101
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Abstract
Transcription in several organisms from certain bacteria to humans has been observed to be stochastic in nature: toggling between active and inactive states. Periods of active nascent RNA synthesis known as bursts represent individual gene activation events in which multiple polymerases are initiated. Therefore, bursting is the single locus illustration of both gene activation and repression. Although transcriptional bursting was originally observed decades ago, only recently have technological advances enabled the field to begin elucidating gene regulation at the single-locus level. In this review, we focus on how biochemical, genomic, and single-cell data describe the regulatory steps of transcriptional bursts.
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Affiliation(s)
- Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, North Carolina 27709, USA
| | - Daniel R. Larson
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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102
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Abstract
Cell-type- and condition-specific profiles of gene expression require coordination between protein-coding gene promoters and cis-regulatory sequences called enhancers. Enhancers can stimulate gene activity at great genomic distances from their targets, raising questions about how enhancers communicate with specific gene promoters and what molecular mechanisms underlie enhancer function. Characterization of enhancer loci has identified the molecular features of active enhancers that accompany the binding of transcription factors and local opening of chromatin. These characteristics include coactivator recruitment, histone modifications, and noncoding RNA transcription. However, it remains unclear which of these features functionally contribute to enhancer activity. Here, we discuss what is known about how enhancers regulate their target genes and how enhancers and promoters communicate. Further, we describe recent data demonstrating many similarities between enhancers and the gene promoters they control, and we highlight unanswered questions in the field, such as the potential roles of transcription at enhancers.
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Affiliation(s)
- Andrew Field
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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103
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Zhang Z, Yu W, Tang D, Zhou Y, Bi M, Wang H, Zheng Y, Chen M, Li L, Xu X, Zhang W, Tao H, Jin VX, Liu Z, Chen L. Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer. RNA Biol 2020; 17:1590-1602. [PMID: 32506995 DOI: 10.1080/15476286.2020.1777769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is one of the most prevalent cancers in women worldwide. Through the regulation of many coding and non-coding target genes, oestrogen (E2 or 17β-oestradiol) and its nuclear receptor ERα play important roles in breast cancer development and progression. Despite the astounding advances in our understanding of oestrogen-regulated coding genes over the past decades, our knowledge on oestrogen-regulated non-coding targets has just begun to expand. Here we leverage epigenomic approaches to systematically analyse oestrogen-regulated long non-coding RNAs (lncRNAs). Similar to the coding targets of ERα, the transcription of oestrogen-regulated lncRNAs correlates with the activation status of ERα enhancers, measured by eRNA production, chromatin accessibility, and the occupancy of the enhancer regulatory components including P300, MED1, and ARID1B. Our 3D chromatin architecture analyses suggest that lncRNAs and their neighbouring E2-resonsive coding genes, exemplified by LINC00160 and RUNX1, might be regulated as a 3D structural unit resulted from enhancer-promoter interactions. Finally, we evaluated the expression levels of LINC00160 and RUNX1 in various types of breast cancer and found that their expression positively correlated with the survival rate in ER+ breast cancer patients, implying that the oestrogen-regulated LINC00160 and its neighbouring RUNX1 might represent potential biomarkers for ER+ breast cancers.
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Affiliation(s)
- Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Wei Yu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA.,Department of Orthopedics, The Second Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou, Zhejiang, China
| | - Dan Tang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA.,Department of General Practice, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi, China
| | - Yufan Zhou
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Mingjun Bi
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Hu Wang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Yan Zheng
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Mingqiu Chen
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University , Fuzhou, China
| | - Li Li
- Department of Oncology, The Second People's Hospital of Jiaozuo , Jiaozuo City, Henan, China
| | - Xinping Xu
- Jiangxi Institute of Respiratory Disease, the Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi, China
| | - Wei Zhang
- Jiangxi Institute of Respiratory Disease, the Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi, China
| | - Huimin Tao
- Department of Orthopedics, The Second Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou, Zhejiang, China
| | - Victor X Jin
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Lizhen Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA.,Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
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104
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Enhancer RNAs are an important regulatory layer of the epigenome. Nat Struct Mol Biol 2020; 27:521-528. [PMID: 32514177 DOI: 10.1038/s41594-020-0446-0] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 05/07/2020] [Indexed: 12/20/2022]
Abstract
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. Leading the charge in the RNA revolution is a class of ncRNAs that are synthesized at active enhancers, called enhancer RNAs (eRNAs). Here, we review recent insights into the biogenesis of eRNAs and the mechanisms underlying their multifaceted functions and consider how these findings could inform future investigations into enhancer transcription and eRNA function.
