1
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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2
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Ravi Sundar Jose Geetha A, Fischer K, Babadei O, Smesnik G, Vogt A, Platanitis E, Müller M, Farlik M, Decker T. Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling. EMBO J 2024; 43:2233-2263. [PMID: 38658796 PMCID: PMC11148166 DOI: 10.1038/s44318-024-00092-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Type I interferons (IFN-I, including IFNβ) and IFNγ produce overlapping, yet clearly distinct immunological activities. Recent data show that the distinctness of global transcriptional responses to the two IFN types is not apparent when comparing their immediate effects. By analyzing nascent transcripts induced by IFN-I or IFNγ over a period of 48 h, we now show that the distinctiveness of the transcriptomes emerges over time and is based on differential employment of the ISGF3 complex as well as of the second-tier transcription factor IRF1. The distinct transcriptional properties of ISGF3 and IRF1 correspond with a largely diverse nuclear protein interactome. Mechanistically, we describe the specific input of ISGF3 and IRF1 into enhancer activation and the regulation of chromatin accessibility at interferon-stimulated genes (ISG). We further report differences between the IFN types in altering RNA polymerase II pausing at ISG 5' ends. Our data provide insight how transcriptional regulators create immunological identities of IFN-I and IFNγ.
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Affiliation(s)
- Aarathy Ravi Sundar Jose Geetha
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Katrin Fischer
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Olga Babadei
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Georg Smesnik
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | | | - Ekaterini Platanitis
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, 1090, Austria
| | - Thomas Decker
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria.
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria.
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3
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Ren G, Ku WL, Ge G, Hoffman JA, Kang JY, Tang Q, Cui K, He Y, Guan Y, Gao B, Liu C, Archer TK, Zhao K. Acute depletion of BRG1 reveals its primary function as an activator of transcription. Nat Commun 2024; 15:4561. [PMID: 38811575 PMCID: PMC11137027 DOI: 10.1038/s41467-024-48911-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
The mammalian SWI/SNF-like BAF complexes play critical roles during animal development and pathological conditions. Previous gene deletion studies and characterization of human gene mutations implicate that the complexes both repress and activate a large number of genes. However, the direct function of the complexes in cells remains largely unclear due to the relatively long-term nature of gene deletion or natural mutation. Here we generate a mouse line by knocking in the auxin-inducible degron tag (AID) to the Smarca4 gene, which encodes BRG1, the essential ATPase subunit of the BAF complexes. We show that the tagged BRG1 can be efficiently depleted by osTIR1 expression and auxin treatment for 6 to 10 h in CD4 + T cells, hepatocytes, and fibroblasts isolated from the knock-in mice. The acute depletion of BRG1 leads to decreases in nascent RNAs and RNA polymerase II binding at a large number of genes, which are positively correlated with the loss of BRG1. Further, these changes are correlated with diminished accessibility at DNase I Hypersensitive Sites (DHSs) and p300 binding. The acute BRG1 depletion results in three major patterns of nucleosome shifts leading to narrower nucleosome spacing surrounding transcription factor motifs and at enhancers and transcription start sites (TSSs), which are correlated with loss of BRG1, decreased chromatin accessibility and decreased nascent RNAs. Acute depletion of BRG1 severely compromises the Trichostatin A (TSA) -induced histone acetylation, suggesting a substantial interplay between the chromatin remodeling activity of BRG1 and histone acetylation. Our data suggest BRG1 mainly plays a direct positive role in chromatin accessibility, RNAPII binding, and nascent RNA production by regulating nucleosome positioning and facilitating transcription factor binding to their target sites.
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Affiliation(s)
- Gang Ren
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
- College of Animal Science and Technology, Northwest Agriculture and Forest University, Yangling, Xianyang, Shaanxi, China
| | - Wai Lim Ku
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Guangzhe Ge
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Jee Youn Kang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Qingsong Tang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Yong He
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Yukun Guan
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.
