TF Activation Profiling Plate Array II Signosis, Inc
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UNIVERSITY of CALIFORNIA, IRVINE Combinatorial Regulation By
UNIVERSITY OF CALIFORNIA, IRVINE Combinatorial regulation by maternal transcription factors during activation of the endoderm gene regulatory network DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biological Sciences by Kitt D. Paraiso Dissertation Committee: Professor Ken W.Y. Cho, Chair Associate Professor Olivier Cinquin Professor Thomas Schilling 2018 Chapter 4 © 2017 Elsevier Ltd. © 2018 Kitt D. Paraiso DEDICATION To the incredibly intelligent and talented people, who in one way or another, helped complete this thesis. ii TABLE OF CONTENTS Page LIST OF FIGURES vii LIST OF TABLES ix LIST OF ABBREVIATIONS X ACKNOWLEDGEMENTS xi CURRICULUM VITAE xii ABSTRACT OF THE DISSERTATION xiv CHAPTER 1: Maternal transcription factors during early endoderm formation in 1 Xenopus Transcription factors co-regulate in a cell type-specific manner 2 Otx1 is expressed in a variety of cell lineages 4 Maternal otx1 in the endodermal conteXt 5 Establishment of enhancers by maternal transcription factors 9 Uncovering the endodermal gene regulatory network 12 Zygotic genome activation and temporal control of gene eXpression 14 The role of maternal transcription factors in early development 18 References 19 CHAPTER 2: Assembly of maternal transcription factors initiates the emergence 26 of tissue-specific zygotic cis-regulatory regions Introduction 28 Identification of maternal vegetally-localized transcription factors 31 Vegt and OtX1 combinatorially regulate the endodermal 33 transcriptome iii -
Interindividual Regulation of the BCRP/ABCG2 Transporter in Term Human Placentas
DMD Fast Forward. Published on January 31, 2018 as DOI: 10.1124/dmd.117.079228 This article has not been copyedited and formatted. The final version may differ from this version. DMD #79228 Title Page Interindividual Regulation of the BCRP/ABCG2 Transporter in Term Human Placentas Kristin M Bircsak, Jamie E Moscovitz, Xia Wen, Faith Archer, Poi Yu Sofia Yuen, Moiz Mohammed, Naureen Memon, Barry I Weinberger, Laura M Saba, Anna M Vetrano, Lauren M Aleksunes Downloaded from Department of Pharmacology and Toxicology, Rutgers, The State University of New Jersey, Ernest Mario School of Pharmacy, Piscataway, NJ, USA (K.M.B., J.E.M., X.W., L.M.A.), dmd.aspetjournals.org Department of Pediatrics, Rutgers University Robert Wood Johnson Medical School, New Brunswick, NJ, USA (F.A., P.Y.S.Y, M.M., N.M., A.M.V.), Hofstra Northwell School of Medicine, Cohen Children’s Medical Center of New York, New Hyde Park, NY, USA (B.I.W.), at ASPET Journals on October 2, 2021 Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA (L.S.), Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA (L.M.A.), Lipid Center, Rutgers, The State University of New Jersey, Piscataway, NJ, USA (L.M.A.) 1 DMD Fast Forward. Published on January 31, 2018 as DOI: 10.1124/dmd.117.079228 This article has not been copyedited and formatted. The final version may differ from this version. DMD #79228 Running Title Page Running title: Interindividual -
Foxh1 Represses Mir-430 During Early Embryonic Development Of
Fischer et al. BMC Biology (2019) 17:61 https://doi.org/10.1186/s12915-019-0683-z RESEARCHARTICLE Open Access FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation Patrick Fischer1, Hao Chen1, Frederic Pacho1, Dietmar Rieder2, Robin A. Kimmel1 and Dirk Meyer1* Abstract Background: FoxH1 is a forkhead transcription factor with conserved key functions in vertebrate mesoderm induction and left-right patterning downstream of the TGF-beta/Nodal signaling pathway. Binding of the forkhead domain (FHD) of FoxH1 to a highly conserved proximal sequence motif was shown to regulate target gene expression. Results: We identify the conserved microRNA-430 