordination. this gene network likely contributes to early mouse embryogenesis. primitive streak | early development | mesoendoderm differentiation Results and Discussion Characterization of in Vitro Primitive Streak Induction. We used the – n the past decade, significant insights have been gained in well-established Activin-A mediated differentiation protocol that Iunderstanding gene-regulatory programs responsible for em- efficiently drives ES cells to form primitive streak cells in vitro (9, bryonic stem (ES) cell pluripotency and self-renewal. However, 14) (SI Appendix,Fig.S1A). We successfully generated two transcriptional control mechanisms underlying finely balanced highly specific polyclonal antibodies directed against the Brachyury lineage-segregation and morphogenetic processes during early protein. At day 4 after differentiation, we detected strong induction of primitive streak markers (Brachyury and Gsc) mammalian embryogenesis remained elusive. During early mouse (SI Appendix,Figs.S1B–D and S2A), indicating a successful gastrulation, Brachyury (T), a classical enhancer-binding transcrip- differentiation of primitive streak cells. To comprehensively tion factor (TF), has been reported to be required for the proper development of primitive streak, allantois, axial, and posterior Significance mesoderm (reviewed in ref. 1). Specifically, mouse embryos that are homozygous for the − − Brachyury (T) deletion die at midgestation (2). T / mutant The gene-regulatory mechanisms for finely balanced cell-fate determination and morphogenesis during early animal de- epiblast cells are compromised in their ability to migrate away velopment remain largely elusive. Here, we combine genomic, from the primitive streak and, therefore, are unable to undergo single-cell imaging and biochemical approaches to chart the the morphogenetic movements carried out by their wild-type molecular pathways mediated by a key developmental regu- (WT) counterparts during gastrulation. In addition to defects in lator—Brachyury. Our results shed light on mechanistic insights the primitive streak, the notochord is absent in posterior portions into the ultrafine organization of Brachyury-bound enhancers of the embryo. Although the anterior portions of T mutant mice and link Brachyury function to cellular differentiation and contain notochordal precursor-like cells, they fail to undergo housekeeping processes critical for coordinating early mouse normal terminal differentiation (3, 4). The embryonic pattern embryogenesis. − − posterior to the forelimb region of T / animals is also disturbed, with somites posterior to the seventh pair absent or abnormal. Author contributions: M.L., P.D.T.V., R.T., and Z.L. designed research; M.L. and Z.L. per- Although neural folds fuse to form the neural tube, they are formed research; M.L. and Z.L. analyzed data; and M.L., R.T., and Z.L. wrote the paper. severely kinked in the caudal region, and the surface ectoderm The authors declare no conflict of interest. tends to form fluid-filled blisters (2, 4, 5). In addition to these Freely available online through the PNAS open access option. well-documented defects, numerous other phenotypic abnormali- Data deposition: The data reported in this paper have been deposited in the Gene Ex- −/− pression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE54985). ties have been reported in T and T mutant embryos, including 1 – To whom correspondence may be addressed. E-mail: [email protected] or tjianr@ left right patterning defects and morphological abnormalities in hhmi.org. heart development (6, 7). Together, these genetic and phenotypic This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. analyses strongly suggest that Brachyury and Brachyury-expressing 1073/pnas.1402612111/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1402612111 PNAS Early Edition | 1of6 Downloaded by guest on September 25, 2021 characterize gene expression changes upon differentiation, we In line with these findings, Brachyury-bound regions were also performed mRNA sequencing (mRNA-seq) with