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Tripathy S, Nagari A, Chiu SP, Nandu T, Camacho CV, Mahendroo M, Kraus WL. Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium by Reducing Estrogen Receptor Alpha Phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589654. [PMID: 38659934 PMCID: PMC11042280 DOI: 10.1101/2024.04.15.589654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Estradiol (E2) and relaxin (Rln) are steroid and polypeptide hormones, respectively, with important roles in the female reproductive tract, including myometrium. Some actions of Rln, which are mediated by its membrane receptor RXFP1, require or are augmented by E2 signaling through its cognate nuclear steroid receptor, estrogen receptor alpha (ERα). In contrast, other actions of Rln act in opposition to the effects of E2. Here we explore the molecular and genomic mechanisms that underlie the functional interplay between E2 and Rln in the myometrium. We used both ovariectomized female mice and immortalized human myometrial cells expressing wild type or mutant ERα (hTERT-HM-ERα cells). Our results indicate that Rln attenuates the genomic actions and biological effects of estrogen in the myometrium and myometrial cells by reducing phosphorylation ERα on serine 118 (S118). Interestingly, we observed a potent inhibitory effect of Rln on the E2-dependent binding of ERα across the genome. The reduction in ERα binding was associated with changes in the hormone-regulated transcriptome, including a decrease in the E2-dependent expression of neighboring genes. The inhibitory effects of Rln cotreatment on the E2-dependent phosphorylation of ERα required the nuclear dual-specificity phosphatases DUSP1 and DUSP5. Moreover, the inhibitory effects of Rln were reflected in a concomitant inhibition of the E2-dependent contraction of myometrial cells. Collectively, our results identify a pathway that integrates Rln/RXFP1 and E2/ERα signaling, resulting in a convergence of membrane and nuclear signaling pathways to control genomic and biological outcomes.
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Affiliation(s)
- Sudeshna Tripathy
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Laboratory of Cervical Remodeling and Preterm Birth, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shu-Ping Chiu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V. Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mala Mahendroo
- Laboratory of Cervical Remodeling and Preterm Birth, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Jones T, Sigauke RF, Sanford L, Taatjes DJ, Allen MA, Dowell RD. A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585303. [PMID: 38559193 PMCID: PMC10980006 DOI: 10.1101/2024.03.15.585303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
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3
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Zheng M, Lin Y, Wang W, Zhao Y, Bao X. Application of nucleoside or nucleotide analogues in RNA dynamics and RNA-binding protein analysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1722. [PMID: 35218164 DOI: 10.1002/wrna.1722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/07/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Cellular RNAs undergo dynamic changes during RNA biological processes, which are tightly orchestrated by RNA-binding proteins (RBPs). Yet, the investigation of RNA dynamics is hurdled by highly abundant steady-state RNAs, which make the signals of dynamic RNAs less detectable. Notably, the exert of nucleoside or nucleotide analogue-based RNA technologies has provided a remarkable platform for RNA dynamics research, revealing diverse unnoticed features in RNA metabolism. In this review, we focus on the application of two types of analogue-based RNA sequencing, antigen-/antibody- and click chemistry-based methodologies, and summarize the RNA dynamics features revealed. Moreover, we discuss emerging single-cell newly transcribed RNA sequencing methodologies based on nucleoside analogue labeling, which provides novel insights into RNA dynamics regulation at single-cell resolution. On the other hand, we also emphasize the identification of RBPs that interact with polyA, non-polyA RNAs, or newly transcribed RNAs and also their associated RNA-binding domains at genomewide level through ultraviolet crosslinking and mass spectrometry in different contexts. We anticipated that further modification and development of these analogue-based RNA and RBP capture technologies will aid in obtaining an unprecedented understanding of RNA biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Meifeng Zheng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Lin
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The Center for Infection and Immunity Study, School of Medicine, Sun Yat-sen University, Guangming Science City, Shenzhen, China
| | - Wei Wang
- Center for Biosafety, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xichen Bao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
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Miller L, Thompson K, Pavlenco C, Mettu VS, Haverkamp H, Skaufel S, Basit A, Prasad B, Larsen J. The Effect of Daily Methylsulfonylmethane (MSM) Consumption on High-Density Lipoprotein Cholesterol in Healthy Overweight and Obese Adults: A Randomized Controlled Trial. Nutrients 2021; 13:nu13103620. [PMID: 34684621 PMCID: PMC8540167 DOI: 10.3390/nu13103620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022] Open
Abstract
Interventions to decrease inflammation and improve metabolic function hold promise for the prevention of obesity-related diseases. Methylsulfonylmethane (MSM) is a naturally occurring compound that demonstrates antioxidant and anti-inflammatory effects. Improvements in measures of metabolic health have been observed in mouse models of obesity and diabetes following MSM treatment. However, the effects of MSM on obesity-related diseases in humans have not been investigated. Therefore, the purpose of this investigation was to determine whether MSM supplementation improves cardiometabolic health, and markers of inflammation and oxidative status. A randomized, double-blind, placebo-controlled design was utilized with a total of 22 overweight or obese adults completing the study. Participants received either a placebo (white rice flour) or 3 g MSM daily for 16 weeks. Measurements occurred at baseline and after 4, 8, and 16 weeks. Outcome measures included fasting glucose, insulin, blood lipids, blood pressure, body composition, metabolic rate, and markers of inflammation and oxidative status. The primary finding of this work shows that high-density lipoprotein cholesterol was elevated at 8 and 16 weeks of daily MSM consumption compared to baseline, (p = 0.008, p = 0.013). Our findings indicate that MSM supplementation may improve the cholesterol profile by resulting in higher levels of high-density lipoprotein cholesterol.