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4
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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5
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Segev A, Heady L, Crewe M, Madabhushi R. Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome. Cell Rep 2024; 43:113809. [PMID: 38377005 PMCID: PMC11064056 DOI: 10.1016/j.celrep.2024.113809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
We trapped catalytically engaged topoisomerase IIβ (TOP2B) in covalent DNA cleavage complexes (TOP2Bccs) and mapped their positions genome-wide in cultured mouse cortical neurons. We report that TOP2Bcc distribution varies with both nucleosome and compartmental chromosome organization. While TOP2Bccs in gene bodies correlate with their level of transcription, highly expressed genes that lack the usually associated chromatin marks, such as H3K36me3, show reduced TOP2Bccs, suggesting that histone posttranslational modifications regulate TOP2B activity. Promoters with high RNA polymerase II occupancy show elevated TOP2B chromatin immunoprecipitation sequencing signals but low TOP2Bccs, indicating that TOP2B catalytic engagement is curtailed at active promoters. Surprisingly, either poisoning or inhibiting TOP2B increases nascent transcription at most genes and enhancers but reduces transcription within long genes. These effects are independent of transcript length and instead correlate with the presence of intragenic enhancers. Together, these results clarify how cells modulate the catalytic engagement of topoisomerases to affect transcription.
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Affiliation(s)
- Amir Segev
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lance Heady
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Morgan Crewe
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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6
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Liu L, Zhao Y, Siepel A. DNA-sequence and epigenomic determinants of local rates of transcription elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572932. [PMID: 38187771 PMCID: PMC10769381 DOI: 10.1101/2023.12.21.572932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Across all branches of life, transcription elongation is a crucial, regulated phase in gene expression. Many recent studies in eukaryotes have focused on the regulation of promoter-proximal pausing of RNA Polymerase II (Pol II), but rates of productive elongation also vary substantially throughout the gene body, both within and across genes. Here, we introduce a probabilistic model for systematically evaluating potential determinants of the local elongation rate based on nascent RNA sequencing (NRS) data. Our model is derived from a unified model for both the kinetics of Pol II movement along the DNA template and the generation of NRS read counts at steady state. It allows for a continuously variable elongation rate along the gene body, with the rate at each nucleotide defined by a generalized linear relationship with nearby genomic and epigenomic features. High-dimensional feature vectors are accommodated through a sparse-regression extension. We show with simulations that the model allows accurate detection of associated features and accurate prediction of local elongation rates. In an analysis of public PRO-seq and epigenomic data, we identify several features that are strongly associated with reductions in the local elongation rate, including DNA methylation, splice sites, RNA stem-loops, CTCF binding sites, and several histone marks, including H3K36me3 and H4K20me1. By contrast, low-complexity sequences and H3K79me2 marks are associated with increases in elongation rate. In an analysis of DNA k -mers, we find that cytosine nucleotides are strongly associated with reductions in local elongation rate, particularly when preceded by guanines and followed by adenines or thymines. Increases in elongation rate are associated with thymines and A+T-rich k -mers. These associations are generally shared across cell types, and by considering them our model is effective at predicting features of held-out PRO-seq data. Overall, our analysis is the first to permit genome-wide predictions of relative nucleotide-specific elongation rates based on complex sets of genomic and epigenomic covariates. We have made predictions available for the K562, CD14+, MCF-7, and HeLa-S3 cell types in a UCSC Genome Browser track.
