1
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Kinkade JA, Seetharam AS, Sachdev S, Bivens NJ, Phinney BS, Grigorean G, Roberts RM, Tuteja G, Rosenfeld CS. Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis†. Biol Reprod 2024; 110:310-328. [PMID: 37883444 PMCID: PMC10873279 DOI: 10.1093/biolre/ioad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023] Open
Abstract
The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. Current studies examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from trophoblast cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the microRNA (miRNA) from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than downregulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta-brain axis.
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Affiliation(s)
- Jessica A Kinkade
- Biomedical Sciences, University of Missouri, Columbia, MO, USA
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Shrikesh Sachdev
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Nathan J Bivens
- Genomics Technology Core Facility, University of Missouri, Columbia, MO, USA
| | - Brett S Phinney
- Proteomics Core UC Davis Genome Center, University of California, Davis, CA, USA
| | - Gabriela Grigorean
- Proteomics Core UC Davis Genome Center, University of California, Davis, CA, USA
| | - R Michael Roberts
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Cheryl S Rosenfeld
- Biomedical Sciences, University of Missouri, Columbia, MO, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Genetics Area Program, University of Missouri, Columbia, MO, USA
- Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, USA
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2
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Iqbal K, Dominguez EM, Nixon B, Moreno-Irusta A, Crnkovich B, Scott RL, Vu HTH, Tuteja G, Vivian JL, Soares MJ. Conditionally mutant animal model for investigating the invasive trophoblast cell lineage. Development 2024; 151:dev202239. [PMID: 38112206 PMCID: PMC10820817 DOI: 10.1242/dev.202239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Placental development involves coordinated expansion and differentiation of trophoblast cell lineages possessing specialized functions. Among the differentiated trophoblast cell lineages are invasive trophoblast cells, which exit the placenta and invade the uterus, where they restructure the uterine parenchyma and facilitate remodeling of uterine spiral arteries. The rat exhibits deep intrauterine trophoblast cell invasion, a feature shared with human placentation, and is also amenable to gene manipulation using genome-editing techniques. In this investigation, we generated a conditional rat model targeting the invasive trophoblast cell lineage. Prolactin family 7, subfamily b, member 1 (Prl7b1) is uniquely and abundantly expressed in the rat invasive trophoblast cell lineage. Disruption of Prl7b1 did not adversely affect placental development. We demonstrated that the Prl7b1 locus could be effectively used to drive the expression of Cre recombinase in invasive trophoblast cells. Our rat model represents a new tool for investigating candidate genes contributing to the regulation of invasive trophoblast cells and their roles in trophoblast-guided uterine spiral artery remodeling.
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Affiliation(s)
- Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Esteban M. Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Brandon Nixon
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Benjamin Crnkovich
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Jay L. Vivian
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO 64018, USA
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO 64108, USA
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3
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Iqbal K, Nixon B, Crnkovich B, Dominguez EM, Moreno-Irusta A, Scott RL, Vu HTH, Tuteja G, Vivian JL, Soares MJ. CONDITIONALLY MUTANT ANIMAL MODEL FOR INVESTIGATING THE INVASIVE TROPHOBLAST CELL LINEAGE. bioRxiv 2023:2023.08.02.551740. [PMID: 37577576 PMCID: PMC10418272 DOI: 10.1101/2023.08.02.551740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Placental development involves coordinated expansion and differentiation of trophoblast cell lineages possessing specialized functions. Among the differentiated trophoblast cell lineages are invasive trophoblast cells, which exit the placenta and invade into the uterus where they restructure the uterine parenchyma and facilitate remodeling of uterine spiral arteries. The rat exhibits deep intrauterine trophoblast cell invasion, a feature shared with human placentation, and is also amenable to gene manipulation using genome editing techniques. In this investigation, we generated a conditional rat model targeting the invasive trophoblast cell lineage. Prolactin family 7, subfamily b, member 1 ( Prl7b1 ) is uniquely and abundantly expressed in the rat invasive trophoblast cell lineage. Disruption of Prl7b1 did not adversely affect placental development. We demonstrated that the Prl7b1 locus could be effectively used to drive the expression of Cre recombinase in invasive trophoblast cells. Our rat model represents a new tool for investigating candidate genes contributing to the regulation of invasive trophoblast cells and their contributions to trophoblast-guided uterine spiral artery remodeling.
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4
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. Core conserved transcriptional regulatory networks define the invasive trophoblast cell lineage. Development 2023; 150:dev201826. [PMID: 37417811 PMCID: PMC10445752 DOI: 10.1242/dev.201826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
The invasive trophoblast cell lineages in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model for studying hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus ATAC-seq data from gestation day 15.5 and 19.5 rat uterine-placental interface tissues, and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial and smooth muscle cells, and compared invasive trophoblast chromatin accessibility with extravillous trophoblast cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy, Kansas City, MO 64108, USA
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
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5
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Vu HTH, Zhang Y, Tuteja G, Dorman KS. Unsupervised contrastive peak caller for ATAC-seq. Genome Res 2023; 33:1133-1144. [PMID: 37217250 PMCID: PMC10538491 DOI: 10.1101/gr.277677.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023]
Abstract
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing. These sequenced regions are quantified and tested for enrichment in a process referred to as "peak calling." Most unsupervised peak calling methods are based on simple statistical models and suffer from elevated false positive rates. Newly developed supervised deep learning methods can be successful, but they rely on high quality labeled data for training, which can be difficult to obtain. Moreover, though biological replicates are recognized to be important, there are no established approaches for using replicates in the deep learning tools, and the approaches available for traditional methods either cannot be applied to ATAC-seq, where control samples may be unavailable, or are post hoc and do not capitalize on potentially complex, but reproducible signal in the read enrichment data. Here, we propose a novel peak caller that uses unsupervised contrastive learning to extract shared signals from multiple replicates. Raw coverage data are encoded to obtain low-dimensional embeddings and optimized to minimize a contrastive loss over biological replicates. These embeddings are passed to another contrastive loss for learning and predicting peaks and decoded to denoised data under an autoencoder loss. We compared our replicative contrastive learner (RCL) method with other existing methods on ATAC-seq data, using annotations from ChromHMM genomic labels and transcription factor ChIP-seq as noisy truth. RCL consistently achieved the best performance.