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Affiliation(s)
- Lindsey Miller
- Department of Physiology, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37934, USA
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA; (K.T.); (C.P.); (H.H.); (S.S.); (J.L.)
- Correspondence:
| | - Kari Thompson
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA; (K.T.); (C.P.); (H.H.); (S.S.); (J.L.)
| | - Carolina Pavlenco
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA; (K.T.); (C.P.); (H.H.); (S.S.); (J.L.)
| | - Vijaya Saradhi Mettu
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (V.S.M.); (A.B.); (B.P.)
| | - Hans Haverkamp
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA; (K.T.); (C.P.); (H.H.); (S.S.); (J.L.)
| | - Samantha Skaufel
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA; (K.T.); (C.P.); (H.H.); (S.S.); (J.L.)
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (V.S.M.); (A.B.); (B.P.)
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (V.S.M.); (A.B.); (B.P.)
| | - Julie Larsen
- Department of Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA; (K.T.); (C.P.); (H.H.); (S.S.); (J.L.)
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5
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Mushimiyimana I, Tomas Bosch V, Niskanen H, Downes NL, Moreau PR, Hartigan K, Ylä-Herttuala S, Laham-Karam N, Kaikkonen MU. Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells. Mol Cell Biol 2021; 41:e0059420. [PMID: 33875575 PMCID: PMC8224232 DOI: 10.1128/mcb.00594-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/29/2020] [Accepted: 04/03/2021] [Indexed: 12/26/2022] Open
Abstract
Vascular endothelial growth factors (VEGFs) are best known as key regulators of angiogenesis and lymphangiogenesis. Although VEGFs have been promising therapeutic targets for various cardiovascular diseases, their regulatory landscape in endothelial cells remains elusive. Several studies have highlighted the involvement of noncoding RNAs (ncRNAs) in the modulation of VEGF expression. In this study, we investigated the role of two classes of ncRNAs, long ncRNAs (lncRNAs) and enhancer RNAs (eRNAs), in the transcriptional regulation of VEGFA and VEGFC. By integrating genome-wide global run-on sequencing (GRO-Seq) and chromosome conformation capture (Hi-C) data, we identified putative lncRNAs and eRNAs associated with VEGFA and VEGFC genes in endothelial cells. A subset of the identified putative enhancers demonstrated regulatory activity in a reporter assay. Importantly, we demonstrate that deletion of enhancers and lncRNAs by CRISPR/Cas9 promoted significant changes in VEGFA and VEGFC expression. Transcriptome sequencing (RNA-Seq) data from lncRNA deletions showed downstream factors implicated in VEGFA- and VEGFC-linked pathways, such as angiogenesis and lymphangiogenesis, suggesting functional roles for these lncRNAs. Our study uncovers novel lncRNAs and eRNAs regulating VEGFA and VEGFC that can be targeted to modulate the expression of these important molecules in endothelial cells.
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Affiliation(s)
- Isidore Mushimiyimana
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vanesa Tomas Bosch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nicholas L. Downes
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pierre R. Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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6
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Rubin JD, Stanley JT, Sigauke RF, Levandowski CB, Maas ZL, Westfall J, Taatjes DJ, Dowell RD. Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment. Commun Biol 2021; 4:661. [PMID: 34079046 PMCID: PMC8172830 DOI: 10.1038/s42003-021-02153-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/20/2021] [Indexed: 02/04/2023] Open
Abstract
Detecting changes in the activity of a transcription factor (TF) in response to a perturbation provides insights into the underlying cellular process. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects positional motif enrichment associated with changes in transcription observed in response to a perturbation. TFEA detects positional motif enrichment within a list of ranked regions of interest (ROIs), typically sites of RNA polymerase initiation inferred from regulatory data such as nascent transcription. Therefore, we also introduce muMerge, a statistically principled method of generating a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data that informs on transcriptional regulation including nascent transcription (eg. PRO-Seq), CAGE, histone ChIP-Seq, and accessibility data (e.g., ATAC-Seq). TFEA not only identifies the key regulators responding to a perturbation, but also temporally unravels regulatory networks with time series data. Consequently, TFEA serves as a hypothesis-generating tool that provides an easy, rigorous, and cost-effective means to broadly assess TF activity yielding new biological insights.
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Affiliation(s)
- Jonathan D Rubin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jacob T Stanley
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Rutendo F Sigauke
- Computational Bioscience Program, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
| | | | - Zachary L Maas
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Jessica Westfall
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.
- Department of Computer Science, University of Colorado, Boulder, CO, USA.
