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Pan H, Cheng X, Rodríguez PFG, Zhang X, Chung I, Jin VX, Li W, Hu Y, Li R. An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing. J Biol Chem 2023; 299:105259. [PMID: 37717699 PMCID: PMC10591015 DOI: 10.1016/j.jbc.2023.105259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023] Open
Abstract
The four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter-proximal regions. Ablation of individual NELF subunits destabilizes the NELF complex and causes cell lethality, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell proliferation. Using separation-of-function mutations, we show here that NELFB function in cell proliferation can be uncoupled from that in Pol II pausing. NELFB mutants sequestered in the cytoplasm and deprived of NELF nuclear function still support cell proliferation and part of the NELFB-dependent transcriptome. Mechanistically, cytoplasmic NELFB physically and functionally interacts with prosurvival signaling kinases, most notably phosphatidylinositol-3-kinase/AKT. Ectopic expression of membrane-tethered phosphatidylinositol-3-kinase/AKT partially bypasses the role of NELFB in cell proliferation, but not Pol II occupancy. Together, these data expand the current understanding of the physiological impact of Pol II pausing and underscore the multiplicity of the biological functions of individual NELF subunits.
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Affiliation(s)
- Haihui Pan
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA.
| | - Xiaolong Cheng
- Department of Genomics & Precision Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA; Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Pedro Felipe Gardeazábal Rodríguez
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Xiaowen Zhang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Inhee Chung
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Victor X Jin
- Institute of Health Equity and Cancer Center, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Wei Li
- Department of Genomics & Precision Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA; Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Yanfen Hu
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA.
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Alexander GM, Heiman-Patterson TD, Bearoff F, Sher RB, Hennessy L, Terek S, Caccavo N, Cox GA, Philip VM, Blankenhorn EA. Identification of quantitative trait loci for survival in the mutant dynactin p150Glued mouse model of motor neuron disease. PLoS One 2022; 17:e0274615. [PMID: 36107978 PMCID: PMC9477371 DOI: 10.1371/journal.pone.0274615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/01/2022] [Indexed: 11/19/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common degenerative motor neuron disorder. Although most cases of ALS are sporadic, 5-10% of cases are familial, with mutations associated with over 40 genes. There is variation of ALS symptoms within families carrying the same mutation; the disease may develop in one sibling and not in another despite the presence of the mutation in both. Although the cause of this phenotypic variation is unknown, it is likely related to genetic modifiers of disease expression. The identification of ALS causing genes has led to the development of transgenic mouse models of motor neuron disease. Similar to families with familial ALS, there are background-dependent differences in disease phenotype in transgenic mouse models of ALS suggesting that, as in human ALS, differences in phenotype may be ascribed to genetic modifiers. These genetic modifiers may not cause ALS rather their expression either exacerbates or ameliorates the effect of the mutant ALS causing genes. We have reported that in both the G93A-hSOD1 and G59S-hDCTN1 mouse models, SJL mice demonstrated a more severe phenotype than C57BL6 mice. From reciprocal intercrosses between G93A-hSOD1 transgenic mice on SJL and C57BL6 strains, we identified a major quantitative trait locus (QTL) on mouse chromosome 17 that results in a significant shift in lifespan. In this study we generated reciprocal intercrosses between transgenic G59S-hDCTN1 mice on SJL and C57BL6 strains and identified survival QTLs on mouse chromosomes 17 and 18. The chromosome 17 survival QTL on G93A-hSOD1 and G59S-hDCTN1 mice partly overlap, suggesting that the genetic modifiers located in this region may be shared by these two ALS models despite the fact that motor neuron degeneration is caused by mutations in different proteins. The overlapping region contains eighty-seven genes with non-synonymous variations predicted to be deleterious and/or damaging. Two genes in this segment, NOTCH3 and Safb/SAFB1, have been associated with motor neuron disease. The identification of genetic modifiers of motor neuron disease, especially those modifiers that are shared by SOD1 and dynactin-1 transgenic mice, may result in the identification of novel targets for therapies that can alter the course of this devastating illness.
