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Dillingham CM, Cormaty H, Morgan EC, Tak AI, Esgdaille DE, Boutz PL, Sridharan R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543088. [PMID: 37398291 PMCID: PMC10312572 DOI: 10.1101/2023.05.31.543088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
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Affiliation(s)
- Caleb M Dillingham
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Harshini Cormaty
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ellen C Morgan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Andrew I Tak
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dakarai E Esgdaille
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry
| | - Paul L Boutz
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
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2
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Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer. Cancer Discov 2023; 13:2470-2487. [PMID: 37694973 PMCID: PMC10618745 DOI: 10.1158/2159-8290.cd-23-0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023]
Abstract
Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state-specific "regulatory transposable elements." Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements. SIGNIFICANCE We show that oncogenesis relies on co-opting transposable elements from pluripotent stem cells as regulatory elements altering the recruitment of lineage-specific transcription factors. We further discover how co-option is dependent on active chromatin states with important implications for developing treatment options against drivers of oncogenesis across the repetitive DNA. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
- Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tina Keshavarzian
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisanne Mout
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ankita Nand
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mona Teng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aditi Qamra
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ken J. Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James R. Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Theodorus H. van der Kwast
- Laboratory Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ganesh V. Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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3
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Bull T, Michelmore R. Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:888425. [PMID: 35615120 PMCID: PMC9125155 DOI: 10.3389/fpls.2022.888425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 05/12/2023]
Abstract
In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).
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Affiliation(s)
- Tawni Bull
- The Genome Center, University of California, Davis, Davis, CA, United States
- Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, United States
| | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Shchuka VM, Abatti LE, Hou H, Khader N, Dorogin A, Wilson MD, Shynlova O, Mitchell JA. The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice. PLoS Biol 2020; 18:e3000710. [PMID: 32667910 PMCID: PMC7384763 DOI: 10.1371/journal.pbio.3000710] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/27/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
During gestation, uterine smooth muscle cells transition from a state of quiescence to one of contractility, but the molecular mechanisms underlying this transition at a genomic level are not well-known. To better understand these events, we evaluated the epigenetic landscape of the mouse myometrium during the pregnant, laboring, and postpartum stages. We generated gestational time point–specific enrichment profiles for histone H3 acetylation on lysine residue 27 (H3K27ac), histone H3 trimethylation of lysine residue 4 (H3K4me3), and RNA polymerase II (RNAPII) occupancy by chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq), as well as gene expression profiles by total RNA-sequencing (RNA-seq). Our findings reveal that 533 genes, including known contractility-driving genes (Gap junction alpha 1 [Gja1], FBJ osteosarcoma oncogene [Fos], Fos-like antigen 2 [Fosl2], Oxytocin receptor [Oxtr], and Prostaglandin G/H synthase 2 (Ptgs2), for example), are up-regulated at day 19 during active labor because of an increase in transcription at gene bodies. Labor-associated promoters and putative intergenic enhancers, however, are epigenetically activated as early as day 15, by which point the majority of genome-wide H3K27ac or H3K4me3 peaks present in term laboring tissue is already established. Despite this early exhibited histone signature, increased noncoding enhancer RNA (eRNA) production at putative intergenic enhancers and recruitment of RNAPII to the gene bodies of labor-associated loci were detected only during labor. Our findings indicate that epigenetic activation of the myometrial genome precedes active labor by at least 4 days in the mouse model, suggesting that the myometrium is poised for rapid activation of contraction-associated genes in order to exit the state of quiescence. A study of the epigenomic and transcriptomic basis of pregnancy and labor onset in a mouse model identifies genes that are epigenetically poised for activation four days before labour onset, and implicates AP-1 transcription factors in the up-regulation of genes during labor.