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7
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Wei Z, Zhao J, Niebler J, Hao JJ, Merrick BA, Xia M. Quantitative Proteomic Profiling of Mitochondrial Toxicants in a Human Cardiomyocyte Cell Line. Front Genet 2020; 11:719. [PMID: 32733541 PMCID: PMC7358379 DOI: 10.3389/fgene.2020.00719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/12/2020] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are essential cellular organelles that participate in important cellular processes, including bioenergetics, metabolism, and signaling. Recent functional and proteomic studies have revealed the remarkable complexity of mitochondrial protein organization. Mitochondrial protein machineries with diverse functions such as protein translocation, respiration, metabolite transport, protein quality control and the control of membrane architecture interact with each other in dynamic networks. The goal of this study was to identify protein expression changes in a human cardiomyocyte cell line treated with several mitochondrial toxicants which inhibit mitochondrial membrane potential (MMP) and mitochondrial respiration. AC16 human cardiomyocyte cells were treated with carbonyl cyanide p-(trifluoromethoxy)phenylhydrazone (FCCP), dinoterb, picoxystrobin, pinacyanol, and triclocarban for 18 h around the IC50 values generated from MMP assay. The samples were harvested and labeled with tandem mass tags with different mass isotopes. Peptide assignment was performed in Proteome Discoverer. Each dataset was analyzed in Ingenuity Pathway Analysis (IPA). In the proteomic profile, these compounds showed dysregulation of a group of mitochondrial proteins (e.g., NDUA, NDUB, BCS1, CYB5B, and SDHF2), as well as proteins involved in lipid metabolism (e.g., CPT, MECR, and LPGAT1), cytoskeleton protein changes (e.g., CROCC, LAMC3, FBLN1, and FMN2) and stress response (e.g., IKBKG, IKBB, SYVN1, SOD2, and CPIN1). Proteomic data from the current study provides key insights into chemical induced cellular pathway dysregulation, supporting the use of proteomic profiling as a sensitive method to further explore molecular functions and disease pathogenesis upon exposure to environmental chemicals.
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Affiliation(s)
- Zhengxi Wei
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Jake Niebler
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | | | - B Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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8
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Hou TY, Nandu T, Li R, Chae M, Murakami S, Kraus WL. Characterization of basal and estrogen-regulated antisense transcription in breast cancer cells: Role in regulating sense transcription. Mol Cell Endocrinol 2020; 506:110746. [PMID: 32035111 PMCID: PMC7089808 DOI: 10.1016/j.mce.2020.110746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 12/27/2022]
Abstract
Estrogen-responsive breast cancer cells exhibit both basal and estrogen-regulated transcriptional programs, which lead to the transcription of many different transcription units (i.e., genes), including those that produce coding and non-coding sense (e.g., mRNA, lncRNA) and antisense (i.e., asRNA) transcripts. We have previously characterized the global basal and estrogen-regulated transcriptomes in estrogen receptor alpha (ERα)-positive MCF-7 breast cancer cells. Herein, we have mined genomic data to define three classes of antisense transcription in MCF-7 cells based on where their antisense transcription termination sites reside relative to their cognate sense mRNA and lncRNA genes. These three classes differ in their response to estrogen treatment, the enrichment of a number of genomic features associated with active promoters (H3K4me3, RNA polymerase II, open chromatin architecture), and the biological functions of their cognate sense genes as analyzed by DAVID gene ontology. We further characterized two estrogen-regulated antisense transcripts arising from the MYC gene in MCF-7 cells, showing that these antisense transcripts are 5'-capped, 3'-polyadenylated, and localized to different compartments of the cell. Together, our analyses have revealed distinct classes of antisense transcription correlated to different biological processes and response to estrogen stimulation, uncovering another layer of hormone-regulated gene regulation.
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Affiliation(s)
- Tim Y Hou
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Rui Li
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Minho Chae
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shino Murakami
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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9
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Burdine RD, Preston CC, Leonard RJ, Bradley TA, Faustino RS. Nucleoporins in cardiovascular disease. J Mol Cell Cardiol 2020; 141:43-52. [PMID: 32209327 DOI: 10.1016/j.yjmcc.2020.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Cardiovascular disease is a pressing health problem with significant global health, societal, and financial burdens. Understanding the molecular basis of polygenic cardiac pathology is thus essential to devising novel approaches for management and treatment. Recent identification of uncharacterized regulatory functions for a class of nuclear envelope proteins called nucleoporins offers the opportunity to understand novel putative mechanisms of cardiac disease development and progression. Consistent reports of nucleoporin deregulation associated with ischemic and dilated cardiomyopathies, arrhythmias and valvular disorders suggests that nucleoporin impairment may be a significant but understudied variable in cardiopathologic disorders. This review discusses and converges existing literature regarding nuclear pore complex proteins and their association with cardiac pathologies, and proposes a role for nucleoporins as facilitators of cardiac disease.
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Affiliation(s)
- Ryan D Burdine
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; School of Health Sciences, University of South Dakota, 414 E Clark St, Vermillion, SD 57069, United States of America
| | - Claudia C Preston
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Riley J Leonard
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Tyler A Bradley
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Randolph S Faustino
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22(nd) Street, Sioux Falls, SD 57105, United States of America.
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10
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Cardiello JF, Sanchez GJ, Allen MA, Dowell RD. Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs. Transcription 2019; 11:3-18. [PMID: 31856658 DOI: 10.1080/21541264.2019.1704128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nascent transcription assays, such as global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq), have uncovered a myriad of unstable RNAs being actively produced from numerous sites genome-wide. These transcripts provide a more complete and immediate picture of the impact of regulatory events. Transcription factors recruit RNA polymerase II, effectively initiating the process of transcription; repressors inhibit polymerase recruitment. Efficiency of recruitment is dictated by sequence elements in and around the RNA polymerase loading zone. A combination of sequence elements and RNA binding proteins subsequently influence the ultimate stability of the resulting transcript. Some of these transcripts are capable of providing feedback on the process, influencing subsequent transcription. By monitoring RNA polymerase activity, nascent assays provide insights into every step of the regulated process of transcription.