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Affiliation(s)
- Ha T H Vu
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
- Department of Genetics, Development and Cell Biology, Ames, Iowa 50011, USA
| | - Yudi Zhang
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Geetu Tuteja
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
- Department of Genetics, Development and Cell Biology, Ames, Iowa 50011, USA
| | - Karin S Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA;
- Department of Genetics, Development and Cell Biology, Ames, Iowa 50011, USA
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
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6
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE. bioRxiv 2023:2023.03.30.534962. [PMID: 37066272 PMCID: PMC10103937 DOI: 10.1101/2023.03.30.534962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The invasive trophoblast cell lineage in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model to study hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus (sn) ATAC-seq data from gestation day (gd) 15.5 and 19.5 rat uterine-placental interface tissues and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial, and smooth muscle cells, and compared invasive trophoblast chromatin accessibility to extravillous trophoblast (EVT) cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, MO, 64108
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
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7
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Vu HT, Kaur H, Kies KR, Starks RR, Tuteja G. Identifying novel regulators of placental development using time-series transcriptome data. Life Sci Alliance 2023; 6:6/2/e202201788. [PMID: 36622342 PMCID: PMC9748866 DOI: 10.26508/lsa.202201788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
The placenta serves as a connection between the mother and the fetus during pregnancy, providing the fetus with oxygen, nutrients, and growth hormones. However, the regulatory mechanisms and dynamic gene interaction networks underlying early placental development are understudied. Here, we generated RNA-sequencing data from mouse fetal placenta at embryonic days 7.5, 8.5, and 9.5 to identify genes with timepoint-specific expression, then inferred gene interaction networks to analyze highly connected network modules. We determined that timepoint-specific gene network modules were associated with distinct developmental processes, and with similar expression profiles to specific human placental cell populations. From each module, we identified hub genes and their direct neighboring genes, which were predicted to govern placental functions. We confirmed that four novel candidate regulators identified through our analyses regulate cell migration in the HTR-8/SVneo cell line. Overall, we predicted several novel regulators of placental development expressed in specific placental cell types using network analysis of bulk RNA-sequencing data. Our findings and analysis approaches will be valuable for future studies investigating the transcriptional landscape of early development.
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Affiliation(s)
- Ha Th Vu
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Haninder Kaur
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Kelby R Kies
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Rebekah R Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA .,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
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8
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Vu HT, Zhang Y, Tuteja G, Dorman K. Unsupervised Contrastive Peak Caller for ATAC-seq. bioRxiv 2023:2023.01.07.523108. [PMID: 36712015 PMCID: PMC9881890 DOI: 10.1101/2023.01.07.523108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing. These sequenced regions are quantified and tested for enrichment in a process referred to as "peak calling". Most unsupervised peak calling methods are based on simple statistical models and suffer from elevated false positive rates. Newly developed supervised deep learning methods can be successful, but they rely on high quality labeled data for training, which can be difficult to obtain. Moreover, though biological replicates are recognized to be important, there are no established approaches for using replicates in the deep learning tools, and the approaches available for traditional methods either cannot be applied to ATAC-seq, where control samples may be unavailable, or are post-hoc and do not capitalize on potentially complex, but reproducible signal in the read enrichment data. Here, we propose a novel peak caller that uses unsupervised contrastive learning to extract shared signals from multiple replicates. Raw coverage data are encoded to obtain low-dimensional embeddings and optimized to minimize a contrastive loss over biological replicates. These embeddings are passed to another contrastive loss for learning and predicting peaks and decoded to denoised data under an autoencoder loss. We compared our Replicative Contrastive Learner (RCL) method with other existing methods on ATAC-seq data, using annotations from ChromHMM genome and transcription factor ChIP-seq as noisy truth. RCL consistently achieved the best performance.
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Affiliation(s)
- Ha T.H. Vu
- Bioinformatics and Computational Biology Program, Iowa State University, Ames IA 50011, USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames IA 50011, USA
| | - Yudi Zhang
- Department of Statistics, Iowa State University, Ames IA 50011, USA
| | - Geetu Tuteja
- Bioinformatics and Computational Biology Program, Iowa State University, Ames IA 50011, USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames IA 50011, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames IA 50011, USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames IA 50011, USA
- Department of Statistics, Iowa State University, Ames IA 50011, USA
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Yu W, Chakravarthi VP, Borosha S, Dilower I, Lee EB, Ratri A, Starks RR, Fields PE, Wolfe MW, Faruque MO, Tuteja G, Rumi MAK. Transcriptional regulation of Satb1 in mouse trophoblast stem cells. Front Cell Dev Biol 2022; 10:918235. [PMID: 36589740 PMCID: PMC9795202 DOI: 10.3389/fcell.2022.918235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
SATB homeobox proteins are important regulators of developmental gene expression. Among the stem cell lineages that emerge during early embryonic development, trophoblast stem (TS) cells exhibit robust SATB expression. Both SATB1 and SATB2 act to maintain the trophoblast stem-state. However, the molecular mechanisms that regulate TS-specific Satb expression are not yet known. We identified Satb1 variant 2 as the predominant transcript in trophoblasts. Histone marks, and RNA polymerase II occupancy in TS cells indicated an active state of the promoter. A novel cis-regulatory region with active histone marks was identified ∼21 kbp upstream of the variant 2 promoter. CRISPR/Cas9 mediated disruption of this sequence decreased Satb1 expression in TS cells and chromosome conformation capture analysis confirmed looping of this distant regulatory region into the proximal promoter. Scanning position weight matrices across the enhancer predicted two ELF5 binding sites in close proximity to SATB1 sites, which were confirmed by chromatin immunoprecipitation. Knockdown of ELF5 downregulated Satb1 expression in TS cells and overexpression of ELF5 increased the enhancer-reporter activity. Interestingly, ELF5 interacts with SATB1 in TS cells, and the enhancer activity was upregulated following SATB overexpression. Our findings indicate that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping of an enhancer that interacts with ELF5 and SATB proteins.