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Affiliation(s)
- Virlana M. Shchuka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (JAM); (OS); (VMS)
| | - Luis E. Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Huayun Hou
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Ontario, Canada
| | - Nawrah Khader
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Anna Dorogin
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Ontario, Canada
| | - Oksana Shynlova
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Obstetrics & Gynaecology, University of Toronto, Ontario, Canada
- * E-mail: (JAM); (OS); (VMS)
| | - Jennifer A. Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (JAM); (OS); (VMS)
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5
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Jia L, Wang Y, Wang C, Du Z, Zhang S, Wen X, Zhou L, Li H, Chen H, Li D, Zhang S, Li W, Xu W, Hoffman AR, Cui J, Hu JF. Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation. Nucleic Acids Res 2020; 48:3935-3948. [PMID: 32055844 PMCID: PMC7144914 DOI: 10.1093/nar/gkaa097] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/03/2023] Open
Abstract
Formation of a pluripotency-specific chromatin network is a critical event in reprogramming somatic cells into pluripotent status. To characterize the regulatory components in this process, we used ‘chromatin RNA in situ reverse transcription sequencing’ (CRIST-seq) to profile RNA components that interact with the pluripotency master gene Oct4. Using this approach, we identified a novel nuclear lncRNA Oplr16 that was closely involved in the initiation of reprogramming. Oplr16 not only interacted with the Oct4 promoter and regulated its activity, but it was also specifically activated during reprogramming to pluripotency. Active expression of Oplr16 was required for optimal maintenance of pluripotency in embryonic stem cells. Oplr16 was also able to enhance reprogramming of fibroblasts into pluripotent cells. RNA reverse transcription-associated trap sequencing (RAT-seq) indicated that Oplr16 interacted with multiple target genes related to stem cell self-renewal. Of note, Oplr16 utilized its 3′-fragment to recruit the chromatin factor SMC1 to orchestrate pluripotency-specific intrachromosomal looping. After binding to the Oct4 promoter, Oplr16 recruited TET2 to induce DNA demethylation and activate Oct4 in fibroblasts, leading to enhanced reprogramming. These data suggest that Oplr16 may act as a pivotal chromatin factor to control stem cell fate by modulating chromatin architecture and DNA demethylation.
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Affiliation(s)
- Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.,Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
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6
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The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194407. [DOI: 10.1016/j.bbagrm.2019.194407] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/17/2022]
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7
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Lee K, Park OS, Choi CY, Seo PJ. ARABIDOPSIS TRITHORAX 4 Facilitates Shoot Identity Establishment during the Plant Regeneration Process. PLANT & CELL PHYSIOLOGY 2019; 60:826-834. [PMID: 30605532 DOI: 10.1093/pcp/pcy248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/24/2018] [Indexed: 05/08/2023]
Abstract
Plant cells have a remarkable plasticity that allows cellular reprogramming from differentiated cells and subsequent tissue regeneration. Callus formation occurs from pericycle-like cells through a lateral root developmental pathway, and even aerial parts can also undergo the cell fate transition. Pluripotent calli are then subjected primarily to shoot regeneration in in vitro tissue culture. Successful completion of plant regeneration from aerial explants thus entails a two-step conversion of tissue identity. Here we show that a single chromatin modifier, ARABIDOPSIS TRITHORAX 4 (ATX4)/SET DOMAIN GROUP 16, is dynamically regulated during plant regeneration to address proper callus formation and shoot regeneration. The ATX4 protein massively activates shoot identity genes by conferring H3K4me3 deposition at the loci. ATX4-deficient mutants display strong silencing of shoot identity and thus enhanced callus formation. Subsequently, de novo shoot organogenesis from calli is impaired in atx4 mutants. These results indicate that a series of epigenetic reprogramming of tissue identity underlies plant regeneration, and molecular components defining tissue identity can be used as invaluable genetic sources for improving crop transformation efficiency.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ok-Sun Park
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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8
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Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports 2019; 10:627-641. [PMID: 29358085 PMCID: PMC5830946 DOI: 10.1016/j.stemcr.2017.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
The heterochromatin protein 1 (HP1) family is involved in various functions with maintenance of chromatin structure. During murine somatic cell reprogramming, we find that early depletion of HP1γ reduces the generation of induced pluripotent stem cells, while late depletion enhances the process, with a concomitant change from a centromeric to nucleoplasmic localization and elongation-associated histone H3.3 enrichment. Depletion of heterochromatin anchoring protein SENP7 increased reprogramming efficiency to a similar extent as HP1γ, indicating the importance of HP1γ release from chromatin for pluripotency acquisition. HP1γ interacted with OCT4 and DPPA4 in HP1α and HP1β knockouts and in H3K9 methylation depleted H3K9M embryonic stem cell (ESC) lines. HP1α and HP1γ complexes in ESCs differed in association with histones, the histone chaperone CAF1 complex, and specific components of chromatin-modifying complexes such as DPY30, implying distinct functional contributions. Taken together, our results reveal the complex contribution of the HP1 proteins to pluripotency. Release of HP1γ from anchoring by Senp7 increases reprogramming efficiency HP1γ switches enrichment from histone H1 to histone H3.3 in pluripotent cells HP1γ interacts with OCT4 and DPPA4 independent of HP1α, HP1β, and H3K9 methylation Proteomic characterization of HP1 protein family in pluripotent cells
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Affiliation(s)
- Nur Zafirah Zaidan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kolin J Walker
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jaime E Brown
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA.