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Affiliation(s)
| | - Gilson J Sanchez
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.,Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
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11
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Braun L, Brenier-Pinchart MP, Hammoudi PM, Cannella D, Kieffer-Jaquinod S, Vollaire J, Josserand V, Touquet B, Couté Y, Tardieux I, Bougdour A, Hakimi MA. The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2. Nat Microbiol 2019; 4:1208-1220. [PMID: 31036909 PMCID: PMC6591128 DOI: 10.1038/s41564-019-0431-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022]
Abstract
The protozoan parasite Toxoplasma gondii has co-evolved with its homeothermic hosts (humans included) strategies that drive its quasi-asymptomatic persistence in hosts, hence optimizing the chance of transmission to new hosts. Persistence, which starts with a small subset of parasites that escape host immune killing and colonize the so-called immune privileged tissues where they differentiate into a low replicating stage, is driven by the interleukin 12 (IL-12)-interferon-γ (IFN-γ) axis. Recent characterization of a family of Toxoplasma effectors that are delivered into the host cell, in which they rewire the host cell gene expression, has allowed the identification of regulators of the IL-12-IFN-γ axis, including repressors. We now report on the dense granule-resident effector, called TEEGR (Toxoplasma E2F4-associated EZH2-inducing gene regulator) that counteracts the nuclear factor-κB (NF-κB) signalling pathway. Once exported into the host cell, TEEGR ends up in the nucleus where it not only complexes with the E2F3 and E2F4 host transcription factors to induce gene expression, but also promotes shaping of a non-permissive chromatin through its capacity to switch on EZH2. Remarkably, EZH2 fosters the epigenetic silencing of a subset of NF-κB-regulated cytokines, thereby strongly contributing to the host immune equilibrium that influences the host immune response and promotes parasite persistence in mice.
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Affiliation(s)
- Laurence Braun
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Marie-Pierre Brenier-Pinchart
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Pierre-Mehdi Hammoudi
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Dominique Cannella
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | | | - Julien Vollaire
- OPTIMAL Small Animal Imaging Facility, Institute for Advanced Biosciences, Grenoble, France
| | - Véronique Josserand
- OPTIMAL Small Animal Imaging Facility, Institute for Advanced Biosciences, Grenoble, France
| | - Bastien Touquet
- Team Membrane and Cell Dynamics of Host Parasite Interactions, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Isabelle Tardieux
- Team Membrane and Cell Dynamics of Host Parasite Interactions, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
| | - Mohamed-Ali Hakimi
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
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12
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Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, Lis JT, Kwak H, Danko CG. Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nat Genet 2018; 50:1553-1564. [PMID: 30349114 PMCID: PMC6204104 DOI: 10.1038/s41588-018-0244-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/21/2018] [Indexed: 11/09/2022]
Abstract
The human genome encodes a variety of poorly understood RNA species that remain challenging to identify using existing genomic tools. We developed chromatin run-on and sequencing (ChRO-seq) to map the location of RNA polymerase for almost any input sample, including samples with degraded RNA that are intractable to RNA sequencing. We used ChRO-seq to map nascent transcription in primary human glioblastoma (GBM) brain tumors. Enhancers identified in primary GBMs resemble open chromatin in the normal human brain. Rare enhancers that are activated in malignant tissue drive regulatory programs similar to the developing nervous system. We identified enhancers that regulate groups of genes that are characteristic of each known GBM subtype and transcription factors that drive them. Finally we discovered a core group of transcription factors that control the expression of genes associated with clinical outcomes. This study characterizes the transcriptional landscape of GBM and introduces ChRO-seq as a method to map regulatory programs that contribute to complex diseases.
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Affiliation(s)
- Tinyi Chu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Graduate field of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - H Hans Salamanca
- Department of Anesthesiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Leighton J Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Sharon L Longo
- Department of Neurological Surgery, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Robert J Corona
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Lawrence S Chin
- Department of Neurological Surgery, SUNY Upstate Medical University, Syracuse, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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13
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Ryu KW, Nandu T, Kim J, Challa S, DeBerardinis RJ, Kraus WL. Metabolic regulation of transcription through compartmentalized NAD + biosynthesis. Science 2018; 360:360/6389/eaan5780. [PMID: 29748257 DOI: 10.1126/science.aan5780] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 12/14/2017] [Accepted: 03/16/2018] [Indexed: 11/02/2022]
Abstract
NAD+ (nicotinamide adenine dinucleotide in its oxidized state) is an essential molecule for a variety of physiological processes. It is synthesized in distinct subcellular compartments by three different synthases (NMNAT-1, -2, and -3). We found that compartmentalized NAD+ synthesis by NMNATs integrates glucose metabolism and adipogenic transcription during adipocyte differentiation. Adipogenic signaling rapidly induces cytoplasmic NMNAT-2, which competes with nuclear NMNAT-1 for the common substrate, nicotinamide mononucleotide, leading to a precipitous reduction in nuclear NAD+ levels. This inhibits the catalytic activity of poly[adenosine diphosphate (ADP)-ribose] polymerase-1 (PARP-1), a NAD+-dependent enzyme that represses adipogenic transcription by ADP-ribosylating the adipogenic transcription factor C/EBPβ. Reversal of PARP-1-mediated repression by NMNAT-2-mediated nuclear NAD+ depletion in response to adipogenic signals drives adipogenesis. Thus, compartmentalized NAD+ synthesis functions as an integrator of cellular metabolism and signal-dependent transcriptional programs.
