1
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Vieira JIG, Braga LG, Chud TCS, Ferreira PH, Guimarães SEF, Martins MF, do Carmo Panetto JC, Machado MA, Silva DBDS, Bonafé CM, Magalhães AFB, da Silva MVGB, Verardo LL. Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile. J Anim Breed Genet 2024. [PMID: 38686591 DOI: 10.1111/jbg.12869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.
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Affiliation(s)
| | - Larissa Graciano Braga
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Lucas Lima Verardo
- Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
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2
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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3
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Dufour A, Kurylo C, Stöckl JB, Laloë D, Bailly Y, Manceau P, Martins F, Turhan AG, Ferchaud S, Pain B, Fröhlich T, Foissac S, Artus J, Acloque H. Cell specification and functional interactions in the pig blastocyst inferred from single-cell transcriptomics and uterine fluids proteomics. Genomics 2024; 116:110780. [PMID: 38211822 DOI: 10.1016/j.ygeno.2023.110780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/08/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
The embryonic development of the pig comprises a long in utero pre- and peri-implantation development, which dramatically differs from mice and humans. During this peri-implantation period, a complex series of paracrine signals establishes an intimate dialogue between the embryo and the uterus. To better understand the biology of the pig blastocyst during this period, we generated a large dataset of single-cell RNAseq from early and hatched blastocysts, spheroid and ovoid conceptus and proteomic datasets from corresponding uterine fluids. Our results confirm the molecular specificity and functionality of the three main cell populations. We also discovered two previously unknown subpopulations of the trophectoderm, one characterised by the expression of LRP2, which could represent progenitor cells, and the other, expressing pro-apoptotic markers, which could correspond to the Rauber's layer. Our work provides new insights into the biology of these populations, their reciprocal functional interactions, and the molecular dialogue with the maternal uterine environment.
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Affiliation(s)
- Adrien Dufour
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy en Josas, France
| | - Cyril Kurylo
- Université de Toulouse, INRAE, ENVT, GenPhySE, Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Jan B Stöckl
- Ludwig-Maximilians-Universität München, Genzentrum, Feodor-Lynen-Str. 25, 81377 München, Germany
| | - Denis Laloë
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy en Josas, France
| | - Yoann Bailly
- INRAE, GenESI, La Gouvanière, 86480 Rouillé, France
| | | | - Frédéric Martins
- Plateforme Genome et Transcriptome (GeT-Santé), GenoToul, Toulouse University, CNRS, INRAE, INSA, Toulouse, France; I2MC - Institut des Maladies Métaboliques et Cardiovasculaires, Inserm, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Ali G Turhan
- Université Paris Saclay, Inserm, UMRS1310, 7 rue Guy Moquet, 94800 Villejuif, France
| | | | - Bertrand Pain
- Université de Lyon, Inserm, INRAE, SBRI, 18 Av. du Doyen Jean Lépine, 69500 Bron, France
| | - Thomas Fröhlich
- Ludwig-Maximilians-Universität München, Genzentrum, Feodor-Lynen-Str. 25, 81377 München, Germany
| | - Sylvain Foissac
- Université de Toulouse, INRAE, ENVT, GenPhySE, Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Jérôme Artus
- Université Paris Saclay, Inserm, UMRS1310, 7 rue Guy Moquet, 94800 Villejuif, France
| | - Hervé Acloque
- Université Paris Saclay, INRAE, AgroParisTech, GABI, Domaine de Vilvert, 78350 Jouy en Josas, France.
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4
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Gao Y, Han W, Dong R, Wei S, Chen L, Gu Z, Liu Y, Guo W, Yan F. Efficient Reprogramming of Mouse Embryonic Stem Cells into Trophoblast Stem-like Cells via Lats Kinase Inhibition. BIOLOGY 2024; 13:71. [PMID: 38392290 PMCID: PMC10886645 DOI: 10.3390/biology13020071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024]
Abstract
Mouse zygotes undergo multiple rounds of cell division, resulting in the formation of preimplantation blastocysts comprising three lineages: trophectoderm (TE), epiblast (EPI), and primitive endoderm (PrE). Cell fate determination plays a crucial role in establishing a healthy pregnancy. The initial separation of lineages gives rise to TE and inner cell mass (ICM), from which trophoblast stem cells (TSC) and embryonic stem cells (ESC) can be derived in vitro. Studying lineage differentiation is greatly facilitated by the clear functional distinction between TSC and ESC. However, transitioning between these two types of cells naturally poses challenges. In this study, we demonstrate that inhibiting LATS kinase promotes the conversion of ICM to TE and also effectively reprograms ESC into stable, self-renewing TS-like cells (TSLC). Compared to TSC, TSLC exhibits similar molecular properties, including the high expression of marker genes such as Cdx2, Eomes, and Tfap2c, as well as hypomethylation of their promoters. Importantly, TSLC not only displays the ability to differentiate into mature trophoblast cells in vitro but also participates in placenta formation in vivo. These findings highlight the efficient reprogramming of ESCs into TSLCs using a small molecular inducer, which provides a new reference for understanding the regulatory network between ESCs and TSCs.
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Affiliation(s)
- Yake Gao
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
- Reproductive Medicine Center, Wuhan Women's and Children's Medical Care Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenrui Han
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Rui Dong
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Shu Wei
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Lu Chen
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Zhaolei Gu
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Yiming Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Wei Guo
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Fang Yan
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
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5
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Guo CC, Xu HE, Ma X. ARID3a from the ARID family: structure, role in autoimmune diseases and drug discovery. Acta Pharmacol Sin 2023; 44:2139-2150. [PMID: 37488425 PMCID: PMC10618457 DOI: 10.1038/s41401-023-01134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/09/2023] [Indexed: 07/26/2023] Open
Abstract
The AT-rich interaction domain (ARID) family of DNA-binding proteins is a group of transcription factors and chromatin regulators with a highly conserved ARID domain that recognizes specific AT-rich DNA sequences. Dysfunction of ARID family members has been implicated in various human diseases including cancers and intellectual disability. Among them, ARID3a has gained increasing attention due to its potential involvement in autoimmunity. In this article we provide an overview of the ARID family, focusing on the structure and biological functions of ARID3a. It explores the role of ARID3a in autoreactive B cells and its contribution to autoimmune diseases such as systemic lupus erythematosus and primary biliary cholangitis. Furthermore, we also discuss the potential for drug discovery targeting ARID3a and present a plan for future research in this field.