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Affiliation(s)
- Lingjie Liu
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY
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7
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Owen DM, Kwon M, Huang X, Nagari A, Nandu T, Kraus WL. Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease†. Biol Reprod 2023; 109:965-981. [PMID: 37694817 PMCID: PMC10724456 DOI: 10.1093/biolre/ioad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 08/07/2023] [Accepted: 09/09/2023] [Indexed: 09/12/2023] Open
Abstract
The placenta is a dynamic organ that must perform a remarkable variety of functions during its relatively short existence in order to support a developing fetus. These functions include nutrient delivery, gas exchange, waste removal, hormone production, and immune barrier protection. Proper placenta development and function are critical for healthy pregnancy outcomes, but the underlying genomic regulatory events that control this process remain largely unknown. We hypothesized that mapping sites of transcriptional enhancer activity and associated changes in gene expression across gestation in human placenta tissue would identify genomic loci and predicted transcription factor activity related to critical placenta functions. We used a suite of genomic assays [i.e., RNA-sequencing (RNA-seq), Precision run-on-sequencing (PRO-seq), and Chromatin immunoprecipitation-sequencing (ChIP-seq)] and computational pipelines to identify a set of >20 000 enhancers that are active at various time points in gestation. Changes in the activity of these enhancers correlate with changes in gene expression. In addition, some of these enhancers encode risk for adverse pregnancy outcomes. We further show that integrating enhancer activity, transcription factor motif analysis, and transcription factor expression can identify distinct sets of transcription factors predicted to be more active either in early pregnancy or at term. Knockdown of selected identified transcription factors in a trophoblast stem cell culture model altered the expression of key placental marker genes. These observations provide a framework for future mechanistic studies of individual enhancer-transcription factor-target gene interactions and have the potential to inform genetic risk prediction for adverse pregnancy outcomes.
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Affiliation(s)
- David M Owen
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of General Obstetrics and Gynecology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Minjung Kwon
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuan Huang
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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8
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Zhao Y, Liu L, Hassett R, Siepel A. Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Res 2023; 51:e106. [PMID: 37889042 PMCID: PMC10681744 DOI: 10.1093/nar/gkad843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions. Here, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations, we show that this model enables accurate estimation of initiation and pause-escape rates. Furthermore, we show by simulation and analysis of real data that pause-escape is often strongly rate-limiting and that steric hindrance can dramatically reduce initiation rates. Our modeling framework is applicable to a variety of inference problems, and our software for estimation and simulation is freely available.
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Affiliation(s)
- Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lingjie Liu
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, USA
| | - Rebecca Hassett
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, USA
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9
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Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics 2023; 24:641. [PMID: 37884859 PMCID: PMC10601309 DOI: 10.1186/s12864-023-09743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. RESULTS We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. CONCLUSION The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Meghan Capeling
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan W Villanueva
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Vera D Rinaldi
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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10
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Barshad G, Lewis JJ, Chivu AG, Abuhashem A, Krietenstein N, Rice EJ, Ma Y, Wang Z, Rando OJ, Hadjantonakis AK, Danko CG. RNA polymerase II dynamics shape enhancer-promoter interactions. Nat Genet 2023; 55:1370-1380. [PMID: 37430091 DOI: 10.1038/s41588-023-01442-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/09/2023] [Indexed: 07/12/2023]
Abstract
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer-promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer-promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer-promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer-promoter communication.
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Affiliation(s)
- Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York City, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York City, NY, USA
| | - Nils Krietenstein
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yitian Ma
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Dalian, China
| | - Zhong Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Dalian, China
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York City, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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11
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Wang N, Wang Z, Danko CG, Chu T. Mapping Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway. Methods Mol Biol 2023; 2599:215-226. [PMID: 36427152 DOI: 10.1007/978-1-0716-2847-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Run-on and sequencing assays like GRO-seq, PRO-seq, and ChRO-seq allow for joint profiling of transcription activity of transcriptional regulatory elements (TREs), i.e., promoters and active enhancers, and target genes. Variation in biological conditions, such as treated vs. control, results in changes in the activity of transcription factors (TFs), which induces concerted changes in TREs and target genes. By modeling the differences between two biological conditions, we developed the computational pipeline known as tfTarget that predicts a set of putative TREs and target genes responding to each TF under the biological condition of interest. In this chapter, we demonstrate the use of the new web-based tfTarget in mapping transcription regulation using run-on sequencing data.
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Affiliation(s)
- Nating Wang
- School of Software Technology, Dalian University of Technology, Dalian, China
| | - Zhong Wang
- School of Software Technology, Dalian University of Technology, Dalian, China
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Tinyi Chu
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.