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Affiliation(s)
- Keun Woo Ryu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiyeon Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. .,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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14
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Tripodi IJ, Allen MA, Dowell RD. Detecting Differential Transcription Factor Activity from ATAC-Seq Data. Molecules 2018; 23:molecules23051136. [PMID: 29748466 PMCID: PMC6099720 DOI: 10.3390/molecules23051136] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 02/06/2023] Open
Abstract
Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases.
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Affiliation(s)
- Ignacio J Tripodi
- Computer Science, University of Colorado, Boulder, CO 80305, USA.
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
| | - Robin D Dowell
- Computer Science, University of Colorado, Boulder, CO 80305, USA.
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80305, USA.
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15
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Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD. Enhancer RNA profiling predicts transcription factor activity. Genome Res 2018; 28:gr.225755.117. [PMID: 29449408 PMCID: PMC5848612 DOI: 10.1101/gr.225755.117] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 01/24/2018] [Indexed: 12/18/2022]
Abstract
Transcription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in coordination of gene expression programs. Active enhancers are often characterized by the presence of short, unstable transcripts termed enhancer RNAs (eRNAs). While their function remains unclear, we demonstrate that eRNAs are a powerful readout of TF activity. We infer sites of eRNA origination across hundreds of publicly available nascent transcription data sets and show that eRNAs initiate from sites of TF binding. By quantifying the colocalization of TF binding motif instances and eRNA origins, we derive a simple statistic capable of inferring TF activity. In doing so, we uncover dozens of previously unexplored links between diverse stimuli and the TFs they affect.
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Affiliation(s)
- Joseph G Azofeifa
- Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Josephina R Hendrix
- Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Timothy Read
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Jonathan D Rubin
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Robin D Dowell
- Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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16
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Dynamic evolution of regulatory element ensembles in primate CD4 + T cells. Nat Ecol Evol 2018; 2:537-548. [PMID: 29379187 DOI: 10.1038/s41559-017-0447-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
How evolutionary changes at enhancers affect the transcription of target genes remains an important open question. Previous comparative studies of gene expression have largely measured the abundance of messenger RNA, which is affected by post-transcriptional regulatory processes, hence limiting inferences about the mechanisms underlying expression differences. Here, we directly measured nascent transcription in primate species, allowing us to separate transcription from post-transcriptional regulation. We used precision run-on and sequencing to map RNA polymerases in resting and activated CD4+ T cells in multiple human, chimpanzee and rhesus macaque individuals, with rodents as outgroups. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. Genes regulated by larger numbers of enhancers are more frequently transcribed at evolutionarily stable levels, despite reduced conservation at individual enhancers. Adaptive nucleotide substitutions are associated with lineage-specific transcription and at one locus, SGPP2, we predict and experimentally validate that multiple substitutions contribute to human-specific transcription. Collectively, our findings suggest a pervasive role for evolutionary compensation across ensembles of enhancers that jointly regulate target genes.
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17
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Franco HL, Nagari A, Malladi VS, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res 2017; 28:159-170. [PMID: 29273624 PMCID: PMC5793780 DOI: 10.1101/gr.226019.117] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022]
Abstract
Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized (“normal”) human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.
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Affiliation(s)
- Hector L Franco
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Venkat S Malladi
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Wenqian Li
- Department of Epigenetics and Molecular Carcinogenesis and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Yuanxin Xi
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Dana Richardson
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kendra L Allton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kaori Tanaka
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jing Li
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shino Murakami
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wei Li
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis and The Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Smithville, Texas 78957, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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18
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PARP-1 Controls the Adipogenic Transcriptional Program by PARylating C/EBPβ and Modulating Its Transcriptional Activity. Mol Cell 2017; 65:260-271. [PMID: 28107648 DOI: 10.1016/j.molcel.2016.11.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 09/06/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins mediated by PARP family members, such as PARP-1. Although PARylation has been studied extensively, few examples of definitive biological roles for site-specific PARylation have been reported. Here we show that C/EBPβ, a key pro-adipogenic transcription factor, is PARylated by PARP-1 on three amino acids in a conserved regulatory domain. PARylation at these sites inhibits C/EBPβ's DNA binding and transcriptional activities and attenuates adipogenesis in various genetic and cell-based models. Interestingly, PARP-1 catalytic activity drops precipitously during the first 48 hr of differentiation, corresponding to a release of C/EBPβ from PARylation-mediated inhibition. This promotes the binding of C/EBPβ at enhancers controlling the expression of adipogenic target genes and continued differentiation. Depletion or chemical inhibition of PARP-1, or mutation of the PARylation sites on C/EBPβ, enhances these early adipogenic events. Collectively, our results provide a clear example of how site-specific PARylation drives biological outcomes.
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19
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Murakami S, Nagari A, Kraus WL. Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching. Genes Dev 2017; 31:1535-1548. [PMID: 28887413 PMCID: PMC5630019 DOI: 10.1101/gad.302182.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022]
Abstract
Although many features of active transcriptional enhancers have been defined by genomic assays, we lack a clear understanding of the order of events leading to enhancer formation and activation as well as the dynamics of coregulator interactions within the enhancer complex. Here, we used selective loss- or gain-of-function mutants of estrogen receptor α (ERα) to define two distinct phases of ligand-dependent enhancer formation. In the first phase (0-20 min), p300 is recruited to ERα by Mediator as well as p300's acetylhistone-binding bromodomain to promote initial enhancer formation, which is not competent for sustained activation. In the second phase (20-45 min), p300 is recruited to ERα by steroid receptor coregulators (SRCs) for enhancer maturation and maintenance. Successful transition between these two phases ("coregulator switching") is required for proper enhancer function. Failure to recruit p300 during either phase leads to abortive enhancer formation and a lack of target gene expression. Our results reveal an ordered and cooperative assembly of ERα enhancers requiring functional interplay among p300, Mediator, and SRCs, which has implications for hormone-dependent gene regulation in breast cancers. More broadly, our results demonstrate the unexpectedly dynamic nature of coregulator interactions within enhancer complexes, which are likely to be a defining feature of all enhancers.