differentiated enriched around genes involved in endoderm development embryoid bodies (EBs; EB day 4) and then compared gene ex- (P < 3.9E-09) and formation (P < 2.6E-05). pression levels to ES cell data. We detected 2,464 up-regulated and 1,329 down-regulated genes (statistics in Dataset S1). Con- Evolutionary Conservation of Brachyury-Mediated Regulation. With sistent with a successful epiblast transition and primitive streak recent Brachyury homolog Ntl ChIP-on-chip (zebrafish) and XBra induction, ES cell ground-state specific genes (Tbx3, Stra8, Pecam1, ChIP-seq (Xenopus tropicalis) data available (12, 13), we next Esrrb, Gbx2,andKlf4) were dramatically down-regulated. However, asked whether a similar set of target genes identified in these mesoderm and definitive endoderm (DE) markers (Cer1, Eomes, studies also bound Brachyury in the mouse. Intriguingly, we Wnt3, Lhx1, Fgf8, Cxcr4, Foxa2, Sox17,andGsc)(15)werestrongly found that ∼10∼13% of the Ntl (zebrafish) and Xbra (X.tropicalis) up-regulated (SI Appendix,Figs.S1C and S2B). We also confirmed target genes (zebrafish, 28/218; X. tropicalis, 113/1,040) have a the expression of Brachyury, Foxa2, and Sox17 at the protein level corresponding homologous gene bound by Brachyury in mouse by immunofluorescence staining (SI Appendix, Fig. S1D). (Fig. 1E and Dataset S3). For example, nine genes (Dusp6, Mesp2, Hoxd8, Cdx2, Irx3, Lefty1, Msgn1, Dhrs3,andSp5)were Brachyury Selectively Binds Key Developmental Genes. We applied bound by Brachyury in all three species (Fig. 1F). We also ob- ChIP sequencing (ChIP-seq) to our in vitro primitive streak served Brachyury-bound genes such as Fgf8, Sox17, Foxa2, Tbx3, formation system. To ensure specific detection of Brachyury Wnt9b, Wnt5b, and Rest that were common targets in mouse and binding, we used two independent anti-Brachyury antibodies for X. tropicalis but not in zebrafish (Fig. 1F and Dataset S3). Con- ChIP-seq experiments. By only calling peaks detected by both versely, Igf1r, Brf1, Gata2, Zfand5, Sox11, Mycn, Notch3,etc.are antibodies, we identified 3,160 high-confidence Brachyury-bound common targets in mouse and zebrafish but not in X. tropicalis.Itis regions in the mouse genome (Dataset S2). These sites display worth noting that the work performed in zebrafish
Load more

Recommended publications
  • FOXA2 Is a Sensitive and Specific Marker for Small Cell Neuroendocrine Carcinoma of the Prostate Jung Wook Park1, John K Lee2,3, Owen N Witte1,4,5 and Jiaoti Huang6
    Modern Pathology (2017) 30, 1262–1272 1262 © 2017 USCAP, Inc All rights reserved 0893-3952/17 $32.00 FOXA2 is a sensitive and specific marker for small cell neuroendocrine carcinoma of the prostate Jung Wook Park1, John K Lee2,3, Owen N Witte1,4,5 and Jiaoti Huang6 1Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, CA, USA; 2Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, CA, USA; 3Molecular Biology Institute, David Geffen School of Medicine, University of California— Los Angeles, Los Angeles, CA, USA; 4Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California—Los Angeles, Los Angeles, CA, USA; 5Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, CA, USA and 6Department of Pathology, Duke University School of Medicine, Durham, NC, USA The median survival of patients with small cell neuroendocrine carcinoma is significantly shorter than that of patients with classic acinar-type adenocarcinoma. Small cell neuroendocrine carcinoma is traditionally diagnosed based on histologic features because expression of current immunohistochemical markers is inconsistent. This is a challenging diagnosis even for expert pathologists and particularly so for pathologists who do not specialize in prostate cancer. New biomarkers to aid in the diagnosis of small cell neuroendocrine carcinoma are therefore urgently needed. We discovered that FOXA2, a pioneer transcription factor, is frequently and specifically expressed in small cell neuroendocrine carcinoma compared with prostate adenocarcinoma from published mRNA-sequencing data of a wide range of human prostate cancers.