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Affiliation(s)
- Wei Yu
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - V. Praveen Chakravarthi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Shaon Borosha
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Iman Dilower
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Eun Bee Lee
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Anamika Ratri
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Rebekah R. Starks
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Patrick E. Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Michael W. Wolfe
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, United States
| | - M. Omar Faruque
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - M. A. Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States,*Correspondence: M. A. Karim Rumi,
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Seetharam AS, Vu HTH, Choi S, Khan T, Sheridan MA, Ezashi T, Roberts RM, Tuteja G. The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion. Stem Cell Reports 2022; 17:1289-1302. [PMID: 35594861 PMCID: PMC9214062 DOI: 10.1016/j.stemcr.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The observation that trophoblast (TB) can be generated from primed pluripotent stem cells (PSCs) by exposure to bone morphogenetic protein-4 (BMP4) when FGF2 and ACTIVIN signaling is minimized has recently been challenged with the suggestion that the procedure instead produces amnion. Here, by analyzing transcriptome data from multiple sources, including bulk and single-cell data, we show that the BMP4 procedure generates bona fide TB with similarities to both placental villous TB and TB generated from TB stem cells. The analyses also suggest that the transcriptomic signatures between embryonic amnion and different forms of TB have commonalities. Our data provide justification for the continued use of TB derived from PSCs as a model for investigating placental development. Cells differentiated by using BAP protocols resemble TB more than embryonic amnion Deviation from the standard BAP protocol results in less differentiated TB Single-cell/nucleus RNA-seq analysis identifies two syncytiotrophoblast populations
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Affiliation(s)
- Arun S Seetharam
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA; Genetics Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Ha T H Vu
- Genetics Development and Cell Biology, Iowa State University, Ames, IA, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Sehee Choi
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Teka Khan
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Megan A Sheridan
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Toshihiko Ezashi
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - R Michael Roberts
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Geetu Tuteja
- Genetics Development and Cell Biology, Iowa State University, Ames, IA, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.
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11
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Adu-Gyamfi EA, Rosenfeld CS, Tuteja G. The impact of bisphenol a (BPA) on the placenta. Biol Reprod 2022; 106:826-834. [PMID: 35020819 DOI: 10.1093/biolre/ioac001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 11/14/2022] Open
Abstract
Bisphenol A (BPA) is an endocrine-disrupting chemical (EDC) that is used in a wide-variety of plastic and common house-hold items. Therefore, there is potential continual exposure to this compound. BPA exposure has been linked to certain placenta-associated obstetric complications such as preeclampsia, fetal growth restriction, miscarriage, and preterm birth. However, how BPA exposure results in these disorders remains uncertain. Hence, we have herein summarized the reported impact of BPA on the morphology and metabolic state of the placenta and have proposed mechanisms by which BPA affects placentation, potentially leading to obstetric complications. Current findings suggest that BPA induces pathological changes in the placenta and disrupts its metabolic activities. Based on exposure concentrations, BPA can elicit apoptotic or anti-apoptotic signals in the trophoblasts; and can exaggerate trophoblast fusion while inhibiting trophoblast migration and invasion to affect pregnancy. Accordingly, the usage of BPA products by pregnant women should be minimized and less harmful alternative chemicals should be explored and employed where possible.
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Affiliation(s)
| | - Cheryl S Rosenfeld
- Department of Biomedical Sciences, University of Missouri, Columbia, MO, USA
- Data Science and Informatics Institute, University of Missouri, Columbia, MO, USA
- Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, USA
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
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12
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Tuteja G, Soares MJ. Editorial: Multi-Omics Approaches to Study Placental Development and Disease. Front Cell Dev Biol 2021; 9:798966. [PMID: 34820389 PMCID: PMC8606685 DOI: 10.3389/fcell.2021.798966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Michael J Soares
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States.,Center for Perinatal Research, Children's Mercy Research Institute, Kansas City, MO, United States.,Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, United States
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13
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Abstract
The placenta is a temporary organ that provides the developing fetus with nutrients, oxygen, and protection in utero. Defects in its development, which may be caused by misregulated gene expression, can lead to devastating outcomes for the mother and fetus. In mouse, placental defects during midgestation commonly lead to embryonic lethality. However, the regulatory mechanisms controlling expression of genes during this period have not been thoroughly investigated. Therefore, we generated and analyzed ChIP-seq data for multiple histone modifications known to mark cis-regulatory regions. We annotated active and poised promoters and enhancers, as well as regions generally associated with repressed gene expression. We found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression. Motif analysis within active enhancers identified a large network of transcription factors, including those that have not been previously studied in the placenta and are candidates for future studies. The data generated and genomic regions annotated provide researchers with a foundation for future studies, aimed at understanding how specific genes in the midgestation mouse placenta are regulated.
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Affiliation(s)
- Rebekah R Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
| | - Haninder Kaur
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA.
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14
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Vu H, Starks RR, Kaur H, Tuteja G. Using transcriptome, active enhancer and open chromatin data to define regulatory networks in the placenta. Placenta 2021. [DOI: 10.1016/j.placenta.2021.07.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Scott RL, Vu THH, Jane A, Iqbal K, Tuteja G, Soares MJ. Trophoblast and Maternal Cell Populations Within the Uterine-Placental Interface. Placenta 2021. [DOI: 10.1016/j.placenta.2021.07.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Mesa AM, Mao J, Medrano TI, Bivens NJ, Jurkevich A, Tuteja G, Cooke PS, Rosenfeld CS. Spatial Transcriptomics analysis of uterine gene expression in enhancer of Zeste homolog 2 (Ezh2) conditional knockout mice. Biol Reprod 2021; 105:1126-1139. [PMID: 34344022 DOI: 10.1093/biolre/ioab147] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
Histone proteins undergo various modifications that alter chromatin structure, including addition of methyl groups. Enhancer of homolog 2 (EZH2), is a histone methyltransferase that methylates lysine residue 27, and thereby, suppresses gene expression. EZH2 plays integral role in the uterus and other reproductive organs. We have previously shown that conditional deletion of uterine EZH2 results in increased proliferation of luminal and glandular epithelial cells, and RNAseq analyses reveal several uterine transcriptomic changes in Ezh2 conditional (c) knockout (KO) mice that can affect estrogen signaling pathways. To pinpoint the origin of such gene expression changes, we used the recently developed spatial transcriptomics (ST) method with the hypotheses that Ezh2cKO mice would predominantly demonstrate changes in epithelial cells and/or ablation of this gene would disrupt normal epithelial/stromal gene expression patterns. Uteri were collected from ovariectomized adult WT and Ezh2cKO mice and analyzed by ST. Asb4, Cxcl14, Dio2, and Igfbp5 were increased, Sult1d1, Mt3, and Lcn2 were reduced in Ezh2cKO uterine epithelium vs. WT epithelium. For Ezh2cKO uterine stroma, differentially expressed key hub genes included Cald1, Fbln1, Myh11, Acta2, and Tagln. Conditional loss of uterine Ezh2 also appears to shift the balance of gene expression profiles in epithelial vs. stromal tissue toward uterine epithelial cell and gland development and proliferation, consistent with uterine gland hyperplasia in these mice. Current findings provide further insight into how EZH2 may selectively affect uterine epithelial and stromal compartments. Additionally, these transcriptome data might provide the mechanistic understanding and valuable biomarkers for human endometrial disorders with epigenetic underpinnings.