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105
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Srivastava D, Mahony S. Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194443. [PMID: 31639474 PMCID: PMC7166147 DOI: 10.1016/j.bbagrm.2019.194443] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin determinants of cell type-specific TF binding specificity. We identify the current challenges and opportunities associated with computational approaches to characterizing, imputing, and predicting cell type-specific TF binding patterns. We further focus on studies that characterize TF binding in dynamic regulatory settings, and we discuss how these studies are leading to a more complex and nuanced understanding of dynamic protein-DNA binding activities. We propose that TF binding activities at individual sites can be viewed along a two-dimensional continuum of local sequence and chromatin context. Under this view, cell type-specific TF binding activities may result from either strongly favorable sequence features or strongly favorable chromatin context.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
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106
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Satoh Y, Takei N, Kawamura S, Takahashi N, Kotani T, Kimura AP. A novel testis-specific long noncoding RNA, Tesra, activates the Prss42/Tessp-2 gene during mouse spermatogenesis†. Biol Reprod 2020; 100:833-848. [PMID: 30379984 PMCID: PMC6437258 DOI: 10.1093/biolre/ioy230] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/06/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023] Open
Abstract
The progression of spermatogenesis is precisely controlled by meiotic stage-specific genes, but the molecular mechanism for activation of such genes is still elusive. Here we found a novel testis-specific long noncoding RNA (lncRNA), Tesra, that was specifically expressed in the mouse testis at the Prss/Tessp gene cluster on chromosome 9. Tesra was transcribed downstream of Prss44/Tessp-4, starting within the gene, as a 4435-nucleotide transcript and developmentally activated at a stage similar to that for Prss/Tessp genes. By in situ hybridization, Tesra was found to be localized in and around germ cells and Leydig cells, being consistent with biochemical data showing its existence in cytoplasmic, nuclear, and extracellular fractions. Based on the finding of more signals in nuclei of pachytene spermatocytes, we explored the possibility that Tesra plays a role in transcriptional activation of Prss/Tessp genes. By a ChIRP assay, the Tesra transcript was found to bind to the Prss42/Tessp-2 promoter region in testicular germ cells, and transient overexpression of Tesra significantly activated endogenous Prss42/Tessp-2 expression and increased Prss42/Tessp-2 promoter activity in a reporter construct. These findings suggest that Tesra activates the Prss42/Tessp-2 gene by binding to the promoter. Finally, we investigated whether Tesra co-functioned with enhancers adjacent to another lncRNA, lncRNA-HSVIII. In the Tet-on system, Tesra transcription significantly increased activity of one enhancer, but Tesra and the enhancer were not interdependent. Collectively, our results proposed a potential function of an lncRNA, Tesra, in transcriptional activation and suggest a novel relationship between an lncRNA and an enhancer.
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Affiliation(s)
- Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Natsumi Takei
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shohei Kawamura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Nobuhiko Takahashi
- Department of Internal Medicine, School of Dentistry, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Japan
| | - Tomoya Kotani
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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107
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Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21103711. [PMID: 32466143 PMCID: PMC7279485 DOI: 10.3390/ijms21103711] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.