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Affiliation(s)
- Cheng-Cen Guo
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
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6
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Magi A, Mattei G, Mingrino A, Caprioli C, Ronchini C, Frigè G, Semeraro R, Bolognini D, Rambaldi A, Candoni A, Colombo E, Mazzarella L, Pelicci PG. High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. Commun Biol 2023; 6:382. [PMID: 37031307 PMCID: PMC10082806 DOI: 10.1038/s42003-023-04756-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Aberrant DNA methylation at CpG dinucleotides is a cancer hallmark that is associated with the emergence of resistance to anti cancer treatment, though molecular mechanisms and biological significance remain elusive. Genome scale methylation maps by currently used methods are based on chemical modification of DNA and are best suited for analyses of methylation at CpG rich regions (CpG islands). We report the first high coverage whole-genome map in cancer using the long read nanopore technology, which allows simultaneous DNA-sequence and -methylation analyses on native DNA. We analyzed clonal epigenomic/genomic evolution in Acute Myeloid Leukemias (AMLs) at diagnosis and relapse, after chemotherapy. Long read sequencing coupled to a novel computational method allowed definition of differential methylation at unprecedented resolution, and showed that the relapse methylome is characterized by hypermethylation at both CpG islands and sparse CpGs regions. Most differentially methylated genes, however, were not differentially expressed nor enriched for chemoresistance genes. A small fraction of under-expressed and hyper-methylated genes at sparse CpGs, in the gene body, was significantly enriched in transcription factors (TFs). Remarkably, these few TFs supported large gene-regulatory networks including 50% of all differentially expressed genes in the relapsed AMLs and highly-enriched in chemoresistance genes. Notably, hypermethylated regions at sparse CpGs were poorly conserved in the relapsed AMLs, under-represented at their genomic positions and showed higher methylation entropy, as compared to CpG islands. Analyses of available datasets confirmed TF binding to their target genes and conservation of the same gene-regulatory networks in large patient cohorts. Relapsed AMLs carried few patient specific structural variants and DNA mutations, apparently not involved in drug resistance. Thus, drug resistance in AMLs can be mainly ascribed to the selection of random epigenetic alterations at sparse CpGs of a few transcription factors, which then induce reprogramming of the relapsing phenotype, independently of clonal genomic evolution.
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Affiliation(s)
- Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy.
- Institute for Biomedical Technologies, National Research Council, Segrate, Milano, Italy.
| | - Gianluca Mattei
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Alessandra Mingrino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Chiara Caprioli
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Chiara Ronchini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - GianMaria Frigè
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Roberto Semeraro
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Davide Bolognini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alessandro Rambaldi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Candoni
- Clinica Ematologica, Azienda Sanitaria Universitaria Integrata di Udine, Udine, Italy
| | - Emanuela Colombo
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
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7
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Cell context-dependent CFI-1/ARID3 functions control neuronal terminal differentiation. Cell Rep 2023; 42:112220. [PMID: 36897776 PMCID: PMC10124151 DOI: 10.1016/j.celrep.2023.112220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
AT-rich interaction domain 3 (ARID3) transcription factors are expressed in the nervous system, but their mechanisms of action are largely unknown. Here, we provide, in vivo, a genome-wide binding map for CFI-1, the sole C. elegans ARID3 ortholog. We identify 6,396 protein-coding genes as putative direct targets of CFI-1, most of which encode neuronal terminal differentiation markers. In head sensory neurons, CFI-1 directly activates multiple terminal differentiation genes, thereby acting as a terminal selector. In motor neurons, however, CFI-1 acts as a direct repressor, continuously antagonizing three transcriptional activators. By focusing on the glr-4/GRIK4 glutamate receptor locus, we identify proximal CFI-1 binding sites and histone methyltransferase activity as necessary for glr-4 repression. Rescue assays reveal functional redundancy between core and extended DNA-binding ARID domains and a strict requirement for REKLES, the ARID3 oligomerization domain. Altogether, this study uncovers cell-context-dependent mechanisms through which a single ARID3 protein controls the terminal differentiation of distinct neuron types.
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8
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Gu C, Gao H, Li K, Dai X, Yang Z, Li R, Wen C, He Y. Copy Number Variation Analysis of Euploid Pregnancy Loss. Front Genet 2022; 13:766492. [PMID: 35401693 PMCID: PMC8984164 DOI: 10.3389/fgene.2022.766492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022] Open
Abstract
Objectives: Copy number variant (CNV) is believed to be the potential genetic cause of pregnancy loss. However, CNVs less than 3 Mb in euploid products of conceptions (POCs) remain largely unexplored. The aim of this study was to investigate the features of CNVs less than 3 Mb in POCs and their potential clinical significance in pregnancy loss/fetal death. Methods: CNV data were extracted from a cohort in our institution and 19 peer-reviewed publications, and only those CNVs less than 3 Mb detected in euploid pregnancy loss/fetal death were included. We conducted a CNV map to analyze the distribution of CNVs in chromosomes using R packages karyoploteR_1.10.5. Gene names and annotated gene types covered by those CNVs were mined from the human Release 19 reference genome file and GENECODE database. We assessed the expression patterns and the consequences of murine knock-out of those genes using TiGER and Mouse Genome Informatics (MGI) databases. Functional enrichment and pathway analysis for genes in CNVs were performed using clusterProfiler V3.12.0. Result: Breakpoints of 564 CNVs less than 3 Mb were obtained from 442 euploid POCs, with 349 gains and 185 losses. The CNV map showed that CNVs were distributed in all chromosomes, with the highest frequency detected in chromosome 22 and the lowest frequency in chromosome Y, and CNVs showed a higher density in the pericentromeric and sub-telomeric regions. A total of 5,414 genes mined from the CNV regions (CNVRs), Gene Ontology (GO), and pathway analysis showed that the genes were significantly enriched in multiple terms, especially in sensory perception, membrane region, and tight junction. A total of 995 protein-coding genes have been reported to present mammalian phenotypes in MGI, and 276 of them lead to embryonic lethality or abnormal embryo/placenta in knock-out mouse models. CNV located at 19p13.3 was the most common CNV of all POCs. Conclusion: CNVs less than 3 Mb in euploid POCs distribute unevenly in all chromosomes, and a higher density was seen in the pericentromeric and sub-telomeric regions. The genes in those CNVRs are significantly enriched in biological processes and pathways that are important to embryonic/fetal development. CNV in 19p13.3 and the variations of ARID3A and FSTL3 might contribute to pregnancy loss.