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Affiliation(s)
- Ana M Mesa
- Department of Physiological Sciences, University of Florida, Gainesville, FL 32610, USA.,Grupo de Investigación en Agrociencias, Biodiversidad y Territorio - GAMMA, Facultad de Ciencias Agrarias, Universidad de Antioquia UdeA, Calle 70 N° 52-21, Medellín, Colombia
| | - Jiude Mao
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Biomedical Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Theresa I Medrano
- Department of Physiological Sciences, University of Florida, Gainesville, FL 32610, USA
| | - Nathan J Bivens
- Genomics Technology, University of Missouri, Columbia, MO 65211, USA
| | - Alexander Jurkevich
- Advanced Light Microscopy Core Facility, University of Missouri, Columbia, MO 65211, USA
| | - Geetu Tuteja
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Paul S Cooke
- Department of Physiological Sciences, University of Florida, Gainesville, FL 32610, USA
| | - Cheryl S Rosenfeld
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Biomedical Sciences, University of Missouri, Columbia, MO 65211, USA.,Data Science and Informatics Institute, University of Missouri, Columbia; MO 65211, USA.,Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, 65211, USA
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17
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Khan T, Seetharam AS, Zhou J, Bivens NJ, Schust DJ, Ezashi T, Tuteja G, Roberts RM. Single Nucleus RNA Sequence (snRNAseq) Analysis of the Spectrum of Trophoblast Lineages Generated From Human Pluripotent Stem Cells in vitro. Front Cell Dev Biol 2021; 9:695248. [PMID: 34368143 PMCID: PMC8334858 DOI: 10.3389/fcell.2021.695248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/21/2021] [Indexed: 02/03/2023] Open
Abstract
One model to study the emergence of the human trophoblast (TB) has been the exposure of pluripotent stem cells to bone morphogenetic protein 4 (BMP4) in presence of inhibitors of ACTIVIN/TGFB; A83-01 and FGF2; PD173074 (BAP), which generates a mixture of cytotrophoblast, syncytiotrophoblast, and cells with similarities to extravillous trophoblast. Here, H1 human embryonic stem cells were BAP-exposed under two O2 conditions (20% and 5%, respectively). At day 8, single nuclei RNA sequencing was used for transcriptomics analysis, thereby allowing profiling of fragile syncytial structures as well as the more resilient mononucleated cells. Following cluster analysis, two major groupings, one comprised of five (2,4,6,7,8) and the second of three (1,3,5) clusters were evident, all of which displayed recognized TB markers. Of these, two (2 and 3) weakly resembled extravillous trophoblast, two (5 and 6) strongly carried the hallmark transcripts of syncytiotrophoblast, while the remaining five were likely different kinds of mononucleated cytotrophoblast. We suggest that the two populations of nuclei within syncytiotrophoblast may have arisen from fusion events involving two distinct species of precursor cells. The number of differentially expressed genes between O2 conditions varied among the clusters, and the number of genes upregulated in cells cultured under 5% O2 was highest in syncytiotrophoblast cluster 6. In summary, the BAP model reveals an unexpectedly complex picture of trophoblast lineage emergence that will need to be resolved further in time-course studies.
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Affiliation(s)
- Teka Khan
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Jie Zhou
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, United States
| | - Nathan J. Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, United States
| | - Danny J. Schust
- Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, United States
| | - Toshihiko Ezashi
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Geetu Tuteja
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - R. Michael Roberts
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
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18
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Starks RR, Abu Alhasan R, Kaur H, Pennington KA, Schulz LC, Tuteja G. Transcription Factor PLAGL1 Is Associated with Angiogenic Gene Expression in the Placenta. Int J Mol Sci 2020; 21:ijms21218317. [PMID: 33171905 PMCID: PMC7664191 DOI: 10.3390/ijms21218317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
During pregnancy, the placenta is important for transporting nutrients and waste between the maternal and fetal blood supply, secreting hormones, and serving as a protective barrier. To better understand placental development, we must understand how placental gene expression is regulated. We used RNA-seq data and ChIP-seq data for the enhancer associated mark, H3k27ac, to study gene regulation in the mouse placenta at embryonic day (e) 9.5, when the placenta is developing a complex network of blood vessels. We identified several upregulated transcription factors with enriched binding sites in e9.5-specific enhancers. The most enriched transcription factor, PLAGL1 had a predicted motif in 233 regions that were significantly associated with vasculature development and response to insulin stimulus genes. We then performed several experiments using mouse placenta and a human trophoblast cell line to understand the role of PLAGL1 in placental development. In the mouse placenta, Plagl1 is expressed in endothelial cells of the labyrinth layer and is differentially expressed in placentas from mice with gestational diabetes compared to placentas from control mice in a sex-specific manner. In human trophoblast cells, siRNA knockdown significantly decreased expression of genes associated with placental vasculature development terms. In a tube assay, decreased PLAGL1 expression led to reduced cord formation. These results suggest that Plagl1 regulates overlapping gene networks in placental trophoblast and endothelial cells, and may play a critical role in placental development in normal and complicated pregnancies.
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Affiliation(s)
- Rebekah R. Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Rabab Abu Alhasan
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
| | - Haninder Kaur
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
| | | | - Laura C. Schulz
- Obstetrics, Gynecology and Women’s Health, University of Missouri, Columba, MO 65212, USA;
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
- Correspondence:
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19
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Green MT, Martin RE, Kinkade JA, Schmidt RR, Bivens NJ, Tuteja G, Mao J, Rosenfeld CS. Maternal oxycodone treatment causes pathophysiological changes in the mouse placenta. Placenta 2020; 100:96-110. [PMID: 32891007 PMCID: PMC8112023 DOI: 10.1016/j.placenta.2020.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Pregnant women are increasingly being prescribed and abusing opioid drugs. As the primary communication organ between mother and conceptus, the placenta may be vulnerable to opioid effects but also holds the key to better understanding how these drugs affect long-term offspring health. We hypothesized that maternal treatment with oxycodone (OXY), the primary opioid at the center of the current crisis, deleteriously affects placental structure and gene expression patterns. METHODS Female mice were treated daily with 5 mg OXY/kg or saline solution (Control, CTL) for two weeks prior to breeding and until placenta were collected at embryonic age 12.5. A portion of the placenta was fixed for histology, and the remainder was frozen for RNA isolation followed by RNAseq. RESULTS Maternal OXY treatment reduced parietal trophoblast giant cell (pTGC) area and decreased the maternal blood vessel area within the labyrinth region. OXY exposure affected placental gene expression profiles in a sex dependent manner with female placenta showing up-regulation of many placental enriched genes, including Ceacam11, Ceacam14, Ceacam12, Ceacam13, Prl7b1, Prl2b1, Ctsq, and Tpbpa. In contrast, placenta of OXY exposed males had alteration of many ribosomal proteins. Weighted correlation network analysis revealed that in OXY female vs. CTL female comparison, select modules correlated with OXY-induced placental histological changes. Such associations were lacking in the male OXY vs. CTL male comparison. DISCUSSION Results suggest OXY exposure alters placental histology. In response to OXY exposure, female placenta responds by upregulating placental enriched transcripts that are either unchanged or downregulated in male placenta. Such changes may shield female offspring from developmental origins of health and disease-based diseases.