family (miR-430) as a novel target of FoxH1. miR-430 levels are increased in foxH1 mutants, resulting in a reduced expression of transcripts that are targeted by miR-430 for degradation. To determine the underlying mechanism of miR-430 repression, we performed chromatin immunoprecipitation studies and overexpression experiments with mutant as well as constitutive active and repressive forms of FoxH1. Our studies reveal a molecular interaction of FoxH1 with miR-430 loci independent of the FHD. Furthermore, we show that previously described mutant forms of FoxH1 that disrupt DNA binding or that lack the C-terminal Smad Interaction Domain (SID) dominantly interfere with miR-430 repression, but not with the regulation of previously described FoxH1 targets. Conclusions: We were able to identify the distinct roles of protein domains of FoxH1 in the regulation process of miR- 430. We provide evidence that the indirect repression of miR-430 loci depends on the connection to a distal repressive chromosome environment via a non-canonical mode. -
82451509.Pdf
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Biology 334 (2009) 513–522 Contents lists available at ScienceDirect Developmental Biology journal homepage: www.elsevier.com/developmentalbiology Genomes & Developmental Control Isl1 is a direct transcriptional target of Forkhead transcription factors in second heart field-derived mesoderm Jione Kang a, Elisha Nathan b, Shan-Mei Xu a, Eldad Tzahor b, Brian L. Black a,⁎ a Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Box 2240, San Francisco, CA 94158-2517, USA b Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel article info abstract Article history: The cells of the second heart field (SHF) contribute to the outflow tract and right ventricle, as well as to parts Received for publication 20 May 2009 of the left ventricle and atria. Isl1, a member of the LIM-homeodomain transcription factor family, is Accepted 27 June 2009 expressed early in this cardiac progenitor population and functions near the top of a transcriptional pathway Available online 4 July 2009 essential for heart development. Isl1 is required for the survival and migration of SHF-derived cells into the early developing heart at the inflow and outflow poles. Despite this important role for Isl1 in early heart Keywords: formation, the transcriptional regulation of Isl1 has remained largely undefined. Therefore, to identify Isl1 Second heart field transcription factors that regulate Isl1 expression in vivo, we screened the conserved noncoding sequences Anterior heart field from the mouse Isl1 locus for enhancer activity in transgenic mouse embryos. -
Tgfβ-Regulated Gene Expression by Smads and Sp1/KLF-Like Transcription Factors in Cancer VOLKER ELLENRIEDER
ANTICANCER RESEARCH 28 : 1531-1540 (2008) Review TGFβ-regulated Gene Expression by Smads and Sp1/KLF-like Transcription Factors in Cancer VOLKER ELLENRIEDER Signal Transduction Laboratory, Internal Medicine, Department of Gastroenterology and Endocrinology, University of Marburg, Marburg, Germany Abstract. Transforming growth factor beta (TGF β) controls complex induces the canonical Smad signaling molecules which vital cellular functions through its ability to regulate gene then translocate into the nucleus to regulate transcription (2). The expression. TGFβ binding to its transmembrane receptor cellular response to TGF β can be extremely variable depending kinases initiates distinct intracellular signalling cascades on the cell type and the activation status of a cell at a given time. including the Smad signalling and transcription factors and also For instance, TGF β induces growth arrest and apoptosis in Smad-independent pathways. In normal epithelial cells, TGF β healthy epithelial cells, whereas it can also promote tumor stimulation induces a cytostatic program which includes the progression