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Affiliation(s)
- Chongjuan Gu
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huan Gao
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Kuanrong Li
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xinyu Dai
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhao Yang
- West China Hospital, Sichuan University, Chengdu, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Canliang Wen
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yaojuan He
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
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9
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Korn SM, Schlundt A. Structures and nucleic acid-binding preferences of the eukaryotic ARID domain. Biol Chem 2022; 403:731-747. [PMID: 35119801 DOI: 10.1515/hsz-2021-0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022]
Abstract
The DNA-binding AT-rich interactive domain (ARID) exists in a wide range of proteins throughout eukaryotic kingdoms. ARID domain-containing proteins are involved in manifold biological processes, such as transcriptional regulation, cell cycle control and chromatin remodeling. Their individual domain composition allows for a sub-classification within higher mammals. ARID is categorized as binder of double-stranded AT-rich DNA, while recent work has suggested ARIDs as capable of binding other DNA motifs and also recognizing RNA. Despite a broad variability on the primary sequence level, ARIDs show a highly conserved fold, which consists of six α-helices and two loop regions. Interestingly, this minimal core domain is often found extended by helices at the N- and/or C-terminus with potential roles in target specificity and, subsequently function. While high-resolution structural information from various types of ARIDs has accumulated over two decades now, there is limited access to ARID-DNA complex structures. We thus find ourselves left at the beginning of understanding ARID domain target specificities and the role of accompanying domains. Here, we systematically summarize ARID domain conservation and compare the various types with a focus on their structural differences and DNA-binding preferences, including the context of multiple other motifs within ARID domain containing proteins.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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10
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Alejo-Valle O, Weigert K, Bhayadia R, Ng M, Issa H, Beyer C, Emmrich S, Schuschel K, Ihling C, Sinz A, Zimmermann M, Wickenhauser C, Flasinski M, Regenyi E, Labuhn M, Reinhardt D, Yaspo ML, Heckl D, Klusmann JH. The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis. Blood 2022; 139:651-665. [PMID: 34570885 PMCID: PMC9632760 DOI: 10.1182/blood.2021012231] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022] Open
Abstract
Given the plasticity of hematopoietic stem and progenitor cells, multiple routes of differentiation must be blocked in the the pathogenesis of acute myeloid leukemia, the molecular basis of which is incompletely understood. We report that posttranscriptional repression of the transcription factor ARID3A by miR-125b is a key event in the pathogenesis of acute megakaryoblastic leukemia (AMKL). AMKL is frequently associated with trisomy 21 and GATA1 mutations (GATA1s), and children with Down syndrome are at a high risk of developing the disease. The results of our study showed that chromosome 21-encoded miR-125b synergizes with Gata1s to drive leukemogenesis in this context. Leveraging forward and reverse genetics, we uncovered Arid3a as the main miR-125b target behind this synergy. We demonstrated that, during normal hematopoiesis, this transcription factor promotes megakaryocytic differentiation in concert with GATA1 and mediates TGFβ-induced apoptosis and cell cycle arrest in complex with SMAD2/3. Although Gata1s mutations perturb erythroid differentiation and induce hyperproliferation of megakaryocytic progenitors, intact ARID3A expression assures their megakaryocytic differentiation and growth restriction. Upon knockdown, these tumor suppressive functions are revoked, causing a blockade of dual megakaryocytic/erythroid differentiation and subsequently of AMKL. Inversely, restoring ARID3A expression relieves the arrest of megakaryocytic differentiation in AMKL patient-derived xenografts. This work illustrates how mutations in lineage-determining transcription factors and perturbation of posttranscriptional gene regulation can interact to block multiple routes of hematopoietic differentiation and cause leukemia. In AMKL, surmounting this differentiation blockade through restoration of the tumor suppressor ARID3A represents a promising strategy for treating this lethal pediatric disease.
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Affiliation(s)
- Oriol Alejo-Valle
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Karoline Weigert
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Raj Bhayadia
- Pediatric Hematology and Oncology, Department of Pediatrics, Goethe University Frankfurt, Frankfurt (Main), Germany
| | - Michelle Ng
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hasan Issa
- Pediatric Hematology and Oncology, Department of Pediatrics, Goethe University Frankfurt, Frankfurt (Main), Germany
| | - Christoph Beyer
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester NY
| | - Konstantin Schuschel
- Pediatric Hematology and Oncology, Department of Pediatrics, Goethe University Frankfurt, Frankfurt (Main), Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Martin Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Marius Flasinski
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Hospital Tauberbischofsheim, Tauberbischofsheim, Germany
| | - Eniko Regenyi
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maurice Labuhn
- Institute for Experimental Virology, Twincore, Center for Experimental and Clinical Infection Research, Hannover, Germany; and
| | - Dirk Reinhardt
- Pediatric Hematology and Oncology, Pediatrics III, University Hospital Essen, Essen, Germany
| | | | - Dirk Heckl
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Jan-Henning Klusmann
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
- Pediatric Hematology and Oncology, Department of Pediatrics, Goethe University Frankfurt, Frankfurt (Main), Germany
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11
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Nazarieh M, Hoeppner M, Helms V. Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. FRONTIERS IN BIOINFORMATICS 2021; 1:653054. [PMID: 36303754 PMCID: PMC9581055 DOI: 10.3389/fbinf.2021.653054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
A blood cell lineage consists of several consecutive developmental stages starting from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks that govern these differentiation processes are not yet fully understood. This is in part due to challenges associated with delineating the interactions between transcription factors (TFs) and their corresponding target genes. A possible step forward in this case is provided by the increasing amount of expression data, as a basis for linking differentiation stages and gene activities. Here, we present a novel hierarchical approach to identify characteristic expression peak patterns that global regulators excert along the differentiation path of cell lineages. Based on such simple patterns, we identified cell state-specific marker genes and extracted TFs that likely drive their differentiation. Integration of the mean expression values of stage-specific “key player” genes yielded a distinct peaking pattern for each lineage that was used to identify further genes in the dataset which behave similarly. Incorporating the set of TFs that regulate these genes led to a set of stage-specific regulators that control the biological process of cell fate. As proof of concept, we considered two expression datasets covering key differentiation events in blood cell formation of mice.
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Affiliation(s)
- Maryam Nazarieh
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Kiel, Germany
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Marc Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Kiel, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
- *Correspondence: Volkhard Helms,
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12
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Zablon HA, Ko CI, Puga A. Converging Roles of the Aryl Hydrocarbon Receptor in Early Embryonic Development, Maintenance of Stemness, and Tissue Repair. Toxicol Sci 2021; 182:1-9. [PMID: 34009372 PMCID: PMC8285021 DOI: 10.1093/toxsci/kfab050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor well-known for its adaptive role as a sensor of environmental toxicants and mediator of the metabolic detoxification of xenobiotic ligands. In addition, a growing body of experimental data has provided indisputable evidence that the AHR regulates critical functions of cell physiology and embryonic development. Recent studies have shown that the naïve AHR-that is, unliganded to xenobiotics but activated endogenously-has a crucial role in maintenance of embryonic stem cell pluripotency, tissue repair, and regulation of cancer stem cell stemness. Depending on the cellular context, AHR silences the expression of pluripotency genes Oct4 and Nanog and potentiates differentiation, whereas curtailing cellular plasticity and stemness. In these processes, AHR-mediated contextual responses and outcomes are dictated by changes of interacting partners in signaling pathways, gene networks, and cell-type-specific genomic structures. In this review, we focus on AHR-mediated changes of genomic architecture as an emerging mechanism for the AHR to regulate gene expression at the transcriptional level. Collective evidence places this receptor as a physiological hub connecting multiple biological processes whose disruption impacts on embryonic development, tissue repair, and maintenance or loss of stemness.