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9
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Ye Y, Li M, Gu L, Chen X, Shi J, Zhang X, Jiang C. Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell Death Differ 2016; 24:409-420. [PMID: 27858939 PMCID: PMC5344203 DOI: 10.1038/cdd.2016.135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 12/25/2022] Open
Abstract
Neurons are a key component of the nervous system and differentiate from multipotent neural stem cells (NSCs). Chromatin remodeling has a critical role in the differentiation process. However, its in vivo epigenetic regulatory role remains unknown. We show here that nucleosome depletion regions (NDRs) form in both proximal promoters and distal enhancers during NSCs differentiating into neurons in the early Drosophila embryonic development. NDR formation in the regulatory regions involves nucleosome shift and eviction. Nucleosome occupancy in promoter NDRs is inversely proportional to the gene activity. Genes with promoter NDR formation during differentiation are enriched for functions related to neuron development and maturation. Active histone-modification signals (H3K4me3 and H3K9ac) in promoters are gained in neurons in two modes: de novo establishment to high levels or increase from the existing levels in NSCs. The gene sets corresponding to the two modes have different neuron-related functions. Dynamic changes of H3K27ac and H3K9ac signals in enhancers and promoters synergistically repress genes associated with neural stem or progenitor cell-related pluripotency and upregulate genes associated with neuron projection morphogenesis, neuron differentiation, and so on. Our results offer new insights into chromatin remodeling during in vivo neuron development and lay a foundation for its epigenetic regulatory mechanism study of other lineage specification.
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Affiliation(s)
- Youqiong Ye
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Min Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Xiaolong Chen
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Jiejun Shi
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
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10
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Abstract
The enabling technologies of synthetic biology are opening up new opportunities for engineering and enhancement of mammalian cells. This will stimulate diverse applications in many life science sectors such as regenerative medicine, development of biosensing cell lines, therapeutic protein production, and generation of new synthetic genetic regulatory circuits. Harnessing the full potential of these new engineering-based approaches requires the design and assembly of large DNA constructs-potentially up to chromosome scale-and the effective delivery of these large DNA payloads to the host cell. Random integration of large transgenes, encoding therapeutic proteins or genetic circuits into host chromosomes, has several drawbacks such as risks of insertional mutagenesis, lack of control over transgene copy-number and position-specific effects; these can compromise the intended functioning of genetic circuits. The development of a system orthogonal to the endogenous genome is therefore beneficial. Mammalian artificial chromosomes (MACs) are functional, add-on chromosomal elements, which behave as normal chromosomes-being replicating and portioned to daughter cells at each cell division. They are deployed as useful gene expression vectors as they remain independent from the host genome. MACs are maintained as a single-copy and can accommodate multiple gene expression cassettes of, in theory, unlimited DNA size (MACs up to 10 megabases have been constructed). MACs therefore enabled control over ectopic gene expression and represent an excellent platform to rapidly prototype and characterize novel synthetic gene circuits without recourse to engineering the host genome. This review describes the obstacles synthetic biologists face when working with mammalian systems and how the development of improved MACs can overcome these-particularly given the spectacular advances in DNA synthesis and assembly that are fuelling this research area.