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Affiliation(s)
| | - Terry D. Heiman-Patterson
- Department of Neurology, Lewis Katz School of Medicine of Temple University, Philadelphia, Pennsylvania, United States of America
| | - Frank Bearoff
- Department of Microbiology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Roger B. Sher
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| | - Laura Hennessy
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Shannon Terek
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Nicole Caccavo
- Department of Neurology, Lewis Katz School of Medicine of Temple University, Philadelphia, Pennsylvania, United States of America
| | - Gregory A. Cox
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Vivek M. Philip
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Elizabeth A. Blankenhorn
- Department of Microbiology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
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3
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Abuhashem A, Chivu AG, Zhao Y, Rice EJ, Siepel A, Danko CG, Hadjantonakis AK. RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes Dev 2022; 36:gad.349565.122. [PMID: 35981753 PMCID: PMC9480856 DOI: 10.1101/gad.349565.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/18/2022] [Indexed: 01/03/2023]
Abstract
Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been predominantly studied in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we found that loss of Pol II pausing stalls pluripotent state transitions within the epiblast of the early mouse embryo. Using Nelfb -/- mice and a NELFB degron mouse pluripotent stem cell model, we show that embryonic stem cells (ESCs) representing the naïve state of pluripotency successfully initiate a transition program but fail to balance levels of induced and repressed genes and enhancers in the absence of NELF. We found an increase in chromatin-associated NELF during transition from the naïve to later pluripotent states. Overall, our work defines the acute and long-term molecular consequences of NELF loss and reveals a role for Pol II pausing in the pluripotency continuum as a modulator of cell state transitions.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
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4
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Abuhashem A, Garg V, Hadjantonakis AK. RNA polymerase II pausing in development: orchestrating transcription. Open Biol 2022; 12:210220. [PMID: 34982944 PMCID: PMC8727152 DOI: 10.1098/rsob.210220] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The coordinated regulation of transcriptional networks underpins cellular identity and developmental progression. RNA polymerase II promoter-proximal pausing (Pol II pausing) is a prevalent mechanism by which cells can control and synchronize transcription. Pol II pausing regulates the productive elongation step of transcription at key genes downstream of a variety of signalling pathways, such as FGF and Nodal. Recent advances in our understanding of the Pol II pausing machinery and its role in transcription call for an assessment of these findings within the context of development. In this review, we discuss our current understanding of the molecular basis of Pol II pausing and its function during organismal development. By critically assessing the tools used to study this process we conclude that combining recently developed genomics approaches with refined perturbation systems has the potential to expand our understanding of Pol II pausing mechanistically and functionally in the context of development and beyond.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA,Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
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5
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Li R, Wang X, Huang Z, Balaji J, Kim TH, Wang T, Zhou L, Deleon A, Cook ME, Marbrey MW, Wu SP, Jeong JW, Arora R, DeMayo FJ. The role of epithelial progesterone receptor isoforms in embryo implantation. iScience 2021; 24:103487. [PMID: 34934913 DOI: 10.1016/j.isci.2021.103487] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/27/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022] Open
Abstract
The loss of uterine epithelial progesterone receptor (PGR) is crucial for successful embryo implantation in both humans and mice. The two major isoforms PGRA and PGRB have divergent functions under both physiological and pathological conditions. The present study compares phenotypes and gene signatures of PGRA and PGRB in uterine epithelium using uterine epithelial-specific constitutively expressed PGRA or PGRB mouse models. The cistrome and transcriptome analysis reveals substantial overlap between epithelial PGRA and PGRB, and both disrupt embryo implantation through FOXO1 pathways. Constitutive epithelial PGRA and PGRB expression impairs ESR1 occupancy at the promoter of Lif leading to reduced Lif transcription and further exaggerates SGK1 expression leading to enhanced PI3K-SGK1 activities, and both contribute to the decline of nuclear FOXO1 expression. Our study demonstrates that PGRA and PGRB in the uterine epithelium act on a similar set of target genes and commonly regulate the LIF-SGK1-FOXO1 signaling pathway for embryo implantation.
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Affiliation(s)
- Rong Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Xiaoqiu Wang
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Zhenyao Huang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Jayani Balaji
- Department of Obstetrics, Gynecology and Reproductive Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing 48823, MI, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing 48823, MI, USA
| | - Tae Hoon Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing 48823, MI, USA
| | - Tianyuan Wang
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Lecong Zhou
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Ashley Deleon
- Laser Capture Microdissection Core Laboratory, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA.,Kelly Government Solutions, Rockville, MD, 20852, USA
| | - Molly E Cook
- Epigenomics and DNA Sequencing Core, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Margeaux W Marbrey
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - San-Pin Wu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Jae Wook Jeong
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing 48823, MI, USA
| | - Ripla Arora