through stimulation of cell proliferation and the transcriptional repression of the c-Myc oncogene and the later induction of an epithelial-to-mesenchymal transition of tumor induction of the cell cycle inhibitors p15 INK4b and p21 Cip1 . cells (1, 3). In the last decade it has become clear that both the During carcinogenesis, however, many tumor cells lose their tumor suppressing and the tumor promoting functions of TGF β ability to respond to TGF β with growth inhibition, and instead, are primarily regulated on the level of gene expression through activate genes involved in cell proliferation, invasion and Smad-dependent and -independent mechanisms (1, 2, 4). -
Supplementary Materials
Supplementary Materials + - NUMB E2F2 PCBP2 CDKN1B MTOR AKT3 HOXA9 HNRNPA1 HNRNPA2B1 HNRNPA2B1 HNRNPK HNRNPA3 PCBP2 AICDA FLT3 SLAMF1 BIC CD34 TAL1 SPI1 GATA1 CD48 PIK3CG RUNX1 PIK3CD SLAMF1 CDKN2B CDKN2A CD34 RUNX1 E2F3 KMT2A RUNX1 T MIXL1 +++ +++ ++++ ++++ +++ 0 0 0 0 hematopoietic potential H1 H1 PB7 PB6 PB6 PB6.1 PB6.1 PB12.1 PB12.1 Figure S1. Unsupervised hierarchical clustering of hPSC-derived EBs according to the mRNA expression of hematopoietic lineage genes (microarray analysis). Hematopoietic-competent cells (H1, PB6.1, PB7) were separated from hematopoietic-deficient ones (PB6, PB12.1). In this experiment, all hPSCs were tested in duplicate, except PB7. Genes under-expressed or over-expressed in blood-deficient hPSCs are indicated in blue and red respectively (related to Table S1). 1 C) Mesoderm B) Endoderm + - KDR HAND1 GATA6 MEF2C DKK1 MSX1 GATA4 WNT3A GATA4 COL2A1 HNF1B ZFPM2 A) Ectoderm GATA4 GATA4 GSC GATA4 T ISL1 NCAM1 FOXH1 NCAM1 MESP1 CER1 WNT3A MIXL1 GATA4 PAX6 CDX2 T PAX6 SOX17 HBB NES GATA6 WT1 SOX1 FN1 ACTC1 ZIC1 FOXA2 MYF5 ZIC1 CXCR4 TBX5 PAX6 NCAM1 TBX20 PAX6 KRT18 DDX4 TUBB3 EPCAM TBX5 SOX2 KRT18 NKX2-5 NES AFP COL1A1 +++ +++ 0 0 0 0 ++++ +++ ++++ +++ +++ ++++ +++ ++++ 0 0 0 0 +++ +++ ++++ +++ ++++ 0 0 0 0 hematopoietic potential H1 H1 H1 H1 H1 H1 PB6 PB6 PB7 PB7 PB6 PB6 PB7 PB6 PB6 PB6.1 PB6.1 PB6.1 PB6.1 PB6.1 PB6.1 PB12.1 PB12.1 PB12.1 PB12.1 PB12.1 PB12.1 Figure S2. Unsupervised hierarchical clustering of hPSC-derived EBs according to the mRNA expression of germ layer differentiation genes (microarray analysis) Selected ectoderm (A), endoderm (B) and mesoderm (C) related genes differentially expressed between hematopoietic-competent (H1, PB6.1, PB7) and -deficient cells (PB6, PB12.1) are shown (related to Table S1). -
A Dissertation Entitled the Androgen Receptor
A Dissertation entitled The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit Submitted to the Graduate Faculty as partial fulfillment of the requirements for the PhD Degree in Biomedical science Dr. Manohar Ratnam, Committee Chair Dr. Lirim Shemshedini, Committee Member Dr. Robert Trumbly, Committee Member Dr. Edwin Sanchez, Committee Member Dr. Beata Lecka -Czernik, Committee Member Dr. Patricia R. Komuniecki, Dean College of Graduate Studies The University of Toledo August 2011 Copyright 2011, Mesfin Gonit This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit As partial fulfillment of the requirements for the PhD Degree in Biomedical science The University of Toledo August 2011 Prostate cancer depends on the androgen receptor (AR) for growth and survival even in the absence of androgen. In the classical models of gene activation by AR, ligand activated AR signals through binding to the androgen response elements (AREs) in the target gene promoter/enhancer. In the present study the role of AREs in the androgen- independent transcriptional signaling was investigated using LP50 cells, derived from parental LNCaP cells through extended passage in vitro. LP50 cells reflected the signature gene overexpression profile of advanced clinical prostate tumors. The growth of LP50 cells was profoundly dependent on nuclear localized AR but was independent of androgen. Nevertheless, in these cells AR was unable to bind to AREs in the absence of androgen. -