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108
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Hou TY, Nandu T, Li R, Chae M, Murakami S, Kraus WL. Characterization of basal and estrogen-regulated antisense transcription in breast cancer cells: Role in regulating sense transcription. Mol Cell Endocrinol 2020; 506:110746. [PMID: 32035111 PMCID: PMC7089808 DOI: 10.1016/j.mce.2020.110746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 12/27/2022]
Abstract
Estrogen-responsive breast cancer cells exhibit both basal and estrogen-regulated transcriptional programs, which lead to the transcription of many different transcription units (i.e., genes), including those that produce coding and non-coding sense (e.g., mRNA, lncRNA) and antisense (i.e., asRNA) transcripts. We have previously characterized the global basal and estrogen-regulated transcriptomes in estrogen receptor alpha (ERα)-positive MCF-7 breast cancer cells. Herein, we have mined genomic data to define three classes of antisense transcription in MCF-7 cells based on where their antisense transcription termination sites reside relative to their cognate sense mRNA and lncRNA genes. These three classes differ in their response to estrogen treatment, the enrichment of a number of genomic features associated with active promoters (H3K4me3, RNA polymerase II, open chromatin architecture), and the biological functions of their cognate sense genes as analyzed by DAVID gene ontology. We further characterized two estrogen-regulated antisense transcripts arising from the MYC gene in MCF-7 cells, showing that these antisense transcripts are 5'-capped, 3'-polyadenylated, and localized to different compartments of the cell. Together, our analyses have revealed distinct classes of antisense transcription correlated to different biological processes and response to estrogen stimulation, uncovering another layer of hormone-regulated gene regulation.
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Affiliation(s)
- Tim Y Hou
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, 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, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Rui Li
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Minho Chae
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shino Murakami
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, 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, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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109
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Guh CY, Hsieh YH, Chu HP. Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs. J Biomed Sci 2020; 27:44. [PMID: 32183863 PMCID: PMC7079490 DOI: 10.1186/s12929-020-00640-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.
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Affiliation(s)
- Chia-Yu Guh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Yu-Hung Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Hsueh-Ping Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China.
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110
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Rodriguez AC, Vahrenkamp JM, Berrett KC, Clark KA, Guillen KP, Scherer SD, Yang CH, Welm BE, Janát-Amsbury MM, Graves BJ, Gertz J. ETV4 Is Necessary for Estrogen Signaling and Growth in Endometrial Cancer Cells. Cancer Res 2020; 80:1234-1245. [PMID: 32046982 PMCID: PMC7073291 DOI: 10.1158/0008-5472.can-19-1382] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 12/09/2019] [Accepted: 01/15/2020] [Indexed: 11/16/2022]
Abstract
Estrogen signaling through estrogen receptor alpha (ER) plays a major role in endometrial cancer risk and progression, however, the molecular mechanisms underlying ER's regulatory role in endometrial cancer are poorly understood. In breast cancer cells, ER genomic binding is enabled by FOXA1 and GATA3, but the transcription factors that control ER genomic binding in endometrial cancer cells remain unknown. We previously identified ETV4 as a candidate factor controlling ER genomic binding in endometrial cancer cells, and here we explore the functional importance of ETV4. Homozygous deletion of ETV4, using CRISPR/Cas9, led to greatly reduced ER binding at the majority of loci normally bound by ER. Consistent with the dramatic loss of ER binding, the gene expression response to estradiol was dampened for most genes. ETV4 contributes to estrogen signaling in two distinct ways. ETV4 loss affects chromatin accessibility at some ER bound loci and impairs ER nuclear translocation. The diminished estrogen signaling upon ETV4 deletion led to decreased growth, particularly in 3D culture, where hollow organoids were formed and in vivo in the context of estrogen-dependent growth. These results show that ETV4 plays an important role in estrogen signaling in endometrial cancer cells. SIGNIFICANCE: Estrogen receptor alpha (ER) is a key oncogene in endometrial cancer. This study uncovers ETV4 as an important factor in controlling the activity of ER and the growth of endometrial cancer cells. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/6/1234/F1.large.jpg.