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Affiliation(s)
| | | | - Alvaro Puga
- Department of Environmental and Public Health Sciences, Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
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13
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Lee BK, Kim J. Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development. Front Cell Dev Biol 2021; 9:673065. [PMID: 34150768 PMCID: PMC8206641 DOI: 10.3389/fcell.2021.673065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
The placenta is a temporary but pivotal organ for human pregnancy. It consists of multiple specialized trophoblast cell types originating from the trophectoderm of the blastocyst stage of the embryo. While impaired trophoblast differentiation results in pregnancy disorders affecting both mother and fetus, the molecular mechanisms underlying early human placenta development have been poorly understood, partially due to the limited access to developing human placentas and the lack of suitable human in vitro trophoblast models. Recent success in establishing human trophoblast stem cells and other human in vitro trophoblast models with their differentiation protocols into more specialized cell types, such as syncytiotrophoblast and extravillous trophoblast, has provided a tremendous opportunity to understand early human placenta development. Unfortunately, while high-throughput research methods and omics tools have addressed numerous molecular-level questions in various research fields, these tools have not been widely applied to the above-mentioned human trophoblast models. This review aims to provide an overview of various omics approaches that can be utilized in the study of human in vitro placenta models by exemplifying some important lessons obtained from omics studies of mouse model systems and introducing recently available human in vitro trophoblast model systems. We also highlight some key unknown questions that might be addressed by such techniques. Integrating high-throughput omics approaches and human in vitro model systems will facilitate our understanding of molecular-level regulatory mechanisms underlying early human placenta development as well as placenta-associated complications.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-State University of New York, Rensselaer, NY, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, United States
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14
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Mayfield RD, Zhu L, Smith TA, Tiwari GR, Tucker HO. The SMYD1 and skNAC transcription factors contribute to neurodegenerative diseases. Brain Behav Immun Health 2020; 9:100129. [PMID: 34589886 PMCID: PMC8474399 DOI: 10.1016/j.bbih.2020.100129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 11/06/2022] Open
Abstract
SMYD1 and the skNAC isoform of the NAC transcription factor have both previously been characterized as transcription factors in hematopoiesis and cardiac/skeletal muscle. Here we report that comparative analysis of genes deregulated by SMYD1 or skNAC knockdown in differentiating C2C12 myoblasts identified transcripts characteristic of neurodegenerative diseases, including Alzheimer's, Parkinson's and Huntington's Diseases (AD, PD, and HD). This led us to determine whether SMYD1 and skNAC function together or independently within the brain. Based on meta-analyses and direct experimentation, we observed SMYD1 and skNAC expression within cortical striata of human brains, mouse brains and transgenic mouse models of these diseases. We observed some of these features in mouse myoblasts induced to differentiate into neurons. Finally, several defining features of Alzheimer's pathology, including the brain-specific, axon-enriched microtubule-associated protein, Tau, are deregulated upon SMYD1 loss.
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Affiliation(s)
- R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
| | - Li Zhu
- Department of Pathology, Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, 94305, USA
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
| | - Tyler A. Smith
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Gayatri R. Tiwari
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Haley O. Tucker
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
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15
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Behjati Ardakani F, Kattler K, Heinen T, Schmidt F, Feuerborn D, Gasparoni G, Lepikhov K, Nell P, Hengstler J, Walter J, Schulz MH. Prediction of single-cell gene expression for transcription factor analysis. Gigascience 2020; 9:giaa113. [PMID: 33124660 PMCID: PMC7596801 DOI: 10.1093/gigascience/giaa113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/20/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing is a powerful technology to discover new cell types and study biological processes in complex biological samples. A current challenge is to predict transcription factor (TF) regulation from single-cell RNA data. RESULTS Here, we propose a novel approach for predicting gene expression at the single-cell level using cis-regulatory motifs, as well as epigenetic features. We designed a tree-guided multi-task learning framework that considers each cell as a task. Through this framework we were able to explain the single-cell gene expression values using either TF binding affinities or TF ChIP-seq data measured at specific genomic regions. TFs identified using these models could be validated by the literature. CONCLUSION Our proposed method allows us to identify distinct TFs that show cell type-specific regulation. This approach is not limited to TFs but can use any type of data that can potentially be used in explaining gene expression at the single-cell level to study factors that drive differentiation or show abnormal regulation in disease. The implementation of our workflow can be accessed under an MIT license via https://github.com/SchulzLab/Triangulate.
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Affiliation(s)
- Fatemeh Behjati Ardakani
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany; Theodor-Stern-Kai 7
- Cluster of Excellence MMCI, Saarland University, Campus E1 7, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Campus E1 4, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Campus E1 3, Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Campus A2 4, 66123 Saarbrücken, Germany
| | - Tobias Heinen
- Cluster of Excellence MMCI, Saarland University, Campus E1 7, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Campus E1 4, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Florian Schmidt
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany; Theodor-Stern-Kai 7
- Cluster of Excellence MMCI, Saarland University, Campus E1 7, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Campus E1 4, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Campus E1 3, Saarbrücken, Germany
| | - David Feuerborn
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystraße 67, 44139 Dortmund, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Campus A2 4, 66123 Saarbrücken, Germany
| | - Konstantin Lepikhov
- Department of Genetics, Saarland University, Campus A2 4, 66123 Saarbrücken, Germany
| | - Patrick Nell
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystraße 67, 44139 Dortmund, Germany
| | - Jan Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystraße 67, 44139 Dortmund, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Campus A2 4, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany; Theodor-Stern-Kai 7
- Cluster of Excellence MMCI, Saarland University, Campus E1 7, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Campus E1 4, Saarland Informatics Campus, 66123 Saarbrücken, Germany
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16
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Oh S, Boo K, Kim J, Baek SA, Jeon Y, You J, Lee H, Choi HJ, Park D, Lee JM, Baek SH. The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes. Nucleic Acids Res 2020; 48:9037-9052. [PMID: 32735658 PMCID: PMC7498345 DOI: 10.1093/nar/gkaa626] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.
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Affiliation(s)
- Sungryong Oh
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyungjin Boo
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jaebeom Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seon Ah Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Jeon
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Junghyun You
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, South Korea
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
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17
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The Role of LIN28- let-7-ARID3B Pathway in Placental Development. Int J Mol Sci 2020; 21:ijms21103637. [PMID: 32455665 PMCID: PMC7279312 DOI: 10.3390/ijms21103637] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Placental disorders are a major cause of pregnancy loss in humans, and 40–60% of embryos are lost between fertilization and birth. Successful embryo implantation and placental development requires rapid proliferation, invasion, and migration of trophoblast cells. In recent years, microRNAs (miRNAs) have emerged as key regulators of molecular pathways involved in trophoblast function. A miRNA binds its target mRNA in the 3ʹ-untranslated region (3ʹ-UTR), causing its degradation or translational repression. Lethal-7 (let-7) miRNAs induce cell differentiation and reduce cell proliferation by targeting proliferation-associated genes. The oncoprotein LIN28 represses the biogenesis of mature let-7 miRNAs. Proliferating cells have high LIN28 and low let-7 miRNAs, whereas differentiating cells have low LIN28 and high let-7 miRNAs. In placenta, low LIN28 and high let-7 miRNAs can lead to reduced proliferation of trophoblast cells, resulting in abnormal placental development. In trophoblast cells, let-7 miRNAs reduce the expression of proliferation factors either directly by binding their mRNA in 3ʹ-UTR or indirectly by targeting the AT-rich interaction domain (ARID)3B complex, a transcription-activating complex comprised of ARID3A, ARID3B, and histone demethylase 4C (KDM4C). In this review, we discuss regulation of trophoblast function by miRNAs, focusing on the role of LIN28-let-7-ARID3B pathway in placental development.