Supplemental Table 1. Primers and Probes for RT-Pcrs
Supplemental Table 1. Primers and probes for RT-PCRs Gene Direction Sequence Quantitative RT-PCR E2F1 Forward Primer 5’-GGA TTT CAC ACC TTT TCC TGG AT-3’ Reverse Primer 5’-CCT GGA AAC TGA CCA TCA GTA CCT-3’ Probe 5’-FAM-CGA GCT GGC CCA CTG CTC TCG-TAMRA-3' E2F2 Forward Primer 5'-TCC CAA TCC CCT CCA GAT C-3' Reverse Primer 5'-CAA GTT GTG CGA TGC CTG C-3' Probe 5' -FAM-TCC TTT TGG CCG GCA GCC G-TAMRA-3' E2F3a Forward Primer 5’-TTT AAA CCA TCT GAG AGG TAC TGA TGA-3’ Reverse Primer 5’-CGG CCC TCC GGC AA-3’ Probe 5’-FAM-CGC TTT CTC CTA GCT CCA GCC TTC G-TAMRA-3’ E2F3b Forward Primer 5’-TTT AAA CCA TCT GAG AGG TAC TGA TGA-3’ Reverse Primer 5’-CCC TTA CAG CAG CAG GCA A-3’ Probe 5’-FAM-CGC TTT CTC CTA GCT CCA GCC TTC G-TAMRA-3’ IRF-1 Forward Primer 5’-TTT GTA TCG GCC TGT GTG AAT G-3’ Reverse Primer 5’-AAG CAT GGC TGG GAC ATC A-3’ Probe 5’-FAM-CAG CTC CGG AAC AAA CAG GCA TCC TT-TAMRA-3' IRF-2 Forward Primer 5'-CGC CCC TCG GCA CTC T-3' Reverse Primer 5'-TCT TCC TAT GCA GAA AGC GAA AC-3' Probe 5'-FAM-TTC ATC GCT GGG CAC ACT ATC AGT-TAMRA-3' TBP Forward Primer 5’-CAC GAA CCA CGG CAC TGA TT-3’ Reverse Primer 5’-TTT TCT TGC TGC CAG TCT GGA C-3’ Probe 5’-FAM-TGT GCA CAG GAG CCA AGA GTG AAG A-BHQ1-3’ Primers and Probes for quantitative RT-PCRs were designed using the computer program “Primer Express” (Applied Biosystems, Foster City, CA, USA). -
The Genetic Factors of Bilaterian Evolution Peter Heger1*, Wen Zheng1†, Anna Rottmann1, Kristen a Panfilio2,3, Thomas Wiehe1
RESEARCH ARTICLE The genetic factors of bilaterian evolution Peter Heger1*, Wen Zheng1†, Anna Rottmann1, Kristen A Panfilio2,3, Thomas Wiehe1 1Institute for Genetics, Cologne Biocenter, University of Cologne, Cologne, Germany; 2Institute for Zoology: Developmental Biology, Cologne Biocenter, University of Cologne, Cologne, Germany; 3School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, United Kingdom Abstract The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo- Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship. *For correspondence: [email protected] Introduction The taxon Bilateria consists of multicellular animals -
Mouse VDR / NR1I1 Protein (His Tag)
Mouse VDR / NR1I1 Protein (His Tag) Catalog Number: 51106-M08B General Information SDS-PAGE: Gene Name Synonym: Nr1i1 Protein Construction: A DNA sequence encoding the mouse VDR (P48281) (Met1-Ser422) was fused with a polyhistidine tag at the C-terminus. Source: Mouse Expression Host: Baculovirus-Insect Cells QC Testing Purity: > 80 % as determined by SDS-PAGE Endotoxin: Protein Description < 1.0 EU per μg of the protein as determined by the LAL method VDR (vitamin D(1,25- dihydroxyvitamin D3)receptor), also known as NR1I1, Stability: belongs to the NR1I family, NR1 subfamily. It is composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ℃ Samples are stable for up to twelve months from date of receipt at -70 ligand-binding domain. Vitamin D receptors (VDRs) are members of the NR1I family, which also includes pregnane X (PXR) and constitutive Met Predicted N terminal: androstane (CAR) receptors, that form heterodimers with members of the Molecular Mass: retinoid X receptor family. VDRs repress expression of 1alpha-hydroxylase (the proximal activator of 1,25(OH)2D3) and induce expression of the The recombinant mouse VDR consists of 432 amino acids and has a 1,25(OH)2D3 inactivating enzyme CYP24. Also, it has recently been calculated molecular mass of 49.2 kDa. The recombinant protein migrates identified as an additional bile acid receptor alongside FXR and may as an approximately 55 kDa band in SDS-PAGE under reducing conditions. function to protect gut against the toxic and carcinogenic effects of these endobiotics. VDR is expressed in the intestine, thyroid and kidney and has Formulation: a vital role in calcium homeostasis. -