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Affiliation(s)
- Shino Murakami
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Anusha Nagari
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
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20
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Kaikkonen MU, Halonen P, Liu OHF, Turunen TA, Pajula J, Moreau P, Selvarajan I, Tuomainen T, Aavik E, Tavi P, Ylä-Herttuala S. Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001702. [DOI: 10.1161/circgenetics.117.001702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/25/2017] [Indexed: 11/16/2022]
Abstract
Background—
Microarrays and RNA sequencing are widely used to profile transcriptome remodeling during myocardial ischemia. However, the steady-state RNA analysis lacks in sensitivity to detect all noncoding RNA species and does not provide separation between transcriptional and post-transcriptional regulations. Here, we provide the first comprehensive analysis of nascent RNA profiles of mRNAs, primary micro-RNAs, long noncoding RNAs, and enhancer RNAs in a large animal model of acute infarction.
Methods and Results—
Acute infarction was induced by cardiac catheterization of domestic swine. Nuclei isolated from healthy, border zone, and ischemic regions of the affected heart were subjected to global run-on sequencing. Global run-on sequencing analysis indicated that half of affected genes are regulated at the level of transcriptional pausing. A gradient of induction of inflammatory mediators and repression of peroxisome proliferator-activated receptor signaling and oxidative phosphorylation was detected when moving from healthy toward infarcted area. In addition, we interrogated the transcriptional regulation of primary micro-RNAs and provide evidence that several arrhythmia-related target genes exhibit repression at post-transcriptional level. We identified 450 long noncoding RNAs differently regulated by ischemia, including novel conserved long noncoding RNAs expressed in antisense orientation to myocardial transcription factors GATA-binding protein 4, GATA-binding protein 6, and Krüppel-like factor 6. Finally, characterization of enhancers exhibiting differential expression of enhancer RNAs pointed a central role for Krüppel-like factor, MEF2C, ETS, NFY, ATF, E2F2, and NRF1 transcription factors in determining transcriptional responses to ischemia.
Conclusions—
Global run-on sequencing allowed us to follow the gradient of gene expression occurring in the ischemic heart and identify novel noncoding RNAs regulated by oxygen deprivation. These findings highlight potential new targets for diagnosis and treatment of myocardial ischemia.
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Affiliation(s)
- Minna U. Kaikkonen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Paavo Halonen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Oscar Hsin-Fu Liu
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Tiia A. Turunen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Juho Pajula
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Pierre Moreau
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Ilakya Selvarajan
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Tomi Tuomainen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Einari Aavik
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Pasi Tavi
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
| | - Seppo Ylä-Herttuala
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (M.U.K., P.H., O.H.-F.L., T.T., J.P., P.M., I.S., T.T., E.A., P.T., S.Y.-H.); and Heart Center and Gene Therapy Unit, Kuopio University Hospital, Finland (S.Y.-H.)
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21
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Nagari A, Murakami S, Malladi VS, Kraus WL. Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers. Methods Mol Biol 2017; 1468:121-138. [PMID: 27662874 PMCID: PMC5522910 DOI: 10.1007/978-1-4939-4035-6_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers.
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Affiliation(s)
- Anusha Nagari
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - Shino Murakami
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Venkat S Malladi
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA.
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA.
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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22
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Gibson BA, Zhang Y, Jiang H, Hussey KM, Shrimp JH, Lin H, Schwede F, Yu Y, Kraus WL. Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science 2016; 353:45-50. [PMID: 27256882 DOI: 10.1126/science.aaf7865] [Citation(s) in RCA: 262] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/19/2016] [Indexed: 12/11/2022]
Abstract
Poly[adenosine diphosphate (ADP)-ribose] polymerases (PARPs) are a family of enzymes that modulate diverse biological processes through covalent transfer of ADP-ribose from the oxidized form of nicotinamide adenine dinucleotide (NAD(+)) onto substrate proteins. Here we report a robust NAD(+) analog-sensitive approach for PARPs, which allows PARP-specific ADP-ribosylation of substrates that is suitable for subsequent copper-catalyzed azide-alkyne cycloaddition reactions. Using this approach, we mapped hundreds of sites of ADP-ribosylation for PARPs 1, 2, and 3 across the proteome, as well as thousands of PARP-1-mediated ADP-ribosylation sites across the genome. We found that PARP-1 ADP-ribosylates and inhibits negative elongation factor (NELF), a protein complex that regulates promoter-proximal pausing by RNA polymerase II (Pol II). Depletion or inhibition of PARP-1 or mutation of the ADP-ribosylation sites on NELF-E promotes Pol II pausing, providing a clear functional link between PARP-1, ADP-ribosylation, and NELF. This analog-sensitive approach should be broadly applicable across the PARP family and has the potential to illuminate the ADP-ribosylated proteome and the molecular mechanisms used by individual PARPs to mediate their responses to cellular signals.