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18
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ARID3A and ARID3B induce stem promoting pathways in ovarian cancer cells. Gene 2020; 738:144458. [PMID: 32061921 DOI: 10.1016/j.gene.2020.144458] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
ARID3A and ARID3B are paralogs from the AT-Rich interactive Domain (ARID) family. ARID3A and ARID3B associate to regulate genes in B-cells and cancer. We were the first to demonstrate that ARID3B regulates stem cell genes and promotes the cancer stem cell phenotype. Importantly, different knockout phenotypes in mice and distinct patterns of expression in adult animals suggests that ARID3A and ARID3B may have unique functions. In addition, high levels of ARID3B but not ARID3A induce cell death. Our goal was to express ARID3A, ARID3B, or both genes at a moderate level (as can be observed in cancer) and then identify ARID3 regulated genes. We transduced ovarian cancer cells with ARID3A-GFP, ARID3B-RFP, or both. RNA-sequencing was conducted. ARID3A and ARID3B regulated nearly identical sets of genes. Few genes (<5%) were uniquely regulated by ARID3A or ARID3B. ARID3A/B induced genes involved in cancer and stem cell processes including: Twist, MYCN, MMP2, GLI2, TIMP3, and WNT5B. We found that ARID3A and ARID3B also induced expression of each other, providing evidence of the cooperativity. While ARID3A and ARID3B likely have unique functions in distinct contexts, they are largely capable of regulating the same stem cell genes in cancer cells. This study provides a comprehensive list of genes and pathways regulated by ARID3A and ARID3B in ovarian cancer cells.
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19
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MiR-574–5p promotes the differentiation of human cardiac fibroblasts via regulating ARID3A. Biochem Biophys Res Commun 2020; 521:427-433. [DOI: 10.1016/j.bbrc.2019.09.107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022]
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20
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Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells. Nat Commun 2019; 10:4749. [PMID: 31628347 PMCID: PMC6802173 DOI: 10.1038/s41467-019-12720-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/26/2019] [Indexed: 02/07/2023] Open
Abstract
Trophectoderm (TE) lineage development is pivotal for proper implantation, placentation, and healthy pregnancy. However, only a few TE-specific transcription factors (TFs) have been systematically characterized, hindering our understanding of the process. To elucidate regulatory mechanisms underlying TE development, here we map super-enhancers (SEs) in trophoblast stem cells (TSCs) as a model. We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Mapping targets of 27 SE-predicted TFs reveals a highly intertwined transcriptional regulatory circuitry. Intriguingly, SE-predicted TFs show 4 distinct expression patterns with dynamic alterations of their targets during TSC differentiation. Furthermore, depletion of a subset of TFs results in dysregulation of the markers for specialized cell types in placenta, suggesting a role during TE differentiation. Collectively, we characterize an expanded TE-specific regulatory network, providing a framework for understanding TE lineage development and placentation. Trophectoderm lineage development is essential for implantation, placentation, and healthy pregnancy. Here the authors map super-enhancers (SEs) in trophoblast stem cells and find both TE-specific master regulators and 150 previous uncharacterised transcription factors that are SE-associated, providing insight into trophectoderm-specific regulatory networks.
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Abstract
Systemic lupus erythematosus (SLE) is a devastating and heterogeneous autoimmune disease that affects multiple organs, and for which the underlying causes are unknown. The majority of SLE patients produce autoantibodies, have increased levels of type-I inflammatory cytokines, and can develop glomerulonephritis. Recent studies indicate an unexpected but strong association between increased disease activity in SLE patients and the expression of the DNA-binding protein ARID3a (A + T rich interaction domain protein 3a) in a number of peripheral blood cell types. ARID3a expression was first associated with autoantibody production in B cells; however, more recent findings also indicate associations with expression of the inflammatory cytokine interferon alpha in SLE plasmacytoid dendritic cells and low-density neutrophils. In addition, ARID3a is expressed in hematopoietic stem cells and some adult kidney progenitor cells. SLE cells expressing enhanced ARID3a levels show differential gene expression patterns compared with homologous healthy control cells, identifying new pathways potentially regulated by ARID3a. The associations of ARID3a expression with increased disease severity in SLE, suggest that it, or its downstream targets, may provide new therapeutic targets for SLE.
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22
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Xu Y, Luo X, Fang Z, Zheng X, Zeng Y, Zhu C, Gu J, Tang F, Hu Y, Hu G, Jin Y, Li H. Transcription coactivator Cited1 acts as an inducer of trophoblast-like state from mouse embryonic stem cells through the activation of BMP signaling. Cell Death Dis 2018; 9:924. [PMID: 30206204 PMCID: PMC6134011 DOI: 10.1038/s41419-018-0991-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/16/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022]
Abstract
Trophoblast lineages, precursors of the placenta, are essential for post-implantation embryo survival. However, the regulatory network of trophoblast development remains incompletely understood. Here, we report that Cited1, a transcription coactivator, is a robust inducer for trophoblast-like state from mouse embryonic stem cells (ESCs). Depletion of Cited1 in ESCs compromises the trophoblast lineage specification induced by BMP signaling. In contrast, overexpression of Cited1 in ESCs induces a trophoblast-like state with elevated expression of trophoblast marker genes in vitro and generation of trophoblastic tumors in vivo. Furthermore, global transcriptome profile analysis indicates that ectopic Cited1 activates a trophoblast-like transcriptional program in ESCs. Mechanistically, Cited1 interacts with Bmpr2 and Smad4 to activate the Cited1–Bmpr2–Smad1/5/8 axis in the cytoplasm and Cited1–Smad4–p300 complexes in the nucleus, respectively. Collectively, our results show that Cited1 plays an important role in regulating trophoblast lineage specification through activating the BMP signaling pathway.
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Affiliation(s)
- Yanli Xu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Xinlong Luo
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China.,KU Leuven Department of Development and Regeneration, Stem Cell Institute Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Zhuoqing Fang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200032, Shanghai, China
| | - Xiaofeng Zheng
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Yanwu Zeng
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Chaonan Zhu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Junjie Gu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Fan Tang
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Yanqin Hu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Ying Jin
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China. .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200032, Shanghai, China.
| | - Hui Li
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China.