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Affiliation(s)
- Madison T Green
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Rachel E Martin
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jessica A Kinkade
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert R Schmidt
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, 65211, USA
| | - Geetu Tuteja
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jiude Mao
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Cheryl S Rosenfeld
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA; Informatics Institute, University of Missouri, Columbia, MO, 65211, USA; Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, 65211, USA; Genetics Area Program, University of Missouri, Columbia, MO, 65211, USA.
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20
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Jain A, Tuteja G. TissueEnrich: Tissue-specific gene enrichment analysis. Bioinformatics 2020; 35:1966-1967. [PMID: 30346488 DOI: 10.1093/bioinformatics/bty890] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/11/2018] [Accepted: 10/19/2018] [Indexed: 01/13/2023] Open
Abstract
SUMMARY RNA-Seq data analysis results in lists of genes that may have a similar function, based on differential gene expression analysis or co-expression network analysis. While tools have been developed to identify biological processes that are enriched in the genes sets, there remains a need for tools that identify enrichment of tissue-specific genes. Therefore, we developed TissueEnrich, a tool that calculates tissue-specific gene enrichment in an input gene set. We demonstrated that TissueEnrich can assign tissue identities to single cell clusters and differentiated embryonic stem cells. AVAILABILITY AND IMPLEMENTATION The TissueEnrich web application is freely available at http://tissueenrich.gdcb.iastate.edu/. The R package is available through Bioconductor at https://bioconductor.org/packages/TissueEnrich. Both the web application and R package are for non-profit academic use under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ashish Jain
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.,Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Geetu Tuteja
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.,Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
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21
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Mao J, Jain A, Denslow ND, Nouri MZ, Chen S, Wang T, Zhu N, Koh J, Sarma SJ, Sumner BW, Lei Z, Sumner LW, Bivens NJ, Roberts RM, Tuteja G, Rosenfeld CS. Bisphenol A and bisphenol S disruptions of the mouse placenta and potential effects on the placenta-brain axis. Proc Natl Acad Sci U S A 2020; 117:4642-4652. [PMID: 32071231 PMCID: PMC7060676 DOI: 10.1073/pnas.1919563117] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Placental trophoblast cells are potentially at risk from circulating endocrine-disrupting chemicals, such as bisphenol A (BPA). To understand how BPA and the reputedly more inert bisphenol S (BPS) affect the placenta, C57BL6J mouse dams were fed 200 μg/kg body weight BPA or BPS daily for 2 wk and then bred. They continued to receive these chemicals until embryonic day 12.5, whereupon placental samples were collected and compared with unexposed controls. BPA and BPS altered the expression of an identical set of 13 genes. Both exposures led to a decrease in the area occupied by spongiotrophoblast relative to trophoblast giant cells (GCs) within the junctional zone, markedly reduced placental serotonin (5-HT) concentrations, and lowered 5-HT GC immunoreactivity. Concentrations of dopamine and 5-hydroxyindoleacetic acid, the main metabolite of serotonin, were increased. GC dopamine immunoreactivity was increased in BPA- and BPS-exposed placentas. A strong positive correlation between 5-HT+ GCs and reductions in spongiotrophoblast to GC area suggests that this neurotransmitter is essential for maintaining cells within the junctional zone. In contrast, a negative correlation existed between dopamine+ GCs and reductions in spongiotrophoblast to GC area ratio. These outcomes lead to the following conclusions. First, BPS exposure causes almost identical placental effects as BPA. Second, a major target of BPA/BPS is either spongiotrophoblast or GCs within the junctional zone. Third, imbalances in neurotransmitter-positive GCs and an observed decrease in docosahexaenoic acid and estradiol, also occurring in response to BPA/BPS exposure, likely affect the placental-brain axis of the developing mouse fetus.
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Affiliation(s)
- Jiude Mao
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
- Biomedical Sciences, University of Missouri, Columbia, MO 65211
| | - Ashish Jain
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
| | - Nancy D Denslow
- Physiological Sciences, University of Florida, Gainesville, FL 32611
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611
| | - Mohammad-Zaman Nouri
- Physiological Sciences, University of Florida, Gainesville, FL 32611
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610
- Proteomics and Mass Spectrometry Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - Tingting Wang
- Proteomics and Mass Spectrometry Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - Ning Zhu
- Proteomics and Mass Spectrometry Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - Jin Koh
- Proteomics and Mass Spectrometry Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - Saurav J Sarma
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
- University of Missouri Metabolomics Center, University of Missouri, Columbia, MO 65211
| | - Barbara W Sumner
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
- University of Missouri Metabolomics Center, University of Missouri, Columbia, MO 65211
| | - Zhentian Lei
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
- University of Missouri Metabolomics Center, University of Missouri, Columbia, MO 65211
- Biochemistry, University of Missouri, Columbia, MO 65211
| | - Lloyd W Sumner
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
- University of Missouri Metabolomics Center, University of Missouri, Columbia, MO 65211
- Biochemistry, University of Missouri, Columbia, MO 65211
| | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO 65211
| | - R Michael Roberts
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211;
- Biochemistry, University of Missouri, Columbia, MO 65211
- Animal Sciences, University of Missouri, Columbia, MO 65211
| | - Geetu Tuteja
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011;
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
| | - Cheryl S Rosenfeld
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211;
- Biomedical Sciences, University of Missouri, Columbia, MO 65211
- Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO 65211
- University of Missouri Informatics Institute, University of Missouri, Columbia, MO 65211
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22
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Abstract
The condition of the placenta is a determinant of the short- and long-term health of the mother and the fetus. However, critical processes occurring in early placental development, such as trophoblast invasion and establishment of placental metabolism, remain poorly understood. To gain a better understanding of the genes involved in regulating these processes, we utilized a multiomics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental time points. We found that incorporating information from both the transcriptome and proteome identifies genes associated with time point-specific biological processes, unlike using the proteome alone. We further inferred genes upregulated on the basis of the proteome data but not the transcriptome data at each time point, leading us to identify 27 genes that we predict to have a role in trophoblast migration or placental metabolism. Finally, using the phosphoproteome data set, we discovered novel phosphosites that may play crucial roles in the regulation of placental transcription factors. By generating the largest proteome and phosphoproteome data sets in the developing placenta, and integrating transcriptome analysis, we uncovered novel aspects of placental gene regulation.