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Affiliation(s)
- Andrea Martella
- School of Biological Sciences, The University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF, U.K
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, The University of Edinburgh , Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, U.K
| | - Junbiao Dai
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yizhi Cai
- School of Biological Sciences, The University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF, U.K
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11
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Elias KM, Emori MM, Westerling T, Long H, Budina-Kolomets A, Li F, MacDuffie E, Davis MR, Holman A, Lawney B, Freedman ML, Quackenbush J, Brown M, Drapkin R. Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors. JCI Insight 2016; 1. [PMID: 27617304 DOI: 10.1172/jci.insight.87988] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulation of lineage-restricted transcription factors has been shown to influence malignant transformation in several types of cancer. Whether similar mechanisms are involved in ovarian cancer pathogenesis is unknown. PAX8 is a nuclear transcription factor that controls the embryologic development of the Müllerian system, including the fallopian tubes. Recent studies have shown that fallopian tube secretory epithelial cells (FTSECs) give rise to the most common form of ovarian cancer, high-grade serous ovarian carcinomas (HGSOCs). We designed the present study in order to understand whether changes in gene expression between FTSECs and HGSOCs relate to alterations in PAX8 binding to chromatin. Using whole transcriptome shotgun sequencing (RNA-Seq) after PAX8 knockdown and ChIP-Seq, we show that FTSECs and HGSOCs are distinguished by marked reprogramming of the PAX8 cistrome. Genes that are significantly altered between FTSECs and HGSOCs are enriched near PAX8 binding sites. These sites are also near TEAD binding sites, and these transcriptional changes may be related to PAX8 interactions with the TEAD/YAP1 signaling pathway. These data suggest that transcriptional changes after transformation in ovarian cancer are closely related to epigenetic remodeling in lineage-specific transcription factors.
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Affiliation(s)
- Kevin M Elias
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA
| | - Megan M Emori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas Westerling
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anna Budina-Kolomets
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Emily MacDuffie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michelle R Davis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander Holman
- Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Brian Lawney
- Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John Quackenbush
- Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ronny Drapkin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA.; Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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12
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Zhang Q, Kota KP, Alam SG, Nickerson JA, Dickinson RB, Lele TP. Coordinated Dynamics of RNA Splicing Speckles in the Nucleus. J Cell Physiol 2015; 231:1269-75. [PMID: 26496460 DOI: 10.1002/jcp.25224] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 12/28/2022]
Abstract
Despite being densely packed with chromatin, nuclear bodies and a nucleoskeletal network, the nucleus is a remarkably dynamic organelle. Chromatin loops form and relax, RNA transcripts and transcription factors move diffusively, and nuclear bodies move. We show here that RNA splicing speckled domains (splicing speckles) fluctuate in constrained nuclear volumes and remodel their shapes. Small speckles move in a directed way toward larger speckles with which they fuse. This directed movement is reduced upon decreasing cellular ATP levels or inhibiting RNA polymerase II activity. The random movement of speckles is reduced upon decreasing cellular ATP levels, moderately reduced after inhibition of SWI/SNF chromatin remodeling and modestly increased upon inhibiting RNA polymerase II activity. To define the paths through which speckles can translocate in the nucleus, we generated a pressure gradient to create flows in the nucleus. In response to the pressure gradient, speckles moved along curvilinear paths in the nucleus. Collectively, our results demonstrate a new type of ATP-dependent motion in the nucleus. We present a model where recycling splicing factors return as part of small sub-speckles from distal sites of RNA processing to larger splicing speckles by a directed ATP-driven mechanism through interchromatin spaces.
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Affiliation(s)
- Qiao Zhang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Krishna P Kota
- Department of Cellular and Tissue Imaging, Perkin Elmer Inc., Waltham, Massachusetts
| | - Samer G Alam
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Richard B Dickinson
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
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