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Lee BK, Uprety N, Jang YJ, Tucker SK, Rhee C, LeBlanc L, Beck S, Kim J. Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells. Stem Cell Res 2017; 26:95-102. [PMID: 29272857 PMCID: PMC5899959 DOI: 10.1016/j.scr.2017.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/05/2017] [Accepted: 12/10/2017] [Indexed: 11/30/2022] Open
Abstract
During early development in placental mammals, proper trophoblast lineage development is essential for implantation and placentation. Defects in this lineage can cause early pregnancy failures and other pregnancy disorders. However, transcription factors controlling trophoblast development remain poorly understood. Here, we utilize Fosl1, previously implicated in trophoblast giant cell development as a member of the AP-1 complex, to trans-differentiate embryonic stem (ES) cells to trophoblast lineage-like cells. We first show that the ectopic expression of Fosl1 is sufficient to induce trophoblast-specific gene expression programs in ES cells. Surprisingly, we find that this transcriptional reprogramming occurs independently of changes in levels of ES cell core factors during the cell fate change. This suggests that Fosl1 acts in a novel way to orchestrate the ES to trophoblast cell fate conversion compared to previously known reprogramming factors. Mapping of Fosl1 targets reveals that Fosl1 directly activates TE lineage-specific genes as a pioneer factor. Our work suggests Fosl1 may be used to reprogram ES cells into differentiated cell types in trophoblast lineage, which not only enhances our knowledge of global trophoblast gene regulation but also may provide a future therapeutic tool for generating induced trophoblast cells from patient-derived pluripotent stem cells.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Nadima Uprety
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Yu Jin Jang
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Scott K Tucker
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Catherine Rhee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Lucy LeBlanc
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Samuel Beck
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States; Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Salisbury Cove, ME 04672, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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24
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Rhee C, Lee BK, Beck S, LeBlanc L, Tucker HO, Kim J. Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells. Nucleic Acids Res 2017; 45:10103-10114. [PMID: 28973471 PMCID: PMC5737334 DOI: 10.1093/nar/gkx692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/02/2017] [Indexed: 11/16/2022] Open
Abstract
Direct reprogramming can be achieved by forced expression of master transcription factors. Yet how such factors mediate repression of initial cell-type-specific genes while activating target cell-type-specific genes is unclear. Through embryonic stem (ES) to trophoblast stem (TS)-like cell reprogramming by introducing individual TS cell-specific ‘CAG’ factors (Cdx2, Arid3a and Gata3), we interrogate their chromosomal target occupancies, modulation of global transcription and chromatin accessibility at the initial stage of reprogramming. From the studies, we uncover a sequential, two-step mechanism of cellular reprogramming in which repression of pre-existing ES cell-associated gene expression program is followed by activation of TS cell-specific genes by CAG factors. Therefore, we reveal that CAG factors function as both decommission and pioneer factors during ES to TS-like cell fate conversion.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel Beck
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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25
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Rhee C, Kim J, Tucker HO. Transcriptional Regulation of the First Cell Fate Decision. JOURNAL OF DEVELOPMENTAL BIOLOGY & REGENERATIVE MEDICINE 2017; 1:102. [PMID: 29658952 PMCID: PMC5897107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding how the first cell fate decision has chosen is a fascinating biological question that was received consider attention over the last decade. Numerous transcription factors are required, and many have been shown to have essential roles in this process. Here we reexamine the function that transcription factors play primarily in the mouse-the model system most thoroughly examined in this process. We address how the first embryonic lineage is established and maintained, with a particular emphasis on subsequent trophectoderm development and the role of the recently established Arid3a transcription factor in this process. In addition, we review relevant aspects of embryonic stem cell reprogramming into trophoblast stem cells -the equivalent of the epiblast (inner cell mass) and the establishment of induced trophoblast stem cells-the in vitro equivalent of the trophectoderm.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge MA 02138, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Haley O. Tucker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
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26
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Khedgikar V, Abbruzzese G, Mathavan K, Szydlo H, Cousin H, Alfandari D. Dual control of pcdh8l/PCNS expression and function in Xenopus laevis neural crest cells by adam13/33 via the transcription factors tfap2α and arid3a. eLife 2017; 6:26898. [PMID: 28829038 PMCID: PMC5601995 DOI: 10.7554/elife.26898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/21/2017] [Indexed: 01/11/2023] Open
Abstract
Adam13/33 is a cell surface metalloprotease critical for cranial neural crest (CNC) cell migration. It can cleave multiple substrates including itself, fibronectin, ephrinB, cadherin-11, pcdh8 and pcdh8l (this work). Cleavage of cadherin-11 produces an extracellular fragment that promotes CNC migration. In addition, the adam13 cytoplasmic domain is cleaved by gamma secretase, translocates into the nucleus and regulates multiple genes. Here, we show that adam13 interacts with the arid3a/dril1/Bright transcription factor. This interaction promotes a proteolytic cleavage of arid3a and its translocation to the nucleus where it regulates another transcription factor: tfap2α. Tfap2α in turn activates multiple genes including the protocadherin pcdh8l (PCNS). The proteolytic activity of adam13 is critical for the release of arid3a from the plasma membrane while the cytoplasmic domain appears critical for the cleavage of arid3a. In addition to this transcriptional control of pcdh8l, adam13 cleaves pcdh8l generating an extracellular fragment that also regulates cell migration.
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Affiliation(s)
- Vikram Khedgikar
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States
| | - Genevieve Abbruzzese
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Ketan Mathavan
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States.,Molecular and Cellular Biology graduate program, University of Massachusetts, Amherst, United States
| | - Hannah Szydlo
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States
| | - Helene Cousin
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States.,Molecular and Cellular Biology graduate program, University of Massachusetts, Amherst, United States
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27
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Piechowski J. Hypothesis about Transdifferentiation As Backbone of Malignancy. Front Oncol 2017; 7:126. [PMID: 28674676 PMCID: PMC5474902 DOI: 10.3389/fonc.2017.00126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022] Open
Abstract
Background Cancer is mainly watched through the prism of random mutations and related corruption of signaling pathways. However, it would seem puzzling to explain the tumor organization, pugnacity and steady evolution of the tumorous disease and, moreover, a systematic ascendancy over the healthy tissues, only through stochastic genomic alterations. Malignancy specific properties Considering the core characteristics of cancer cells, it appears that two major sets of properties are emerging, corresponding to well-identified physiological phenotypes, i.e., (1) the trophoblastic logistical functions for cell survival, protection, expansion, migration, and host-tissue conditioning for angiogenesis and immune tolerance and (2) the sexual functions for genome maintenance. To explain the resurgence of these trophoblastic and sexual phenotypes, a particular cell reprogramming, to be called “malignant transdifferentiation” in view of its key role in the precancer-to-cancer shift, appears to be a convincing hypothesis. Perspectives The concept of malignant transdifferentiation, in addition to oncogenic mutations, would determine a more rational approach of oncogenesis and would open so far unexplored ways of therapeutic actions. Indeed, the trophoblastic phenotype would be a good candidate for therapeutic purposes because, on the one hand, it covers numerous properties that all are vital for the tumor, and on the other hand, it can be targeted with potentially no risk of affecting the healthy tissues as it is not expressed there after birth.
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28
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Rhee C, Edwards M, Dang C, Harris J, Brown M, Kim J, Tucker HO. ARID3A is required for mammalian placenta development. Dev Biol 2017; 422:83-91. [PMID: 27965054 PMCID: PMC5540318 DOI: 10.1016/j.ydbio.2016.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/17/2022]
Abstract
Previous studies in the mouse indicated that ARID3A plays a critical role in the first cell fate decision required for generation of trophectoderm (TE). Here, we demonstrate that ARID3A is widely expressed during mouse and human placentation and essential for early embryonic viability. ARID3A localizes to trophoblast giant cells and other trophoblast-derived cell subtypes in the junctional and labyrinth zones of the placenta. Conventional Arid3a knockout embryos suffer restricted intrauterine growth with severe defects in placental structural organization. Arid3a null placentas show aberrant expression of subtype-specific markers as well as significant alteration in cytokines, chemokines and inflammatory response-related genes, including previously established markers of human placentation disorders. BMP4-mediated induction of trophoblast stem (TS)-like cells from human induced pluripotent stem cells results in ARID3A up-regulation and cytoplasmic to nuclear translocation. Overexpression of ARID3A in BMP4-mediated TS-like cells up-regulates TE markers, whereas pluripotency markers are down-regulated. Our results reveal an essential, conserved function for ARID3A in mammalian placental development through regulation of both intrinsic and extrinsic developmental programs.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Melissa Edwards
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Christine Dang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - June Harris
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Mark Brown
- Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Haley O Tucker
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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29
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Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. Nat Struct Mol Biol 2017; 24:226-233. [PMID: 28134930 DOI: 10.1038/nsmb.3365] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022]
Abstract
The long noncoding RNA Xist is expressed from only the paternal X chromosome in mouse preimplantation female embryos and mediates transcriptional silencing of that chromosome. In females, absence of Xist leads to postimplantation lethality. Here, through single-cell RNA sequencing of early preimplantation mouse embryos, we found that the initiation of imprinted X-chromosome inactivation absolutely requires Xist. Lack of paternal Xist leads to genome-wide transcriptional misregulation in the early blastocyst and to failure to activate the extraembryonic pathway that is essential for postimplantation development. We also demonstrate that the expression dynamics of X-linked genes depends on the strain and parent of origin as well as on the location along the X chromosome, particularly at the first 'entry' sites of Xist. This study demonstrates that dosage-compensation failure has an effect as early as the blastocyst stage and reveals genetic and epigenetic contributions to orchestrating transcriptional silencing of the X chromosome during early embryogenesis.