Selective Inhibition of TGF-B Responsive Genes by Smad-Interacting Peptide Aptamers from Foxh1, Lef1 and CBP
Oncogene (2005) 24, 3864–3874 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc Selective inhibition of TGF-b responsive genes by Smad-interacting peptide aptamers from FoxH1, Lef1 and CBP Qiqi Cui1, Sang Kyun Lim1, Bryan Zhao1 and Francis Michael Hoffmann*,1,2 1McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA; 2Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA Transforming growth factor beta (TGF-b)stimulation several pathological conditions including cancer and results in the assembly of Smad-containing protein com- fibrosis (Derynck et al., 2001; Wakefield and Roberts, plexes that mediate activation or repression of TGF-b 2002). TGF-b alters cellular gene expression and cell responsive genes. To determine if disruption of specific behavior by binding and activating the Type II and Smad protein–protein interactions would selectively Type I serine kinase receptors on the cell membrane. inhibit responses to TGF-b or generally interfere with Activated Type I receptor phosphorylates Smad2 and Smad-dependent signaling, we developed three Smad- Smad3, which form heterodimeric or heterotrimeric binding peptide aptamers by introducing Smad interaction complexes with Smad4 that accumulate in the cell motifs from Smad-binding proteins CBP, FoxH1 and nucleus (ten Dijke and Hill, 2004). The Smad2–Smad4 Lef1 into the scaffold protein E. coli thioredoxin A (Trx). and Smad3–Smad4 protein complexes bind over 20 All three classes of aptamers bound to Smads by GST different nuclear proteins including DNA-binding proteins, pulldown assays and co-immunoprecipitation from mam- transcription activators and transcription repressors malian cells. -
Review Vitamin D in Neurological Diseases: a Rationale for a Pathogenic Impact
Review Vitamin D in Neurological Diseases: A Rationale for a Pathogenic Impact Rita Moretti, Maria Elisa Morelli and Paola Caruso * Neurology Clinic, Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy; [email protected] (R.M.); [email protected] (M.E.M.) * Correspondence: [email protected] Received: 27 June 2018; Accepted: 26 July 2018; Published: 31 July 2018 Abstract: It is widely known that vitamin D receptors have been found in neurons and glial cells, and their highest expression is in the hippocampus, hypothalamus, thalamus and subcortical grey nuclei, and substantia nigra. Vitamin D helps the regulation of neurotrophin, neural differentiation, and maturation, through the control operation of growing factors synthesis (i.e., neural growth factor [NGF] and glial cell line-derived growth factor (GDNF), the trafficking of the septohippocampal pathway, and the control of the synthesis process of different neuromodulators (such as acetylcholine [Ach], dopamine [DA], and gamma-aminobutyric [GABA]). Based on these assumptions, we have written this review to summarize the potential role of vitamin D in neurological pathologies. This work could be titanic and the results might have been very fuzzy and even incoherent had we not conjectured to taper our first intentions and devoted our interests towards three mainstreams, demyelinating pathologies, vascular syndromes, and neurodegeneration. As a result of the lack of useful therapeutic options, apart from the disease- modifying strategies, the role of different risk factors should be investigated in neurology, as their correction may lead to the improvement of the cerebral conditions. We have explored the relationships between the gene-environmental influence and long-term vitamin D deficiency, as a risk factor for the development of different types of neurological disorders, along with the role and the rationale of therapeutic trials with vitamin D implementation.