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Affiliation(s)
- Bryan A Gibson
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences and The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yajie Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hong Jiang
- Howard Hughes Medical Institute and Department of Chemistry, Cornell University, Ithaca, NY 14850, USA
| | | | - Jonathan H Shrimp
- Howard Hughes Medical Institute and Department of Chemistry, Cornell University, Ithaca, NY 14850, USA
| | - Hening Lin
- Howard Hughes Medical Institute and Department of Chemistry, Cornell University, Ithaca, NY 14850, USA
| | - Frank Schwede
- Biolog Life Science Institute, D-28199 Bremen, Germany
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences and The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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23
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Liu X, Kraus WL, Bai X. Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci 2015; 40:516-25. [PMID: 26254229 DOI: 10.1016/j.tibs.2015.07.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/07/2015] [Accepted: 07/06/2015] [Indexed: 01/06/2023]
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a well-established mechanism to control the timing, rate, and possibly the magnitude of transcriptional responses. Recent studies have shown that cellular signaling pathways can regulate gene transcription and signaling outcomes by controlling Pol II pausing in a wide array of biological systems. Identification of the proteins and small molecules that affect the establishment and release of paused Pol II is shedding new light on the mechanisms and biology of Pol II pausing. This review focuses on the interplay between cellular signaling pathways and Pol II pausing during normal development and under disease conditions.
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Affiliation(s)
- Xiuli Liu
- Molecular Genetics of Blood Development Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Signaling and Gene Regulation Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoying Bai
- Molecular Genetics of Blood Development Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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24
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Chae M, Danko CG, Kraus WL. groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. BMC Bioinformatics 2015; 16:222. [PMID: 26173492 PMCID: PMC4502638 DOI: 10.1186/s12859-015-0656-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
Background Global run-on coupled with deep sequencing (GRO-seq) provides extensive information on the location and function of coding and non-coding transcripts, including primary microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and enhancer RNAs (eRNAs), as well as yet undiscovered classes of transcripts. However, few computational tools tailored toward this new type of sequencing data are available, limiting the applicability of GRO-seq data for identifying novel transcription units. Results Here, we present groHMM, a computational tool in R, which defines the boundaries of transcription units de novo using a two state hidden-Markov model (HMM). A systematic comparison of the performance between groHMM and two existing peak-calling methods tuned to identify broad regions (SICER and HOMER) favorably supports our approach on existing GRO-seq data from MCF-7 breast cancer cells. To demonstrate the broader utility of our approach, we have used groHMM to annotate a diverse array of transcription units (i.e., primary transcripts) from four GRO-seq data sets derived from cells representing a variety of different human tissue types, including non-transformed cells (cardiomyocytes and lung fibroblasts) and transformed cells (LNCaP and MCF-7 cancer cells), as well as non-mammalian cells (from flies and worms). As an example of the utility of groHMM and its application to questions about the transcriptome, we show how groHMM can be used to analyze cell type-specific enhancers as defined by newly annotated enhancer transcripts. Conclusions Our results show that groHMM can reveal new insights into cell type-specific transcription by identifying novel transcription units, and serve as a complete and useful tool for evaluating functional genomic elements in cells. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0656-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Minho Chae
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 75390, Dallas, TX, USA. .,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 75390, Dallas, TX, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, 14853, Ithaca, NY, USA.
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 75390, Dallas, TX, USA. .,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 75390, Dallas, TX, USA.
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25
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Cook DJ, Patra B, Kuttippurathu L, Hoek JB, Vadigepalli R. A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes. Front Physiol 2015. [PMID: 26217230 PMCID: PMC4493398 DOI: 10.3389/fphys.2015.00189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Following partial hepatectomy, a coordinated series of molecular events occurs to regulate hepatocyte entry into the cell cycle to recover lost mass. In rats during the first 6 h following resection, hepatocytes are primed by a tightly controlled cytokine response to prepare hepatocytes to begin replication. Although it appears to be a critical element driving regeneration, the cytokine response to resection has not yet been fully characterized. Specifically, the role of one of the key response elements to cytokine signaling (NF-κB) remains incompletely characterized. In this study, we present a novel, genome-wide, pattern-based analysis characterizing NF-κB binding during the priming phase of liver regeneration. We interrogated the dynamic regulation of priming by NF-κB through categorizing NF-κB binding in different temporal profiles: immediate sustained response, early transient response, and delayed response to partial hepatectomy. We then identified functional regulation of NF-κB binding by relating the temporal response profile to differential gene expression. We found that NF-κB bound genes govern negative regulation of cell growth and inflammatory response immediately following hepatectomy. NF-κB also transiently regulates genes responsible for lipid biosynthesis and transport as well as induction of apoptosis following hepatectomy. By the end of the priming phase, NF-κB regulation of genes involved in inflammatory response, negative regulation of cell death, and extracellular structure organization became prominent. These results suggest that NF-κB regulates target genes through binding and unbinding in immediate, transient, and delayed patterns. Such dynamic switch-like patterns of NF-κB binding may govern different functional transitions that drive the onset of regeneration.