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Affiliation(s)
- Adriana C Rodriguez
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Kristofer C Berrett
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Kathleen A Clark
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Katrin P Guillen
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Sandra D Scherer
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Chieh-Hsiang Yang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah
- Department of Bioengineering, University of Utah, Salt Lake City, Utah
| | - Bryan E Welm
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Margit M Janát-Amsbury
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah
- Department of Bioengineering, University of Utah, Salt Lake City, Utah
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
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111
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Vasquez YM, Nandu TS, Kelleher AM, Ramos EI, Gadad SS, Kraus WL. Genome-wide analysis and functional prediction of the estrogen-regulated transcriptional response in the mouse uterus†. Biol Reprod 2020; 102:327-338. [PMID: 31511857 PMCID: PMC7016285 DOI: 10.1093/biolre/ioz183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022] Open
Abstract
The ovarian hormones estrogen and progesterone orchestrate the transcriptional programs required to direct functions of the uterus for initiation and maintenance of pregnancy. Estrogen, acting via estrogen receptor alpha, regulates gene expression by activating and repressing distinct genes involved in signaling pathways that regulate cellular and physiological responses including cell division, water influx, and immune cell recruitment. Historically, these transcriptional responses have been postulated to reflect a biphasic physiological response. In this study, we explored the transcriptional responses of the ovariectomized mouse uterus to 17β-estradiol (E2) by RNA-seq to obtain global expression profiles of protein-coding transcripts (mRNAs) and long noncoding RNAs (lncRNAs) following 0.5, 1, 2, and 6 hours of treatment. The E2-regulated mRNA and lncRNA expression profiles in the mouse uterus indicate an association between lncRNAs and mRNAs that regulate E2-driven pathways and reproductive phenotypes in the mouse. The transient E2-regulated transcriptome is reflected in the time-dependent shifting of biological processes regulated in the uterus in response to E2. Moreover, high expression of some conserved lncRNAs that are E2 regulated in the mouse uterus are predictive of low overall survival in endometrial carcinoma patients (e.g., H19, KCNQ1OT1, MIR17HG, and FTX). Collectively, this study (1) describes a genomic approach for identifying E2-regulated lncRNAs that may serve critical function in the uterus and (2) provides new insights into our understanding of the regulation of hormone-regulated transcriptional responses with implications in pregnancy and endometrial pathologies.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/mortality
- Databases, Genetic
- Estradiol/pharmacology
- Female
- Gene Expression Regulation/drug effects
- Gene Ontology
- Genital Neoplasms, Female/genetics
- Genital Neoplasms, Female/metabolism
- Genital Neoplasms, Female/mortality
- Humans
- Mice
- Ovariectomy
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Survival Rate
- Transcriptome/drug effects
- Uterus/drug effects
- Uterus/metabolism
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Affiliation(s)
- Yasmin M Vasquez
- 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 S 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
| | - Andrew M Kelleher
- 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
| | - Enrique I Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Shrikanth S Gadad
- 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
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, 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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112
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Hossan T, Kundu S, Alam SS, Nagarajan S. Epigenetic Modifications Associated with the Pathogenesis of Type 2 Diabetes Mellitus. Endocr Metab Immune Disord Drug Targets 2020; 19:775-786. [PMID: 30827271 DOI: 10.2174/1871530319666190301145545] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Type 2 diabetes mellitus (T2DM) is a multifactorial metabolic disorder. Pancreatic β-cell dysfunction and insulin resistance are the most common and crucial events of T2DM. Increasing evidence suggests the association of epigenetic modifications with the pathogenesis of T2DM through the changes in important biological processes including pancreatic β- cell differentiation, development and maintenance of normal β-cell function. Insulin sensitivity by the peripheral glucose uptake tissues is also changed by the altered epigenetic mechanisms. In this review, we discussed the major epigenetic alterations and their effects on β-cell function, insulin secretion and insulin resistance in context of T2DM. METHODS We investigated the presently available epigenetic modifications including DNA methylation, posttranslational histone modifications, ATP-dependent chromatin remodeling and non-coding RNAs related to the pathogenesis of T2DM. Published literatures on this topic were searched both on Google Scholar and Pubmed with related keywords and investigated for relevant information. RESULTS The epigenetic modifications introduce changes in gene expression which are essential for appropriate β-cell development and functions, insulin secretion and sensitivity resulting in the pathogenesis of T2DM. Interestingly, T2DM could also be a prominent reason for the mentioned epigenetic alterations. CONCLUSION This review article emphasized on the epigenetic modifications associated with T2DM and discussed the consequences in deterioration of the disease condition.