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12
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Todero JE, Koch-Laskowski K, Shi Q, Kanke M, Hung YH, Beck R, Styblo M, Sethupathy P. Candidate master microRNA regulator of arsenic-induced pancreatic beta cell impairment revealed by multi-omics analysis. Arch Toxicol 2022; 96:1685-1699. [PMID: 35314868 PMCID: PMC9095563 DOI: 10.1007/s00204-022-03263-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/17/2022] [Indexed: 02/05/2023]
Abstract
Arsenic is a pervasive environmental toxin that is listed as the top priority for investigation by the Agency for Toxic Substance and Disease Registry. While chronic exposure to arsenic is associated with type 2 diabetes (T2D), the underlying mechanisms are largely unknown. We have recently demonstrated that arsenic treatment of INS-1 832/13 pancreatic beta cells impairs glucose-stimulated insulin secretion (GSIS), a T2D hallmark. We have also shown that arsenic alters the microRNA profile of beta cells. MicroRNAs have a well-established post-transcriptional regulatory role in both normal beta cell function and T2D pathogenesis. We hypothesized that there are microRNA master regulators that shape beta cell gene expression in pathways pertinent to GSIS after exposure to arsenicals. To test this hypothesis, we first treated INS-1 832/13 beta cells with either inorganic arsenic (iAsIII) or monomethylarsenite (MAsIII) and confirmed GSIS impairment. We then performed multi-omic analysis using chromatin run-on sequencing, RNA-sequencing, and small RNA-sequencing to define profiles of transcription, gene expression, and microRNAs, respectively. Integrating across these data sets, we first showed that genes downregulated by iAsIII treatment are enriched in insulin secretion and T2D pathways, whereas genes downregulated by MAsIII treatment are enriched in cell cycle and critical beta cell maintenance factors. We also defined the genes that are subject primarily to post-transcriptional control in response to arsenicals and demonstrated that miR-29a is the top candidate master regulator of these genes. Our results highlight the importance of microRNAs in arsenical-induced beta cell dysfunction and reveal both shared and unique mechanisms between iAsIII and MAsIII.
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Affiliation(s)
- Jenna E Todero
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kieran Koch-Laskowski
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Qing Shi
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Rowan Beck
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miroslav Styblo
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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13
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Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O’Neill RJ. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 2022; 376:eabk3112. [PMID: 35357925 PMCID: PMC9301658 DOI: 10.1126/science.abk3112] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.
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Affiliation(s)
- Savannah J. Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Gabrielle A. Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Patrick G. S. Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Luke Wojenski
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Matias Rodriguez
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leighton J. Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | | | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Michael C. Schatz
- Department of Computer Science and Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Rachel J. O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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14
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Shanahan MT, Kanke M, Oyesola OO, Hung YH, Koch-Laskowski K, Singh AP, Peck BCE, Biraud M, Sheahan B, Cortes JE, Gong H, Sahoo DK, Cubitt R, Kurpios NA, Mochel JP, Allenspach K, McElroy SJ, Ding S, von Moltke J, Dekaney CM, Tait-Wojno ED, Sethupathy P. Multiomic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and reveals novel markers of almost all major cell types. Am J Physiol Gastrointest Liver Physiol 2021; 321:G668-G681. [PMID: 34643097 PMCID: PMC8887887 DOI: 10.1152/ajpgi.00222.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 01/31/2023]
Abstract
MicroRNA-mediated regulation is critical for the proper development and function of the small intestinal (SI) epithelium. However, it is not known which microRNAs are expressed in each of the cell types of the SI epithelium. To bridge this important knowledge gap, we performed comprehensive microRNA profiling in all major cell types of the mouse SI epithelium. We used flow cytometry and fluorescence-activated cell sorting with multiple reporter mouse models to isolate intestinal stem cells, enterocytes, goblet cells, Paneth cells, enteroendocrine cells, tuft cells, and secretory progenitors. We then subjected these cell populations to small RNA-sequencing. The resulting atlas revealed highly enriched microRNA markers for almost every major cell type (https://sethupathy-lab.shinyapps.io/SI_miRNA/). Several of these lineage-enriched microRNAs (LEMs) were observed to be embedded in annotated host genes. We used chromatin-run-on sequencing to determine which of these LEMs are likely cotranscribed with their host genes. We then performed single-cell RNA-sequencing to define the cell type specificity of the host genes and embedded LEMs. We observed that the two most enriched microRNAs in secretory progenitors are miR-1224 and miR-672, the latter of which we found is deleted in hominin species. Finally, using several in vivo models, we established that miR-152 is a Paneth cell-specific microRNA.NEW & NOTEWORTHY In this study, first, microRNA atlas (and searchable web server) across all major small intestinal epithelial cell types is presented. We have demonstrated microRNAs that uniquely mark several lineages, including enteroendocrine and tuft. Identification of a key marker of mouse secretory progenitor cells, miR-672, which we show is deleted in humans. We have used several in vivo models to establish miR-152 as a specific marker of Paneth cells, which are highly understudied in terms of microRNAs.