- Department of Obstetrics, Gynecology and Reproductive Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing 48823, MI, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing 48823, MI, USA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
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Barron L, Khadka S, Schenken R, He L, Blenis J, Blagg J, Chen SF, Tsai KL, Boyer TG. Identification and characterization of the mediator kinase-dependent myometrial stem cell phosphoproteome. F&S SCIENCE 2021; 2:383-395. [PMID: 35559861 PMCID: PMC10906282 DOI: 10.1016/j.xfss.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To identify, in myometrial stem/progenitor cells, the presumptive cell of origin for uterine fibroids, substrates of Mediator-associated cyclin dependent kinase 8/19 (CDK8/19), which is known to be disrupted by uterine fibroid driver mutations in Mediator complex subunit 12 (MED12). DESIGN Experimental study. SETTING Academic research laboratory. PATIENT(S) Women undergoing hysterectomy for uterine fibroids. INTERVENTION(S) Stable isotopic labeling of amino acids in cell culture (SILAC) coupled with chemical inhibition of CDK8/19 and downstream quantitative phosphoproteomics and transcriptomic analyses in myometrial stem/progenitor cells. MAIN OUTCOME MEASURE(S) High-confidence Mediator kinase substrates identified by SILAC-based quantitative phosphoproteomics were determined using an empirical Bayes analysis and validated orthogonally by in vitro kinase assay featuring reconstituted Mediator kinase modules comprising wild-type or G44D mutant MED12 corresponding to the most frequent uterine fibroid driver mutation in MED12. Mediator kinase-regulated transcripts identified by RNA sequencing were linked to Mediator kinase substrates by computational analyses. RESULT(S) A total of 296 unique phosphosites in 166 proteins were significantly decreased (≥ twofold) upon CDK8/19 inhibition, including 118 phosphosites in 71 nuclear proteins representing high-confidence Mediator kinase substrates linked to RNA polymerase II transcription, RNA processing and transport, chromatin modification, cytoskeletal architecture, and DNA replication and repair. Orthogonal validation confirmed a subset of these proteins, including Cut Like Homeobox 1 (CUX1) and Forkhead Box K1 (FOXK1), to be direct targets of MED12-dependent CDK8 phosphorylation in a manner abrogated by the most common uterine fibroid driver mutation (G44D) in MED12, implicating these substrates in disease pathogenesis. Transcriptome-wide profiling of Mediator kinase-inhibited myometrial stem/progenitor cells revealed alterations in cell cycle and myogenic gene expression programs to which Mediator kinase substrates could be linked directly. Among these, CUX1 is an established transcriptional regulator of the cell cycle whose corresponding gene on chromosome 7q is the locus for a recurrent breakpoint in uterine fibroids, linking MED12 and Mediator kinase with CUX1 for the first time in uterine fibroid pathogenesis. FOXK1, a transcriptional regulator of myogenic stem cell fate, was found to be coordinately enriched along with kinase, but not core, Mediator subunits in myometrial stem/progenitor cells compared with differentiated uterine smooth muscle cells. CONCLUSION(S) These studies identify a new catalog of pathologically and biologically relevant Mediator kinase substrates implicated in the pathogenesis of MED12 mutation-positive uterine fibroids, and further uncover a biochemical basis to link Mediator kinase activity with CUX1 and FOXK1 in the regulation of myometrial stem/progenitor cell fate.
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Affiliation(s)
- Lindsey Barron
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas
| | - Subash Khadka
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas
| | - Robert Schenken
- Department of Obstetrics and Gynecology, University of Texas Health Science Center San Antonio, San Antonio, Texas
| | - Long He
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - John Blenis
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Julian Blagg
- NeoPhore Ltd. and Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas.
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Hewitt SC, Grimm SA, Wu SP, DeMayo FJ, Korach KS. Estrogen receptor α (ERα)-binding super-enhancers drive key mediators that control uterine estrogen responses in mice. J Biol Chem 2020; 295:8387-8400. [PMID: 32354741 DOI: 10.1074/jbc.ra120.013666] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
Estrogen receptor α (ERα) modulates gene expression by interacting with chromatin regions that are frequently distal from the promoters of estrogen-regulated genes. Active chromatin-enriched "super-enhancer" (SE) regions, mainly observed in in vitro culture systems, often control production of key cell type-determining transcription factors. Here, we defined super-enhancers that bind to ERα in vivo within hormone-responsive uterine tissue in mice. We found that SEs are already formed prior to estrogen exposure at the onset of puberty. The genes at SEs encoded critical developmental factors, including retinoic acid receptor α (RARA) and homeobox D (HOXD). Using high-throughput chromosome conformation capture (Hi-C) along with DNA sequence analysis, we demonstrate that most SEs are located at a chromatin loop end and that most uterine genes in loop ends associated with these SEs are regulated by estrogen. Although the SEs were formed before puberty, SE-associated genes acquired optimal ERα-dependent expression after reproductive maturity, indicating that pubertal processes that occur after SE assembly and ERα binding are needed for gene responses. Genes associated with these SEs affected key estrogen-mediated uterine functions, including transforming growth factor β (TGFβ) and LIF interleukin-6 family cytokine (LIF) signaling pathways. To the best of our knowledge, this is the first identification of SE interactions that underlie hormonal regulation of genes in uterine tissue and optimal development of estrogen responses in this tissue.
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Affiliation(s)
- Sylvia C Hewitt
- Reproductive and Developmental Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Sara A Grimm
- Integrative Bioinformatics Support Group, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - San-Pin Wu
- Reproductive and Developmental Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Kenneth S Korach
- Reproductive and Developmental Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
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