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Affiliation(s)
- Tareq Hossan
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Shoumik Kundu
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sayeda Sadia Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sankari Nagarajan
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
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113
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Lee JH, Xiong F, Li W. Enhancer RNAs in cancer: regulation, mechanisms and therapeutic potential. RNA Biol 2020; 17:1550-1559. [PMID: 31916476 DOI: 10.1080/15476286.2020.1712895] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enhancers are distal genomic elements critical for gene regulation and cell identify control during development and diseases. Many human cancers were found to associate with enhancer malfunction, due to genetic and epigenetic alterations, which in some cases directly drive tumour growth. Conventionally, enhancers are known to provide DNA binding motifs to recruit transcription factors (TFs) and to control target genes. However, recent progress found that most, if not all, active enhancers pervasively transcribe noncoding RNAs that are referred to as enhancer RNAs (eRNAs). Increasing evidence points to functional roles of at least a subset of eRNAs in gene regulation in both normal and cancer cells, adding new insights into the action mechanisms of enhancers. eRNA expression was observed to be widespread but also specific to tumour types and individual patients, serving as opportunities to exploit them as potential diagnosis markers or therapeutic targets. In this review, we discuss the brief history of eRNA research, their functional mechanisms and importance in cancer gene regulation, as well as their therapeutic and diagnostic values in cancer. We propose that further studies of eRNAs in cancer will offer a promising 'eRNA targeted therapy' for human cancer intervention.
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Affiliation(s)
- Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA.,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth , Houston, TX, USA
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114
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Abstract
Enhancers are cis-acting elements with many sites bound by transcription factors and activate transcription over long distance. Histone modifications are critical for enhancer activity and utilized as hallmarks for the identification of putative enhancers. Monomethylation of histone H3 lysine 4 (H3K4me1) is the mark for enhancer priming; acetylation of histone H3 lysine 27 (H3K27ac) for active enhancers and trimethylation of histone H3 lysine 27 (H3K27me3) for silent enhancers. Recent studies from multiple groups have provided evidence that enhancer reprogramming, especially gain of enhancer activity, is closely related to tumorigenesis and cancer development. In this review, we will summarize the recent discoveries about enhancer regulation and the mechanisms of enhancer reprogramming in tumorigenesis, and discuss the potential application of enhancer manipulation in precision medicine.
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Affiliation(s)
- Jie Yao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Ji Chen
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Lian-Yun Li
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Min Wu
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
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115
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Arnold PR, Wells AD, Li XC. Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate. Front Cell Dev Biol 2020; 7:377. [PMID: 31993419 PMCID: PMC6971116 DOI: 10.3389/fcell.2019.00377] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
Enhancers are cis-regulatory elements in the genome that cooperate with promoters to control target gene transcription. Unlike promoters, enhancers are not necessarily adjacent to target genes and can exert their functions regardless of enhancer orientations, positions and spatial segregations from target genes. Thus, for a long time, the question as to how enhancers act in a temporal and spatial manner attracted considerable attention. The recent discovery that enhancers are also abundantly transcribed raises interesting questions about the exact roles of enhancer RNA (eRNA) in gene regulation. In this review, we highlight the process of enhancer transcription and the diverse features of eRNA. We review eRNA functions, which include enhancer-promoter looping, chromatin modifying, and transcription regulating. As eRNA are transcribed from active enhancers, they exhibit tissue and lineage specificity, and serve as markers of cell state and function. Finally, we discuss the unique relationship between eRNA and super enhancers in phase separation wherein eRNA may contribute significantly to cell fate decisions.