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Affiliation(s)
- Majd Abdulghani
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Haninder Kaur
- Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Justin W Walley
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Geetu Tuteja
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
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23
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Starks RR, Biswas A, Jain A, Tuteja G. Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. Epigenetics Chromatin 2019; 12:16. [PMID: 30795793 PMCID: PMC6385419 DOI: 10.1186/s13072-019-0260-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The assay for transposase-accessible chromatin (ATAC-seq) is a powerful method to examine chromatin accessibility. While many studies have reported a positive correlation between gene expression and promoter accessibility, few have investigated the genes that deviate from this trend. In this study, we aimed to understand the relationship between gene expression and promoter accessibility in multiple cell types while also identifying gene regulatory networks in the placenta, an understudied organ that is critical for a successful pregnancy. RESULTS We started by assaying the open chromatin landscape in the mid-gestation placenta, when the fetal vasculature has started developing. After incorporating transcriptomic data generated in the placenta at the same time point, we grouped genes based on their expression levels and ATAC-seq promoter coverage. We found that the genes with the strongest correlation (high expression and high coverage) are likely involved in housekeeping functions, whereas tissue-specific genes were highly expressed and had only medium-low coverage. We also predicted that genes with medium-low expression and high promoter coverage were actively repressed. Within this group, we extracted a protein-protein interaction network enriched for neuronal functions, likely preventing the cells from adopting a neuronal fate. We further confirmed that a repressive histone mark is bound to the promoters of genes in this network. Finally, we ran our pipeline using ATAC-seq and RNA-seq data generated in ten additional cell types. We again found that genes with the strongest correlation are enriched for housekeeping functions and that genes with medium-low promoter coverage and high expression are more likely to be tissue-specific. These results demonstrate that only two data types, both of which require relatively low starting material to generate and are becoming more commonly available, can be integrated to understand multiple aspects of gene regulation. CONCLUSIONS Within the placenta, we identified an active placenta-specific gene network as well as a repressed neuronal network. Beyond the placenta, we demonstrate that ATAC-seq data and RNA-seq data can be integrated to identify tissue-specific genes and actively repressed gene networks in multiple cell types.
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Affiliation(s)
- Rebekah R Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
| | - Anilisa Biswas
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Molecular, Cellular, and Developmental Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ashish Jain
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA. .,Molecular, Cellular, and Developmental Biology, Iowa State University, Ames, IA, 50011, USA.
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Jain A, Ezashi T, Roberts RM, Tuteja G. Deciphering transcriptional regulation in human embryonic stem cells specified towards a trophoblast fate. Sci Rep 2017; 7:17257. [PMID: 29222466 PMCID: PMC5722916 DOI: 10.1038/s41598-017-17614-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
Differentiated human embryonic stem cells (hESC) continue to provide a model for studying early trophoblast cells (TB), but many questions have been raised regarding their true identity. Therefore, we carried out a global and unbiased analysis on previously published transcriptomic profiles for hESC differentiated to TB by means of bone morphogenetic protein-4 and inhibitors of activin A and fibroblast growth factor-2 signaling (BAP treatment). Our results confirm that BAP treated hESC (ESCd) lack a mesoderm signature and are a subtype of placental cells unlike those present at term. ESCd display a high level of expression of genes implicated in migration and invasion compared to commonly used, immortalized TB cell lines and primary cells from term placenta. Co-expression network analysis also identified gene modules involved in cell migration and adhesion, processes that are likely critical during the beginning stages of placentation. Finally, protein-protein interaction analysis predicted several additional genes that may play important roles in early stages of placental development. Together, our analyses provide novel insights into the transcriptional programs that are active in ESCd.
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Affiliation(s)
- Ashish Jain
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.,Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Toshihiko Ezashi
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - R Michael Roberts
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Geetu Tuteja
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA. .,Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
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Tran Q, Strong J, Al Rebh H, Gatz J, Pope K, Jenkins R, Nguyen T, Tuteja G, Vuchula S, Chang WT. 123 Emergency Providers Adequately Manage Mechanical Ventilation in Critically Ill Patients With Spontaneous Intracranial Hemorrhage and Elevated Intracranial Pressure. Ann Emerg Med 2017. [DOI: 10.1016/j.annemergmed.2017.07.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Albrecht C, Baker JC, Blundell C, Chavez SL, Carbone L, Chamley L, Hannibal RL, Illsley N, Kurre P, Laurent LC, McKenzie C, Morales-Prieto D, Pantham P, Paquette A, Powell K, Price N, Rao BM, Sadovsky Y, Salomon C, Tuteja G, Wilson S, O'Tierney-Ginn PF. IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems. Placenta 2017; 60 Suppl 1:S5-S9. [PMID: 28108031 DOI: 10.1016/j.placenta.2017.01.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 11/17/2022]
Abstract
Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2016 there were twelve themed workshops, four of which are summarized in this report. These workshops covered innovative technologies applied to new and traditional areas of placental research: 1) genomic communication; 2) bioinformatics; 3) trophoblast biology and pathology; 4) placental transport systems.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peter Kurre
- Oregon Health and Science University, Oregon, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - P F O'Tierney-Ginn
- Center for Reproductive Health, MetroHealth Medical Center, Case Western Reserve University, Cleveland, OH, USA.