    [Show full text]
  • Zfp57 Mutant ES Cell Lines Directly Derived from Blastocysts
    Stem Cell Research 16 (2016) 282–286 Contents lists available at ScienceDirect Stem Cell Research journal homepage: www.elsevier.com/locate/scr Lab Resource: Stem Cell Line Zfp57 mutant ES cell lines directly derived from blastocysts Ho-Tak Lau a, Lizhi Liu a, Xiajun Li a,b,⁎ a Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA b Department of Oncological Sciences, Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA article info abstract Article history: Zfp57 is a master regulator of genomic imprinting in mouse embryos. To further test its functions, we have Received 25 November 2015 derived multiple Zfp57 mutant ES clones directly from mouse blastocysts. Indeed, we found DNA methylation im- Received in revised form 30 December 2015 print was lost at most examined imprinting control regions in these Zfp57 mutant ES clones, similar to what was Accepted 31 December 2015 observed in Zfp57 mutant embryos in the previous studies. This result indicates that these blastocyst-derived Available online 6 January 2016 Zfp57 mutant ES clones can be employed for functional analyses of Zfp57 in genomic imprinting. © 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Resource table heterozygous female mice and Zfp57−/− homozygous male mice, whereas five Zfp57−/− (M−Z−) ES clones were derived from the cross between Zfp57−/− homozygous female mice and Zfp57−/− homozygous male mice.
    [Show full text]
  • Estrogen Receptor Α AF-2 Mutation Results in Antagonist Reversal and Reveals Tissue Selective Function of Estrogen Receptor Modulators
    Estrogen receptor α AF-2 mutation results in antagonist reversal and reveals tissue selective function of estrogen receptor modulators Yukitomo Araoa, Katherine J. Hamiltona, Manas K. Rayb, Gregory Scottb, Yuji Mishinac, and Kenneth S. Koracha,1 aReceptor Biology Section, Laboratory of Reproductive and Developmental Toxicology and bKnock Out Core, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709; and cSchool of Dentistry, University of Michigan, Ann Arbor, MI 48109 Edited by David J. Mangelsdorf, University of Texas Southwestern Medical Center, Dallas, TX, and approved July 22, 2011 (received for review June 10, 2011) The estrogen receptor (ER) is a ligand-dependent transcription and that may be related to the cell type specific functionality factor containing two transcriptional activation domains. AF-1 is in of TAM (12). However, it is still not entirely clear how TAM the N terminus of the receptor protein and AF-2 activity is manifests agonist activities through ERα WT in different tissues. dependent on helix 12 of the C-terminal ligand-binding domain. We focused on the L543A and L544A mutations in the ERα Two point mutations of leucines 543 and 544 to alanines (L543A, AF-2 domain (AF2ER) to evaluate the ERα AF-1 and AF-2 L544A) in helix 12 minimized estrogen-dependent transcriptional functions in vivo and the SERM functionality in the tissues. α α activation and reversed the activity of the estrogen antagonists The ER -KO ( ERKO) mouse is an established model for α α ICI182780 (ICI) and tamoxifen (TAM) into agonists in a similar evaluating ER function in vivo.
    [Show full text]
  • Mechanism of Nucleosome Targeting by Pioneer Transcription Factors
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2019 Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors Meilin Mary Fernandez Garcia University of Pennsylvania Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons, and the Biophysics Commons Recommended Citation Fernandez Garcia, Meilin Mary, "Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors" (2019). Publicly Accessible Penn Dissertations. 3624. https://repository.upenn.edu/edissertations/3624 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/3624 For more information, please contact [email protected]. Mechanism Of Nucleosome Targeting By Pioneer Transcription Factors Abstract Transcription factors (TFs) forage the genome to instruct cell plasticity, identity, and differentiation. These developmental processes are elicited through TF engagement with chromatin. Yet, how and which TFs can engage with chromatin and thus, nucleosomes, remains largely unexplored. Pioneer TFs are TF that display a high affinity for nucleosomes. Extensive genetic and biochemical studies on the pioneer TF FOXA, a driver of fibroblast to hepatocyte reprogramming, revealed its nucleosome binding ability and chromatin targeting lead to chromatin accessibility and subsequent cooperative binding of TFs. Similarly, a number of reprogramming TFs have been suggested to have pioneering activity due to their ability to target compact chromatin and increase accessibility and enhancer formation in vivo. But whether these factors directly interact with nucleosomes remains to be assessed. Here we test the nucleosome binding ability of the cell reprogramming TFs, Oct4, Sox2, Klf4 and cMyc, that are required for the generation of induced pluripotent stem cells. In addition, we also test neuronal and macrophage reprogramming TFs.