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Affiliation(s)
- Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Oyebola O Oyesola
- Department of Immunology, University of Washington, Seattle, Washington
| | - Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Kieran Koch-Laskowski
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ajeet P Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Bailey C E Peck
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Mandy Biraud
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Breanna Sheahan
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Josca E Cortes
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Huiyu Gong
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa
| | - Dipak K Sahoo
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Natasza A Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Jonathan P Mochel
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Karin Allenspach
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Steven J McElroy
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina
| | - Jakob von Moltke
- Department of Immunology, University of Washington, Seattle, Washington
| | - Christopher M Dekaney
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Elia D Tait-Wojno
- Department of Immunology, University of Washington, Seattle, Washington
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
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15
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Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A. Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics 2021; 37:4727-4736. [PMID: 34382072 PMCID: PMC8665767 DOI: 10.1093/bioinformatics/btab582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Motivation Quantification of isoform abundance has been extensively studied at the mature RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA sequencing. Results We address this problem with a new computational method called Deconvolution of Expression for Nascent RNA-sequencing data (DENR), which models nascent RNA-sequencing read-counts as a mixture of user-provided isoforms. The baseline algorithm is enhanced by machine-learning predictions of active transcription start sites and an adjustment for the typical ‘shape profile’ of read-counts along a transcription unit. We show that DENR outperforms simple read-count-based methods for estimating gene and isoform abundances, and that transcription of multiple pre-RNA isoforms per gene is widespread, with frequent differences between cell types. In addition, we provide evidence that a majority of human isoform diversity derives from primary transcription rather than from post-transcriptional processes. Availability and implementation DENR and nascentRNASim are freely available at https://github.com/CshlSiepelLab/DENR (version v1.0.0) and https://github.com/CshlSiepelLab/nascentRNASim (version v0.3.0). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Shushan Toneyan
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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16
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Hung YH, Huang S, Dame MK, Yu Q, Yu QC, Zeng YA, Camp JG, Spence JR, Sethupathy P. Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Nucleic Acids Res 2021; 49:726-744. [PMID: 33406262 PMCID: PMC7826262 DOI: 10.1093/nar/gkaa1204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The establishment of the small intestinal (SI) lineage during human embryogenesis ensures functional integrity of the intestine after birth. The chromatin dynamics that drive SI lineage formation and regional patterning in humans are essentially unknown. To fill this knowledge void, we apply a cutting-edge genomic technology to a state-of-the-art human model of early SI development. Specifically, we leverage chromatin run-on sequencing (ChRO-seq) to define the landscape of active promoters, enhancers and gene bodies across distinct stages of directed differentiation of human pluripotent stem cells into SI spheroids with regional specification. Through comprehensive ChRO-seq analysis we identify candidate stage-specific chromatin activity states, novel markers and enhancer hotspots during the directed differentiation. Moreover, we propose a detailed transcriptional network associated with SI lineage formation or regional patterning. Our ChRO-seq analyses uncover a previously undescribed pattern of enhancer activity and transcription at HOX gene loci underlying SI regional patterning. We also validated this unique HOX dynamics by the analysis of single cell RNA-seq data from human fetal SI. Overall, the results lead to a new proposed working model for the regulatory underpinnings of human SI development, thereby adding a novel dimension to the literature that has relied almost exclusively on non-human models.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael K Dame
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basal, Basel 4056, Switzerland
| | - Qing C Yu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yi A Zeng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basal, Basel 4056, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4001, Switzerland