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Affiliation(s)
- Daniel J Cook
- Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University Philadelphia, PA, USA ; Department of Chemical and Biomolecular Engineering, University of Delaware Newark, DE, USA
| | - Biswanath Patra
- Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University Philadelphia, PA, USA
| | - Lakshmi Kuttippurathu
- Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University Philadelphia, PA, USA
| | - Jan B Hoek
- Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University Philadelphia, PA, USA
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University Philadelphia, PA, USA ; Department of Chemical and Biomolecular Engineering, University of Delaware Newark, DE, USA
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26
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Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends Genet 2015; 31:426-33. [PMID: 26073855 DOI: 10.1016/j.tig.2015.05.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential to enhance transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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27
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Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods 2015; 12:433-8. [PMID: 25799441 PMCID: PMC4507281 DOI: 10.1038/nmeth.3329] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/24/2015] [Indexed: 12/26/2022]
Abstract
Modifications to the global run-on and sequencing (GRO-seq) protocol that enrich for 5'-capped RNAs can be used to reveal active transcriptional regulatory elements (TREs) with high accuracy. Here, we introduce discriminative regulatory-element detection from GRO-seq (dREG), a sensitive machine learning method that uses support vector regression to identify active TREs from GRO-seq data without requiring cap-based enrichment (https://github.com/Danko-Lab/dREG/). This approach allows TREs to be assayed together with gene expression levels and other transcriptional features in a single experiment. Predicted TREs are more enriched for several marks of transcriptional activation—including expression quantitative trait loci, disease-associated polymorphisms, acetylated histone 3 lysine 27 (H3K27ac) and transcription factor binding—than those identified by alternative functional assays. Using dREG, we surveyed TREs in eight human cell types and provide new insights into global patterns of TRE function.
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Affiliation(s)
- Charles G. Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY,USA
| | - Stephanie L. Hyland
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Leighton J. Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Andre L. Martins
- Graduate Field in Computational Biology, Cornell University, Ithaca, NY, USA
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Hyung Won Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Vivian G. Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John T. Lis
- Graduate Field in Computational Biology, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY,USA
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Abstract
In recent year, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological conditions. Besides small noncoding RNAs (eg, microRNAs), >200-nucleotide long transcripts, namely long noncoding RNAs (lncRNAs), can interfere with gene expressions and signaling pathways at various stages. In the cardiovascular system, studies have detected and characterized the expression of lncRNAs under normal physiological condition and in disease states. Several lncRNAs are regulated during acute myocardial infarction (eg, Novlnc6) and heart failure (eg, Mhrt), whereas others control hypertrophy, mitochondrial function and apoptosis of cardiomyocytes. In the vascular system, the endothelial-expressed lncRNAs (eg, MALAT1 and Tie-1-AS) can regulate vessel growth and function, whereas the smooth-muscle-expressed lncRNA smooth muscle and endothelial cell-enriched migration/differentiation-associated long noncoding RNA was recently shown to control the contractile phenotype of smooth muscle cells. This review article summarizes the data on lncRNA expressions in mouse and human and highlights identified cardiovascular lncRNAs that might play a role in cardiovascular diseases. Although our understanding of lncRNAs is still in its infancy, these examples may provide helpful insights how lncRNAs interfere with cardiovascular diseases.
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Affiliation(s)
- Shizuka Uchida
- From the Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany (S.U., S.D.); and German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt, Germany (S.U., S.D.)
| | - Stefanie Dimmeler
- From the Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany (S.U., S.D.); and German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt, Germany (S.U., S.D.).
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29
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Franco HL, Nagari A, Kraus WL. TNFα signaling exposes latent estrogen receptor binding sites to alter the breast cancer cell transcriptome. Mol Cell 2015; 58:21-34. [PMID: 25752574 DOI: 10.1016/j.molcel.2015.02.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/18/2014] [Accepted: 01/27/2015] [Indexed: 01/08/2023]
Abstract
The interplay between mitogenic and proinflammatory signaling pathways plays key roles in determining the phenotypes and clinical outcomes of breast cancers. Using GRO-seq in MCF-7 cells, we defined the immediate transcriptional effects of crosstalk between estradiol (E2) and TNFα, identifying a large set of target genes whose expression is rapidly altered with combined E2 + TNFα treatment, but not with either agent alone. The pleiotropic effects on gene transcription in response to E2 + TNFα are orchestrated by extensive remodeling of the ERα enhancer landscape in an NF-κB- and FoxA1-dependent manner. In addition, expression of the de novo and synergistically regulated genes is strongly associated with clinical outcomes in breast cancers. Together, our genomic and molecular analyses indicate that TNFα signaling, acting in pathways culminating in the redistribution of NF-κB and FoxA1 binding sites across the genome, creates latent ERα binding sites that underlie altered patterns of gene expression and clinically relevant cellular responses.
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Affiliation(s)
- Hector L Franco
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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30
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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31
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Fuchs G, Voichek Y, Benjamin S, Gilad S, Amit I, Oren M. 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol 2014; 15:R69. [PMID: 24887486 PMCID: PMC4072947 DOI: 10.1186/gb-2014-15-5-r69] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022] Open
Abstract
Although transcriptional elongation by RNA polymerase II is coupled with many RNA-related processes, genomewide elongation rates remain unknown. We describe a method, called 4sUDRB-seq, based on reversible inhibition of transcription elongation coupled with tagging newly transcribed RNA with 4-thiouridine and high throughput sequencing to measure simultaneously with high confidence genome-wide transcription elongation rates in cells. We find that most genes are transcribed at about 3.5 Kb/min, with elongation rates varying between 2 Kb/min and 6 Kb/min. 4sUDRB-seq can facilitate genomewide exploration of the involvement of specific elongation factors in transcription and the contribution of deregulated transcription elongation to various pathologies.
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