    [Show full text]
  • Genomic Imprinting Defect in Zfp57 Mutant Ips Cell Lines
    Stem Cell Research 16 (2016) 259–263 Contents lists available at ScienceDirect Stem Cell Research journal homepage: www.elsevier.com/locate/scr Lab Resource: Stem Cell Line Genomic imprinting defect in Zfp57 mutant iPS cell lines Carol M. McDonald a, Lizhi Liu a,LijuanXiaoa, Christoph Schaniel a,b, Xiajun Li a,c,⁎ a Black Family Stem Cell Institute, Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA b Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA c Department of Oncological Sciences, Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA article info abstract Article history: ZFP57 maintains genomic imprinting in mouse embryos and ES cells. To test its roles during iPS reprogramming, Received 1 January 2016 we derived iPS clones by utilizing retroviral infection to express reprogramming factors in mouse MEF cells. After Received in revised form 17 January 2016 analyzing four imprinted regions, we found that parentally derived DNA methylation imprint was largely main- Accepted 19 January 2016 tained in the iPS clones with Zfp57 but missing in those without maternal or zygotic Zfp57. Intriguingly, DNA Available online 21 January 2016 methylation imprint was lost at the Peg1 and Peg3 but retained at the Snrpn and Dlk1-Dio3 imprinted regions in the iPS clones without zygotic Zfp57.Thisfinding will be pursued in future studies. © 2016 The Authors.
    [Show full text]
  • Virtual Chip-Seq: Predicting Transcription Factor Binding
    bioRxiv preprint doi: https://doi.org/10.1101/168419; this version posted March 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Virtual ChIP-seq: predicting transcription factor binding 2 by learning from the transcriptome 1,2,3 1,2,3,4,5 3 Mehran Karimzadeh and Michael M. Hoffman 1 4 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada 2 5 Princess Margaret Cancer Centre, Toronto, ON, Canada 3 6 Vector Institute, Toronto, ON, Canada 4 7 Department of Computer Science, University of Toronto, Toronto, ON, Canada 5 8 Lead contact: michael.hoff[email protected] 9 March 8, 2019 10 Abstract 11 Motivation: 12 Identifying transcription factor binding sites is the first step in pinpointing non-coding mutations 13 that disrupt the regulatory function of transcription factors and promote disease. ChIP-seq is 14 the most common method for identifying binding sites, but performing it on patient samples is 15 hampered by the amount of available biological material and the cost of the experiment. Existing 16 methods for computational prediction of regulatory elements primarily predict binding in genomic 17 regions with sequence similarity to known transcription factor sequence preferences. This has limited 18 efficacy since most binding sites do not resemble known transcription factor sequence motifs, and 19 many transcription factors are not even sequence-specific. 20 Results: 21 We developed Virtual ChIP-seq, which predicts binding of individual transcription factors in new 22 cell types using an artificial neural network that integrates ChIP-seq results from other cell types 23 and chromatin accessibility data in the new cell type.
    [Show full text]
  • Aberrant Development of Pancreatic Beta Cells Derived from Human Ipscs with FOXA2 Deficiency Ahmed K
    Elsayed et al. Cell Death and Disease (2021) 12:103 https://doi.org/10.1038/s41419-021-03390-8 Cell Death & Disease ARTICLE Open Access Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency Ahmed K. Elsayed1, Ihab Younis2, Gowher Ali1, Khalid Hussain3 and Essam M. Abdelalim 1,4 Abstract FOXA2 has been identified as an essential factor for pancreas development and emerging evidence supports an association between FOXA2 and diabetes. Although the role of FOXA2 during pancreatic development is well-studied in animal models, its role during human islet cell development remains unclear. Here, we generated induced pluripotent stem cells (iPSCs) from a patient with FOXA2 haploinsufficiency (FOXA2+/− iPSCs) followed by beta-cell differentiation to understand the role of FOXA2 during pancreatic beta-cell development. Our results showed that FOXA2 haploinsufficiency resulted in aberrant expression of genes essential for the differentiation and proper functioning of beta cells. At pancreatic progenitor (PP2) and endocrine progenitor (EPs) stages, transcriptome analysis showed downregulation in genes associated with pancreatic development and diabetes and upregulation in genes associated with nervous system development and WNT signaling pathway. Knockout of FOXA2 in control iPSCs (FOXA2−/− iPSCs) led to severe phenotypes in EPs and beta-cell stages. The expression of NGN3 and its downstream targets at EPs as well as INSUILIN and GLUCAGON at the beta-cell stage, were almost absent in the cells derived from FOXA2−/− iPSCs. These findings indicate that FOXA2 is crucial for human pancreatic endocrine development and its defect may lead to diabetes based on FOXA2 dosage. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction TFs lead to neonatal diabetes, which can be associated During human development, early endodermal tissue with pancreatic hypoplasia/agenesis in some mutations4.
