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Kelly MR, Wisniewska K, Regner MJ, Lewis MW, Perreault AA, Davis ES, Phanstiel DH, Parker JS, Franco HL. A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer. Nat Commun 2022; 13:4247. [PMID: 35869079 PMCID: PMC9307778 DOI: 10.1038/s41467-022-31919-8] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/08/2022] [Indexed: 01/14/2023] Open
Abstract
The human genome contains regulatory elements, such as enhancers, that are often rewired by cancer cells for the activation of genes that promote tumorigenesis and resistance to therapy. This is especially true for cancers that have little or no known driver mutations within protein coding genes, such as ovarian cancer. Herein, we utilize an integrated set of genomic and epigenomic datasets to identify clinically relevant super-enhancers that are preferentially amplified in ovarian cancer patients. We systematically probe the top 86 super-enhancers, using CRISPR-interference and CRISPR-deletion assays coupled to RNA-sequencing, to nominate two salient super-enhancers that drive proliferation and migration of cancer cells. Utilizing Hi-C, we construct chromatin interaction maps that enable the annotation of direct target genes for these super-enhancers and confirm their activity specifically within the cancer cell compartment of human tumors using single-cell genomics data. Together, our multi-omic approach examines a number of fundamental questions about how regulatory information encoded into super-enhancers drives gene expression networks that underlie the biology of ovarian cancer.
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Affiliation(s)
- Michael R Kelly
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael W Lewis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea A Perreault
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eric S Davis
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Douglas H Phanstiel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hector L Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Perreault AA, Brown JD, Venters BJ. Erythropoietin Regulates Transcription and YY1 Dynamics in a Pre-established Chromatin Architecture. iScience 2020; 23:101583. [PMID: 33089097 PMCID: PMC7559257 DOI: 10.1016/j.isci.2020.101583] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional architecture of the genome plays an essential role in establishing and maintaining cell identity. However, the magnitude and temporal kinetics of changes in chromatin structure that arise during cell differentiation remain poorly understood. Here, we leverage a murine model of erythropoiesis to study the relationship between chromatin conformation, the epigenome, and transcription in erythroid cells. We discover that acute transcriptional responses induced by erythropoietin (EPO), the hormone necessary for erythroid differentiation, occur within an invariant chromatin topology. Within this pre-established landscape, Yin Yang 1 (YY1) occupancy dynamically redistributes to sites in proximity of EPO-regulated genes. Using HiChIP, we identify chromatin contacts mediated by H3K27ac and YY1 that are enriched for enhancer-promoter interactions of EPO-responsive genes. Taken together, these data are consistent with an emerging model that rapid, signal-dependent transcription occurs in the context of a pre-established chromatin architecture. EPO induces rapid RNA Pol II response at a key subset of genes YY1 is redistributed in the genome following 1 h EPO stimulation CTCF and YY1 bind different locations pre and post 1 h EPO stimulation E-P loops mediated by H3K27ac are largely invariant in response to EPO
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Affiliation(s)
- Andrea A Perreault
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37232, USA.,Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Jonathan D Brown
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Bryan J Venters
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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Abstract
The human HCC1806 cell line is frequently used as a preclinical model for triple negative breast cancer (TNBC). Given that dysregulated epigenetic mechanisms are involved in cancer pathogenesis, emerging therapeutic strategies target chromatin regulators, such as histone deacetylases. A comprehensive understanding of the epigenome and transcription profiling in HCC1806 provides the framework for evaluating efficacy and molecular mechanisms of epigenetic therapies. Thus, to study the interplay of transcription and chromatin in the HCC1806 preclinical model, we performed nascent transcription profiling using Precision Run-On coupled to sequencing (PRO-seq). Additionally, we mapped the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, seven histone modifications, and CTCF using ChIP-exo. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq with near base pair precision mapping of protein-DNA interactions. In this Data Descriptor, we present detailed information on experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the nascent transcription and chromatin.
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Affiliation(s)
- Andrea A. Perreault
- Chemical and Physical Biology Program at Vanderbilt University, Nashville, TN, USA
| | - Danielle M. Sprunger
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Bryan J. Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
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Abstract
The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.
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Affiliation(s)
- Zenab F. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrea A. Perreault
- Chemical and Physical Biology Program at Vanderbilt University, Nashville, TN 37232, USA
| | - Bryan J. Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, USA
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Perreault AA, Benton ML, Koury MJ, Brandt SJ, Venters BJ. Epo reprograms the epigenome of erythroid cells. Exp Hematol 2017; 51:47-62. [PMID: 28410882 DOI: 10.1016/j.exphem.2017.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/25/2022]
Abstract
The hormone erythropoietin (Epo) is required for erythropoiesis, yet its molecular mechanism of action remains poorly understood, particularly with respect to chromatin dynamics. To investigate how Epo modulates the erythroid epigenome, we performed epigenetic profiling using an ex vivo murine cell system that undergoes synchronous erythroid maturation in response to Epo stimulation. Our findings define the repertoire of Epo-modulated enhancers, illuminating a new facet of Epo signaling. First, a large number of enhancers rapidly responded to Epo stimulation, revealing a cis-regulatory network of Epo-responsive enhancers. In contrast, most of the other identified enhancers remained in an active acetylated state during Epo signaling, suggesting that most erythroid enhancers are established at an earlier precursor stage. Second, we identified several hundred super-enhancers that were linked to key erythroid genes, such as Tal1, Bcl11a, and Mir144/451. Third, experimental and computational validation revealed that many predicted enhancer regions were occupied by TAL1 and enriched with DNA-binding motifs for GATA1, KLF1, TAL1/E-box, and STAT5. Additionally, many of these cis-regulatory regions were conserved evolutionarily and displayed correlated enhancer:promoter acetylation. Together, these findings define a cis-regulatory enhancer network for Epo signaling during erythropoiesis, and provide the framework for future studies involving the interplay of epigenetics and Epo signaling.
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Affiliation(s)
- Andrea A Perreault
- Department of Molecular Physiology and Biophysics, Chemical and Physical Biology Program, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Mary Lauren Benton
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Mark J Koury
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Stephen J Brandt
- Department of Cancer Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Chemical and Physical Biology Program, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN.
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Abstract
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise. The key distinction of the ChIP-exo methodology is the incorporation of lambda exonuclease digestion in the library preparation workflow to effectively footprint the left and right 5' DNA borders of the protein-DNA crosslink site. The ChIP-exo libraries are then subjected to high throughput sequencing. The resulting data can be leveraged to provide unique and ultra-high resolution insights into the functional organization of the genome. Here, we describe the ChIP-exo method that we have optimized and streamlined for mammalian systems and next-generation sequencing-by-synthesis platform.
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Affiliation(s)
- Andrea A Perreault
- Department of Molecular Physiology and Biophysics, Vanderbilt University
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt University;
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