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30
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Popowski M, Lee BK, Rhee C, Iyer VR, Tucker HO. Arid3a regulates mesoderm differentiation in mouse embryonic stem cells. JOURNAL OF STEM CELL THERAPY AND TRANSPLANTATION 2017; 1:52-62. [PMID: 31080945 PMCID: PMC6510499 DOI: 10.29328/journal.jsctt.1001005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Research into regulation of the differentiation of stem cells is critical to understanding early developmental decisions and later development growth. The transcription factor ARID3A previously was shown to be critical for trophectoderm and hematopoetic development. Expression of ARID3A increases during embryonic differentiation, but the underlying reason remained unclear. Here we show that Arid3a null embryonic stem (ES) cells maintain an undifferentiated gene expression pattern and form teratomas in immune-compromised mice. However, Arid3a null ES cells differentiated in vitro into embryoid bodies (EBs) significantly faster than control ES cells, and the majority forming large cystic embryoid EBs. Analysis of gene expression during this transition indicated that Arid3a nulls differentiated spontaneously into mesoderm and neuroectoderm lineages. While young ARID3A-deficient mice showed no gross tissue morphology, proliferative and structural abnormalities were observed in the kidneys of older null mice. Together these data suggest that ARID3A is not only required hematopoiesis, but is critical for early mesoderm differentiation.
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Affiliation(s)
- Melissa Popowski
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-kyu Lee
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Cathy Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vishwanath R Iyer
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Address for Correspondence: Haley O Tucker, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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31
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Baines K, Renaud S. Transcription Factors That Regulate Trophoblast Development and Function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 145:39-88. [DOI: 10.1016/bs.pmbts.2016.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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32
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Vaiman D. Genes, epigenetics and miRNA regulation in the placenta. Placenta 2016; 52:127-133. [PMID: 28043658 DOI: 10.1016/j.placenta.2016.12.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 10/24/2016] [Accepted: 12/23/2016] [Indexed: 12/19/2022]
Abstract
This text reviews briefly the context in which epigenetics regulate gene expression in trophoblast development and function. It is an attempt to focus on a limited number of recent papers that, according to the author, shed new light on placental development, and constitute possible trails for improving knowledge and women follow-up in pathological pregnancies.
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Affiliation(s)
- Daniel Vaiman
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris-Descartes, 24, rue du Faubourg St-Jacques, 75014, Paris, France.
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ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle. J Virol 2016; 90:9543-55. [PMID: 27512077 PMCID: PMC5044832 DOI: 10.1128/jvi.03262-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 07/18/2016] [Indexed: 12/11/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of commonly fatal malignancies of immunocompromised individuals, including primary effusion lymphoma (PEL) and Kaposi's sarcoma (KS). A hallmark of all herpesviruses is their biphasic life cycle—viral latency and the productive lytic cycle—and it is well established that reactivation of the KSHV lytic cycle is associated with KS pathogenesis. Therefore, a thorough appreciation of the mechanisms that govern reactivation is required to better understand disease progression. The viral protein replication and transcription activator (RTA) is the KSHV lytic switch protein due to its ability to drive the expression of various lytic genes, leading to reactivation of the entire lytic cycle. While the mechanisms for activating lytic gene expression have received much attention, how RTA impacts cellular function is less well understood. To address this, we developed a cell line with doxycycline-inducible RTA expression and applied stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics. Using this methodology, we have identified a novel cellular protein (AT-rich interacting domain containing 3B [ARID3B]) whose expression was enhanced by RTA and that relocalized to replication compartments upon lytic reactivation. We also show that small interfering RNA (siRNA) knockdown or overexpression of ARID3B led to an enhancement or inhibition of lytic reactivation, respectively. Furthermore, DNA affinity and chromatin immunoprecipitation assays demonstrated that ARID3B specifically interacts with A/T-rich elements in the KSHV origin of lytic replication (oriLyt), and this was dependent on lytic cycle reactivation. Therefore, we have identified a novel cellular protein whose expression is enhanced by KSHV RTA with the ability to inhibit KSHV reactivation.
IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of fatal malignancies of immunocompromised individuals, including Kaposi's sarcoma (KS). Herpesviruses are able to establish a latent infection, in which they escape immune detection by restricting viral gene expression. Importantly, however, reactivation of productive viral replication (the lytic cycle) is necessary for the pathogenesis of KS. Therefore, it is important that we comprehensively understand the mechanisms that govern lytic reactivation, to better understand disease progression. In this study, we have identified a novel cellular protein (AT-rich interacting domain protein 3B [ARID3B]) that we show is able to temper lytic reactivation. We showed that the master lytic switch protein, RTA, enhanced ARID3B levels, which then interacted with viral DNA in a lytic cycle-dependent manner. Therefore, we have added a new factor to the list of cellular proteins that regulate the KSHV lytic cycle, which has implications for our understanding of KSHV biology.