    [Show full text]
  • Foxa2 and Mafa Regulate Islet-Specific Glucose-6
    315 Foxa2 and MafA regulate islet-specific glucose-6-phosphatase catalytic subunit-related protein gene expression Cyrus C Martin, Brian P Flemming, Yingda Wang, James K Oeser and Richard M O’Brien Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, 8415 MRB IV, 2213 Garland Avenue, Nashville, Tennessee 37232, USA (Correspondence should be addressed to R M O’Brien; Email: [email protected]) Abstract Islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP/G6PC2) is a major autoantigen in both mouse and human type 1 diabetes. IGRP is selectively expressed in islet b cells and polymorphisms in the IGRP gene have recently been associated with variations in fasting blood glucose levels and cardiovascular-associated mortality in humans. Chromatin immunoprecipitation (ChIP) assays have shown that the IGRP promoter binds the islet-enriched transcription factors Pax-6 and BETA2. We show here, again using ChIP assays, that the IGRP promoter also binds the islet-enriched transcription factors MafA and Foxa2. Single binding sites for these factors were identified in the proximal IGRP promoter, mutation of which resulted in decreased IGRP fusion gene expression in bTC-3, Hamster insulinoma tumor (HIT), and Min6 cells. ChiP assays have shown that the islet-enriched transcription factor Pdx-1 also binds the IGRP promoter, but mutational analysis of four Pdx-1 binding sites in the proximal IGRP promoter revealed surprisingly little effect of Pdx-1 binding on IGRP fusion gene expression in bTC-3 cells. In contrast, in both HIT and Min6 cells mutation of these four Pdx-1 binding sites resulted in a w50% reduction in fusion gene expression.
    [Show full text]
  • Integrated Computational Approach to the Analysis of RNA-Seq Data Reveals New Transcriptional Regulators of Psoriasis
    OPEN Experimental & Molecular Medicine (2016) 48, e268; doi:10.1038/emm.2016.97 & 2016 KSBMB. All rights reserved 2092-6413/16 www.nature.com/emm ORIGINAL ARTICLE Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis Alena Zolotarenko1, Evgeny Chekalin1, Alexandre Mesentsev1, Ludmila Kiseleva2, Elena Gribanova2, Rohini Mehta3, Ancha Baranova3,4,5,6, Tatiana V Tatarinova6,7,8, Eleonora S Piruzian1 and Sergey Bruskin1,5 Psoriasis is a common inflammatory skin disease with complex etiology and chronic progression. To provide novel insights into the regulatory molecular mechanisms of the disease, we performed RNA sequencing analysis of 14 pairs of skin samples collected from patients with psoriasis. Subsequent pathway analysis and extraction of the transcriptional regulators governing psoriasis-associated pathways was executed using a combination of the MetaCore Interactome enrichment tool and the cisExpress algorithm, followed by comparison to a set of previously described psoriasis response elements. A comparative approach allowed us to identify 42 core transcriptional regulators of the disease associated with inflammation (NFκB, IRF9, JUN, FOS, SRF), the activity of T cells in psoriatic lesions (STAT6, FOXP3, NFATC2, GATA3, TCF7, RUNX1), the hyper- proliferation and migration of keratinocytes (JUN, FOS, NFIB, TFAP2A, TFAP2C) and lipid metabolism (TFAP2, RARA, VDR). In addition to the core regulators, we identified 38 transcription factors previously not associated with the disease that can clarify the pathogenesis of psoriasis. To illustrate these findings, we analyzed the regulatory role of one of the identified transcription factors (TFs), FOXA1. Using ChIP-seq and RNA-seq data, we concluded that the atypical expression of the FOXA1 TF is an important player in the disease as it inhibits the maturation of naive T cells into the (CD4+FOXA1+CD47+CD69+PD-L1(hi) FOXP3 − ) regulatory T cell subpopulation, therefore contributing to the development of psoriatic skin lesions.