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Starks R, Tuteja G. Integrating multi-dimensional genomics data to build regulatory maps of placental development. Placenta 2016. [DOI: 10.1016/j.placenta.2016.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Yu W, Tuteja G, Hong Y, Ratri A, Borosha S, Wolfe M, Rumi M. Regulation of SATB homeobox 1 gene expression in trophoblast stem cells. Placenta 2016. [DOI: 10.1016/j.placenta.2016.06.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Tuteja G, Chung T, Bejerano G. Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. Placenta 2015; 37:45-55. [PMID: 26604129 DOI: 10.1016/j.placenta.2015.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Trophoblast invasion establishes adequate blood flow between mother and fetus in early placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. We aimed to identify enhancer elements that are active during trophoblast invasion, and build a trophoblast invasion gene-enhancer network. METHODS We carried out ChIP-Seq for an enhancer-associated mark (H3k27Ac) at two time points during early placental development in mouse. One time point when invasion is at its peak (e7.5) and another time point shortly afterwards (e9.5). We use computational analysis to identify putative enhancers, as well as the transcription factor binding sites within them, that are specific to the time point of trophoblast invasion. RESULTS We compared read profiles at e7.5 and e9.5 to identify 1,977 e7.5-specific enhancers. Within a subset of e7.5-specific enhancers, we discovered a cell migration associated regulatory code, consisting of three transcription factor motifs: AP1, Ets, and Tcfap2. To validate differential expression of the transcription factors that bind these motifs, we performed RNA-Seq in the same context. Finally, we integrated these data with publicly available protein-protein interaction data and constructed a trophoblast invasion gene-enhancer network. DISCUSSION The data we generated and analysis we carried out improves our understanding of the regulatory mechanisms of trophoblast invasion, by suggesting a transcriptional code exists in the enhancers of cell migration genes. Furthermore, the network we constructed highlights novel candidate genes that may be critical for trophoblast invasion.
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Affiliation(s)
- Geetu Tuteja
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tisha Chung
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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Tuteja G, Bejerano G. Assaying the enhancer landscape during early placental development to identify a trophoblast invasion transcriptional code and gene-enhancer network. Placenta 2015. [DOI: 10.1016/j.placenta.2015.07.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G. Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. PLoS Comput Biol 2014; 10:e1003449. [PMID: 24499934 PMCID: PMC3907286 DOI: 10.1371/journal.pcbi.1003449] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/09/2013] [Indexed: 12/01/2022] Open
Abstract
Identifying enhancers regulating gene expression remains an important and challenging task. While recent sequencing-based methods provide epigenomic characteristics that correlate well with enhancer activity, it remains onerous to comprehensively identify all enhancers across development. Here we introduce a computational framework to identify tissue-specific enhancers evolving under purifying selection. First, we incorporate high-confidence binding site predictions with target gene functional enrichment analysis to identify transcription factors (TFs) likely functioning in a particular context. We then search the genome for clusters of binding sites for these TFs, overcoming previous constraints associated with biased manual curation of TFs or enhancers. Applying our method to the placenta, we find 33 known and implicate 17 novel TFs in placental function, and discover 2,216 putative placenta enhancers. Using luciferase reporter assays, 31/36 (86%) tested candidates drive activity in placental cells. Our predictions agree well with recent epigenomic data in human and mouse, yet over half our loci, including 7/8 (87%) tested regions, are novel. Finally, we establish that our method is generalizable by applying it to 5 additional tissues: heart, pancreas, blood vessel, bone marrow, and liver. Enhancers are distal gene regulatory elements that can activate tissue- and time-point specific gene expression. Identification of active enhancers is challenging, and is the subject of intense investigation. We developed an automated computational framework to predict transcription factors (TFs) and enhancers that target a tissue of interest by combining two growing resources: TF binding motifs and target gene function annotations. We applied our framework to the placenta, and confirmed our enhancer predictions are more active in placental cell types than others. To demonstrate generalizability, we applied our approach to 5 additional tissues. The combination of experimental sampling with computational prediction approaches will aid in the identification of those enhancers that are most likely active in a particular tissue, as well as the characterization of groups of TFs associated with these enhancers.
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Affiliation(s)
- Geetu Tuteja
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Karen Betancourt Moreira
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Tisha Chung
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Jenny Chen
- Biomedical Informatics Program, Stanford University, Stanford, California, United States of America
| | - Aaron M. Wenger
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- Department of Computer Science, Stanford University, Stanford, California, United States of America
- * E-mail:
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Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G. The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genet 2013; 9:e1003728. [PMID: 24009522 PMCID: PMC3757057 DOI: 10.1371/journal.pgen.1003728] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 07/03/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. Over 95% of the peaks we measure are conserved to human. Eight of ten (80%) candidates tested using mouse transgenesis drive activity in restricted laminar patterns within the neocortex. GREAT based computational analysis reveals highly significant correlation with genes expressed at E14.5 in key areas for neocortex development, and allows the grouping of enhancers by known biological functions and pathways for further studies. We find that multiple genes are flanked by dozens of candidate enhancers each, including well-known key neocortical genes as well as suspected and novel genes. Nearly a quarter of our candidate enhancers are conserved well beyond mammals. Human and zebrafish regions orthologous to our candidate enhancers are shown to most often function in other aspects of central nervous system development. Finally, we find strong evidence that specific interspersed repeat families have contributed potentially key developmental enhancers via co-option. Our analysis expands the methodologies available for extracting the richness of information found in genome-wide functional maps.
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Affiliation(s)
- Aaron M. Wenger
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Shoa L. Clarke
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - James H. Notwell
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Tisha Chung
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Geetu Tuteja
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Harendra Guturu
- Department of Electrical Engineering, Stanford University, Stanford, California, United States of America
| | - Bruce T. Schaar
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell 2013; 151:1608-16. [PMID: 23260146 DOI: 10.1016/j.cell.2012.11.018] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 08/30/2012] [Accepted: 11/01/2012] [Indexed: 10/27/2022]
Abstract
Nucleosome occupancy is fundamental for establishing chromatin architecture. However, little is known about the relationship between nucleosome dynamics and initial cell lineage specification. Here, we determine the mechanisms that control global nucleosome dynamics during embryonic stem (ES) cell differentiation into endoderm. Both nucleosome depletion and de novo occupation occur during the differentiation process, with higher overall nucleosome density after differentiation. The variant histone H2A.Z and the winged helix transcription factor Foxa2 both act to regulate nucleosome depletion and gene activation, thus promoting ES cell differentiation, whereas DNA methylation promotes nucleosome occupation and suppresses gene expression. Nucleosome depletion during ES cell differentiation is dependent on Nap1l1-coupled SWI/SNF and INO80 chromatin remodeling complexes. Thus, both epigenetic and genetic regulators cooperate to control nucleosome dynamics during ES cell fate decisions.