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Liu J, Luo X, Xu Y, Gu J, Tang F, Jin Y, Li H. Single-stranded DNA binding protein Ssbp3 induces differentiation of mouse embryonic stem cells into trophoblast-like cells. Stem Cell Res Ther 2016; 7:79. [PMID: 27236334 PMCID: PMC4884356 DOI: 10.1186/s13287-016-0340-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/04/2016] [Accepted: 05/11/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intrinsic factors and extrinsic signals which control unlimited self-renewal and developmental pluripotency in embryonic stem cells (ESCs) have been extensively investigated. However, a much smaller number of factors involved in extra-embryonic trophoblast differentiation from ESCs have been studied. In this study, we investigated the role of the single-stranded DNA binding protein, Ssbp3, for the induction of trophoblast-like differentiation from mouse ESCs. METHODS Gain- and loss-of-function experiments were carried out through overexpression or knockdown of Ssbp3 in mouse ESCs under self-renewal culture conditions. Expression levels of pluripotency and lineage markers were detected by real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analyses. The global gene expression profile in Ssbp3-overexpressing cells was determined by affymetrix microarray. Gene ontology and pathway terms were analyzed and further validated by qRT-PCR and Western blotting. The methylation status of the Elf5 promoter in Ssbp3-overexpressing cells was detected by bisulfite sequencing. The trophoblast-like phenotype induced by Ssbp3 was also evaluated by teratoma formation and early embryo injection assays. RESULTS Forced expression of Ssbp3 in mouse ESCs upregulated expression levels of lineage-associated genes, with trophoblast cell markers being the highest. In contrast, depletion of Ssbp3 attenuated the expression of trophoblast lineage marker genes induced by downregulation of Oct4 or treatment with BMP4 and bFGF in ESCs. Interestingly, global gene expression profiling analysis indicated that Ssbp3 overexpression did not significantly alter the transcript levels of pluripotency-associated transcription factors. Instead, Ssbp3 promoted the expression of early trophectoderm transcription factors such as Cdx2 and activated MAPK/Erk1/2 and TGF-β pathways. Furthermore, overexpression of Ssbp3 reduced the methylation level of the Elf5 promoter and promoted the generation of teratomas with internal hemorrhage, indicative of the presence of trophoblast cells. CONCLUSIONS This study identifies Ssbp3, a single-stranded DNA binding protein, as a regulator for mouse ESCs to differentiate into trophoblast-like cells. This finding is helpful to understand the regulatory networks for ESC differentiation into extra-embryonic lineages.
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Affiliation(s)
- Jifeng Liu
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinlong Luo
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Present address: KU Leuven Department of Development and Regeneration, Stem Cell Institute Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Yanli Xu
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junjie Gu
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, New Life Science Building A, Room 1328, 320 Yue Yang Road, Shanghai, 200032, China
| | - Fan Tang
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, New Life Science Building A, Room 1328, 320 Yue Yang Road, Shanghai, 200032, China
| | - Ying Jin
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, New Life Science Building A, Room 1328, 320 Yue Yang Road, Shanghai, 200032, China.
| | - Hui Li
- Laboratory of Molecular Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, New Life Science Building A, Room 1328, 320 Yue Yang Road, Shanghai, 200032, China.
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35
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Piechowski J. Trophoblastic-like transdifferentiation: A key to oncogenesis. Crit Rev Oncol Hematol 2016; 101:1-11. [DOI: 10.1016/j.critrevonc.2016.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/29/2015] [Accepted: 01/19/2016] [Indexed: 12/18/2022] Open
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36
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Liao TT, Hsu WH, Ho CH, Hwang WL, Lan HY, Lo T, Chang CC, Tai SK, Yang MH. let-7 Modulates Chromatin Configuration and Target Gene Repression through Regulation of the ARID3B Complex. Cell Rep 2016; 14:520-533. [PMID: 26776511 DOI: 10.1016/j.celrep.2015.12.064] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/05/2015] [Accepted: 12/13/2015] [Indexed: 12/22/2022] Open
Abstract
Let-7 is crucial for both stem cell differentiation and tumor suppression. Here, we demonstrate a chromatin-dependent mechanism of let-7 in regulating target gene expression in cancer cells. Let-7 directly represses the expression of AT-rich interacting domain 3B (ARID3B), ARID3A, and importin-9. In the absence of let-7, importin-9 facilitates the nuclear import of ARID3A, which then forms a complex with ARID3B. The nuclear ARID3B complex recruits histone demethylase 4C to reduce histone 3 lysine 9 trimethylation and promotes the transcription of stemness factors. Functionally, expression of ARID3B is critical for the tumor initiation in let-7-depleted cancer cells. An inverse association between let-7 and ARID3A/ARID3B and prognostic significance is demonstrated in head and neck cancer patients. These results highlight a chromatin-dependent mechanism where let-7 regulates cancer stemness through ARID3B.
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Affiliation(s)
- Tsai-Tsen Liao
- Institute of Clinical Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan
| | - Wen-Hao Hsu
- Institute of Clinical Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan
| | - Chien-Hsin Ho
- Institute of Clinical Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan
| | - Wei-Lun Hwang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, No. 250, Wuxing Street, Taipei 11031, Taiwan
| | - Hsin-Yi Lan
- Institute of Clinical Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan
| | - Ting Lo
- Institute of Clinical Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan
| | - Cheng-Chi Chang
- Graduate Institute of Oral Biology, School of Dentistry, National Taiwan University, No. 1, Changde Street, Taipei 10048, Taiwan
| | - Shyh-Kuan Tai
- Department of Otolaryngology, Taipei Veterans General Hospital, No. 201, Section 2, Shih-Pai Road, Taipei 11217, Taiwan
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan; Institute of Biotechnology in Medicine, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan; Genomic Research Center, National Yang-Ming University, No. 155, Section 2, Li-Nong Street, Taipei 11221, Taiwan; Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, No. 201, Section 2, Shih-Pai Road, Taipei 11217, Taiwan; Genomic Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 11529, Taiwan.
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Bobbs A, Gellerman K, Hallas WM, Joseph S, Yang C, Kurkewich J, Cowden Dahl KD. ARID3B Directly Regulates Ovarian Cancer Promoting Genes. PLoS One 2015; 10:e0131961. [PMID: 26121572 PMCID: PMC4486168 DOI: 10.1371/journal.pone.0131961] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/08/2015] [Indexed: 01/22/2023] Open
Abstract
The DNA-binding protein AT-Rich Interactive Domain 3B (ARID3B) is elevated in ovarian cancer and increases tumor growth in a xenograft model of ovarian cancer. However, relatively little is known about ARID3B's function. In this study we perform the first genome wide screen for ARID3B direct target genes and ARID3B regulated pathways. We identified and confirmed numerous ARID3B target genes by chromatin immunoprecipitation (ChIP) followed by microarray and quantitative RT-PCR. Using motif-finding algorithms, we characterized a binding site for ARID3B, which is similar to the previously known site for the ARID3B paralogue ARID3A. Functionality of this predicted site was demonstrated by ChIP analysis. We next demonstrated that ARID3B induces expression of its targets in ovarian cancer cell lines. We validated that ARID3B binds to an epidermal growth factor receptor (EGFR) enhancer and increases mRNA expression. ARID3B also binds to the promoter of Wnt5A and its receptor FZD5. FZD5 is highly expressed in ovarian cancer cell lines, and is upregulated by exogenous ARID3B. Both ARID3B and FZD5 expression increase adhesion to extracellular matrix (ECM) components including collagen IV, fibronectin and vitronectin. ARID3B-increased adhesion to collagens II and IV require FZD5. This study directly demonstrates that ARID3B binds target genes in a sequence-specific manner, resulting in increased gene expression. Furthermore, our data indicate that ARID3B regulation of direct target genes in the Wnt pathway promotes adhesion of ovarian cancer cells.
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Affiliation(s)
- Alexander Bobbs
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, Indiana, United States of America
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
| | - Katrina Gellerman
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - William Morgan Hallas
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Stancy Joseph
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, Indiana, United States of America
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
| | - Chao Yang
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jeffrey Kurkewich
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Karen D. Cowden Dahl
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, Indiana, United States of America
- Harper Cancer Research Institute, South Bend, Indiana, United States of America
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- * E-mail:
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