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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17
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Mukai C, Choi E, Sams KL, Klampen EZ, Anguish L, Marks BA, Rice EJ, Wang Z, Choate LA, Chou SP, Kato Y, Miller AD, Danko CG, Coonrod SA. Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis. BMC Vet Res 2020; 16:206. [PMID: 32571313 PMCID: PMC7310061 DOI: 10.1186/s12917-020-02395-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/29/2020] [Indexed: 01/20/2023] Open
Abstract
Background Canine visceral hemangiosarcoma (HSA) is a highly aggressive cancer of endothelial origin that closely resembles visceral angiosarcoma in humans, both clinically and histopathologically. Currently there is an unmet need for new diagnostics and therapies for both forms of this disease. The goal of this study was to utilize Chromatin run-on sequencing (ChRO-seq) and immunohistochemistry (IHC) to identify gene and protein expression signatures that may be important drivers of HSA progression. Results ChRO-seq was performed on tissue isolated from 17 HSA samples and 4 normal splenic samples. Computational analysis was then used to identify differentially expressed genes and these factors were subjected to gene ontology analysis. ChRO-seq analysis revealed over a thousand differentially expressed genes in HSA tissue compared with normal splenic tissue (FDR < 0.005). Interestingly, the majority of genes overexpressed in HSA tumor tissue were associated with extracellular matrix (ECM) remodeling. This observation correlated well with our histological analysis, which found that HSA tumors contain a rich and complex collagen network. Additionally, we characterized the protein expression patterns of two highly overexpressed molecules identified in ChRO-seq analysis, podoplanin (PDPN) and laminin alpha 4 (LAMA4). We found that the expression of these two ECM-associated factors appeared to be largely limited to transformed endothelial cells within the HSA lesions. Conclusion Outcomes from this study suggest that ECM remodeling plays an important role in HSA progression. Additionally, our study identified two potential novel biomarkers of HSA, PDPN and LAMA4. Interestingly, given that function-blocking anti-PDPN antibodies have shown anti-tumor effects in mouse models of canine melanoma, our studies raise the possibility that these types of therapeutic strategies could potentially be developed for treating canine HSA.
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Affiliation(s)
- Chinatsu Mukai
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - Eunju Choi
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kelly L Sams
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elena Zu Klampen
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Lynne Anguish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Brooke A Marks
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shao-Pei Chou
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan.,New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Andrew D Miller
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Scott A Coonrod
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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18
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Gao T, Qian J. EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. Nucleic Acids Res 2020; 48:D58-D64. [PMID: 31740966 PMCID: PMC7145677 DOI: 10.1093/nar/gkz980] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/02/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023] Open
Abstract
Enhancers are distal cis-regulatory elements that activate the transcription of their target genes. They regulate a wide range of important biological functions and processes, including embryogenesis, development, and homeostasis. As more and more large-scale technologies were developed for enhancer identification, a comprehensive database is highly desirable for enhancer annotation based on various genome-wide profiling datasets across different species. Here, we present an updated database EnhancerAtlas 2.0 (http://www.enhanceratlas.org/indexv2.php), covering 586 tissue/cell types that include a large number of normal tissues, cancer cell lines, and cells at different development stages across nine species. Overall, the database contains 13 494 603 enhancers, which were obtained from 16 055 datasets using 12 high-throughput experiment methods (e.g. H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq and MPRA). The updated version is a huge expansion of the first version, which only contains the enhancers in human cells. In addition, we predicted enhancer–target gene relationships in human, mouse and fly. Finally, the users can search enhancers and enhancer–target gene relationships through five user-friendly, interactive modules. We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facilitate users to perform useful functional analysis of enhancers in various genomes.
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Affiliation(s)
- Tianshun Gao
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Jiang Qian
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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