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Affiliation(s)
- Zhaoyu Li
- Department of Genetics and Institute of Diabetes, Obesity and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Li Z, Tuteja G, Schug J, Kaestner KH. Abstract 5112: Foxa1 and Foxa2 are essential for gender dimorphism in liver cancer. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hepatocellular carcinoma (HCC) is sexually dimorphic in both rodents and humans, with significantly higher incidence in males, an effect that is dependent on sex hormones. The molecular mechanisms by which estrogens prevent and androgens promote liver cancer remain unclear. Here, we discover that sexually-dimorphic HCC is completely reversed in Foxa1- and Foxa2-deficient mice after diethylnitrosamine-induced hepatocarcinogenesis. Co-regulation of target genes by Foxa1/a2 and either the estrogen receptor (ERalpha) or the androgen receptor (AR) was increased during hepatocarcinogenesis in normal female or male mice, respectively, but was lost in Foxa1/2-deficient mice. Thus, both estrogen-dependent resistance to and androgen-mediated facilitation of HCC depend on Foxa1/2. Strikingly, single nucleotide polymorphisms at FOXA2 binding sites reduce binding of both FOXA2 and ERalpha to their targets in human liver, and correlate with HCC development in women. Thus, Foxa factors and their targets are central for the sexual dimorphism of HCC. (Cell, accepted in press)
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5112. doi:1538-7445.AM2012-5112
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Affiliation(s)
- Zhaoyu Li
- 1University of Pennsylvania, Philadelphia, PA
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Tuteja G, Rout C, Bishnoi N. Quantification of Polycyclic Aromatic Hydrocarbons in Leafy and Underground Vegetables: A Case Study Around Panipat City, Haryana, India. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/jest.2011.611.620] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Soccio RE, Tuteja G, Everett LJ, Li Z, Lazar MA, Kaestner KH. Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol 2011; 25:694-706. [PMID: 21292830 DOI: 10.1210/me.2010-0454] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The winged helix protein FOXA2 and the nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) are highly conserved, regionally expressed transcription factors (TFs) that regulate networks of genes controlling complex metabolic functions. Cistrome analysis for Foxa2 in mouse liver and PPARγ in mouse adipocytes has previously produced consensus-binding sites that are nearly identical to those used by the corresponding TFs in human cells. We report here that, despite the conservation of the canonical binding motif, the great majority of binding regions for FOXA2 in human liver and for PPARγ in human adipocytes are not in the orthologous locations corresponding to the mouse genome, and vice versa. Of note, TF binding can be absent in one species despite sequence conservation, including motifs that do support binding in the other species, demonstrating a major limitation of in silico binding site prediction. Whereas only approximately 10% of binding sites are conserved, gene-centric analysis reveals that about 50% of genes with nearby TF occupancy are shared across species for both hepatic FOXA2 and adipocyte PPARγ. Remarkably, for both TFs, many of the shared genes function in tissue-specific metabolic pathways, whereas species-unique genes fail to show enrichment for these pathways. Nonetheless, the species-unique genes, like the shared genes, showed the expected transcriptional regulation by the TFs in loss-of-function experiments. Thus, species-specific strategies underlie the biological functions of metabolic TFs that are highly conserved across mammalian species. Analysis of factor binding in multiple species may be necessary to distinguish apparent species-unique noise and reveal functionally relevant information.
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Affiliation(s)
- Raymond E Soccio
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6149, USA
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Abstract
ChIP-Seq technology, which combines chromatin immunoprecipitation (ChIP) with massively parallel sequencing, is rapidly replacing ChIP-on-chip for the genome-wide identification of transcription factor binding events. Identifying bound regions from the large number of sequence tags produced by ChIP-Seq is a challenging task. Here, we present GLITR (GLobal Identifier of Target Regions), which accurately identifies enriched regions in target data by calculating a fold-change based on random samples of control (input chromatin) data. GLITR uses a classification method to identify regions in ChIP data that have a peak height and fold-change which do not resemble regions in an input sample. We compare GLITR to several recent methods and show that GLITR has improved sensitivity for identifying bound regions closely matching the consensus sequence of a given transcription factor, and can detect bona fide transcription factor targets missed by other programs. We also use GLITR to address the issue of sequencing depth, and show that sequencing biological replicates identifies far more binding regions than re-sequencing the same sample.
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Affiliation(s)
| | | | | | - Klaus H. Kaestner
- *To whom correspondence should be addressed. Tel: +215 898 8759; Fax: +215 573 5892;
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Li Z, White P, Tuteja G, Rubins N, Sackett S, Kaestner KH. Foxa1 and Foxa2 regulate bile duct development in mice. J Clin Invest 2009; 119:1537-45. [PMID: 19436110 DOI: 10.1172/jci38201] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 03/10/2009] [Indexed: 01/01/2023] Open
Abstract
The forkhead box proteins A1 and A2 (Foxa1 and Foxa2) are transcription factors with critical roles in establishing the developmental competence of the foregut endoderm and in initiating liver specification. Using conditional gene ablation during a later phase of liver development, we show here that deletion of both Foxa1 and Foxa2 (Foxa1/2) in the embryonic liver caused hyperplasia of the biliary tree. Abnormal bile duct formation in Foxa1/2-deficient liver was due, at least in part, to activation of IL-6 expression, a proliferative signal for cholangiocytes. The glucocorticoid receptor is a negative regulator of IL-6 transcription; in the absence of Foxa1/2, the glucocorticoid receptor failed to bind to the IL-6 promoter, causing enhanced IL-6 expression. Thus, after liver specification, Foxa1/2 are required for normal bile duct development through prevention of excess cholangiocyte proliferation. Our data suggest that Foxa1/2 function as terminators of bile duct expansion in the adult liver through inhibition of IL-6 expression.
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Affiliation(s)
- Zhaoyu Li
- Department of Genetics and Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6145, USA
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Tuteja G, Jensen ST, White P, Kaestner KH. Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Res 2008; 36:4149-57. [PMID: 18556755 PMCID: PMC2475634 DOI: 10.1093/nar/gkn366] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Foxa2 is a critical transcription factor that controls liver development and plays an important role in hepatic gluconeogensis in adult mice. Here, we use genome-wide location analysis for Foxa2 to identify its targets in the adult liver. We then show by computational analyses that Foxa2 containing cis-regulatory modules are not constructed from a random assortment of binding sites for other transcription factors expressed in the liver, but rather that their composition depends on the strength of the Foxa2 consensus site present. Genes containing a cis-regulatory module with a medium or weak Foxa2 consensus site are much more liver-specific than the genes with a strong consensus site. We not only provide a better understanding of the mechanisms of Foxa2 regulation but also introduce a novel method for identification of different cis-regulatory modules involving a single factor.
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Affiliation(s)
- Geetu Tuteja
- Department of Genetics, Genomics and Computational Biology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Affiliation(s)
- Geetu Tuteja
- Department of Genetics, University fo Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Affiliation(s)
- Geetu Tuteja
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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