    [Show full text]
  • Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2
    Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2 The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Bochkis, Irina M. et al. “Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2.” Ed. Michael Snyder. PLoS Genetics 8.6 (2012): e1002770. As Published http://dx.doi.org/10.1371/journal.pgen.1002770 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/73529 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.5/ Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2 Irina M. Bochkis1¤, Jonathan Schug1, Diana Z. Ye1, Svitlana Kurinna2, Sabrina A. Stratton2, Michelle C. Barton2, Klaus H. Kaestner1* 1 Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America, 2 Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America Abstract Gene duplication is a powerful driver of evolution. Newly duplicated genes acquire new roles that are relevant to fitness, or they will be lost over time. A potential path to functional relevance is mutation of the coding sequence leading to the acquisition of novel biochemical properties, as analyzed here for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators. We determine by genome-wide location analysis (ChIP-Seq) that, although Foxa1 and Foxa2 share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo.
    [Show full text]
  • Ligand-Free Estrogen Receptor Alpha (ESR1) As Master Regulator for the Expression of CYP3A4 and Other Cytochrome P450s (Cyps) in Human Liver*
    Molecular Pharmacology Fast Forward. Published on August 9, 2019 as DOI: 10.1124/mol.119.116897 This article has not been copyedited and formatted. The final version may differ from this version. MOL# 116897 Ligand-Free Estrogen Receptor Alpha (ESR1) as Master Regulator for the Expression of CYP3A4 and other Cytochrome P450s (CYPs) in Human Liver* Danxin Wang, Rong Lu, Grzegorz Rempala, and Wolfgang Sadee Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, USA (D.W); Downloaded from Department of Clinical Sciences, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas, 75235, USA (R.L); molpharm.aspetjournals.org Mathematical Bioscience Institute, The Ohio State University, Columbus, Ohio 43210, USA (G.R); Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA (W.S) at ASPET Journals on September 26, 2021 1 Molecular Pharmacology Fast Forward. Published on August 9, 2019 as DOI: 10.1124/mol.119.116897 This article has not been copyedited and formatted. The final version may differ from this version. MOL# 116897 Running title: Ligand-free ESR1 as CYP3A4 master regulator Corresponding author: Danxin Wang, MD, Ph.D Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, PO Box 100486, 1345 Center Drive MSB PG-05B, Gainesville, FL 32610 Tel: 352-273-7673; Fax:
    [Show full text]
  • Ikkalpha Mediated NOTCH1 Activation Promotes Tumorigenesis Via FOXA2 Suppression
    The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 8-2012 IKKalpha mediated NOTCH1 Activation Promotes Tumorigenesis via FOXA2 Suppression Mo Liu Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Medicine and Health Sciences Commons Recommended Citation Liu, Mo, "IKKalpha mediated NOTCH1 Activation Promotes Tumorigenesis via FOXA2 Suppression" (2012). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 261. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/261 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. IKKα Mediated NOTCH1 Activation Promotes Tumorigenesis via FOXA2 Suppression By Mo Liu APPROVED: ____________________________ Mien-Chie Hung, Ph.D., Supervisor _____________________________ Dihua Yu, M.D., Ph.D. ______________________________ Elsa R. Flores, Ph.D. ______________________________ Hui-Kuan Lin, Ph.D. ______________________________ Andrew Bean, Ph.D. APPROVED: ___________________________________ DEAN, THE UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON GRADUATE SCHOOL OF BIOMEDICAL SCIENCES IKKα Mediated NOTCH1 Activation Promotes Tumorigenesis via FOXA2 Suppression A DISSERTATION Presented to the Faculty of The University of Texas Health Science Center at Houston and The University of Texas M.
    [Show full text]