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Affiliation(s)
- Preston R Arnold
- Texas A&M Health Science Center, College of Medicine, Bryan, TX, United States.,Immunobiology and Transplant Sciences, Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xian C Li
- Immunobiology and Transplant Sciences, Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
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116
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lncRNA CISAL Inhibits BRCA1 Transcription by Forming a Tertiary Structure at Its Promoter. iScience 2020; 23:100835. [PMID: 32000125 PMCID: PMC7033639 DOI: 10.1016/j.isci.2020.100835] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/25/2019] [Accepted: 01/08/2020] [Indexed: 11/21/2022] Open
Abstract
Cisplatin-based neoadjuvant chemotherapy has been shown to improve survival in patients with squamous cell carcinoma (SCC), but clinical biomarkers to predict chemosensitivity remain elusive. Here, we show the long noncoding RNA (lncRNA) LINC01011, which we termed cisplatin-sensitivity-associated lncRNA (CISAL), controls mitochondrial fission and cisplatin sensitivity by inhibiting BRCA1 transcription in tongue SCC (TSCC) models. Mechanistically, we found CISAL directly binds the BRCA1 promoter and forms an RNA-DNA triplex structure, sequestering BRCA1 transcription factor-GABPA away from the downstream regulatory binding region. Importantly, the clinical relevance of these findings is suggested by the significant association of CISAL and BRCA1 expression levels in TSCC tumors with neoadjuvant chemosensitivity and overall survival. We propose a new model where lncRNAs are tethered at gene promoter by RNA-DNA triplex formation, spatially sequestering transcription factors away from DNA-binding sites. Our study uncovers the potential of CISAL-BRCA1 signaling as a potential target to predict or improve chemosensitivity. CISAL enhances mitochondrial fission and cisplatin sensitivity in TSCC cells through BRCA1 CISAL directly binds the BRCA1 promoter and forms an RNA-DNA triplex structure CISAL sequesters GABPA away from regulatory binding at BRCA1 promoter High CISAL predicts favorable neoadjuvant chemosensitivity and prognosis of TSCC patients
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117
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Czimmerer Z, Halasz L, Nagy L. Unorthodox Transcriptional Mechanisms of Lipid-Sensing Nuclear Receptors in Macrophages: Are We Opening a New Chapter? Front Endocrinol (Lausanne) 2020; 11:609099. [PMID: 33362723 PMCID: PMC7758493 DOI: 10.3389/fendo.2020.609099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022] Open
Abstract
Work over the past 30 years has shown that lipid-activated nuclear receptors form a bridge between metabolism and immunity integrating metabolic and inflammatory signaling in innate immune cells. Ligand-induced direct transcriptional activation and protein-protein interaction-based transrepression were identified as the most common mechanisms of liganded-nuclear receptor-mediated transcriptional regulation. However, the integration of different next-generation sequencing-based methodologies including chromatin immunoprecipitation followed by sequencing and global run-on sequencing allowed to investigate the DNA binding and ligand responsiveness of nuclear receptors at the whole-genome level. Surprisingly, these studies have raised the notion that a major portion of lipid-sensing nuclear receptor cistromes are not necessarily responsive to ligand activation. Although the biological role of the ligand insensitive portion of nuclear receptor cistromes is largely unknown, recent findings indicate that they may play roles in the organization of chromatin structure, in the regulation of transcriptional memory, and the epigenomic modification of responsiveness to other microenvironmental signals in macrophages. In this review, we will provide an overview and discuss recent advances of our understanding of lipid-activated nuclear receptor-mediated non-classical or unorthodox actions in macrophages.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
- *Correspondence: Laszlo Nagy,
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118
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Cardiello JF, Sanchez GJ, Allen MA, Dowell RD. Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs. Transcription 2019; 11:3-18. [PMID: 31856658 DOI: 10.1080/21541264.2019.1704128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nascent transcription assays, such as global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq), have uncovered a myriad of unstable RNAs being actively produced from numerous sites genome-wide. These transcripts provide a more complete and immediate picture of the impact of regulatory events. Transcription factors recruit RNA polymerase II, effectively initiating the process of transcription; repressors inhibit polymerase recruitment. Efficiency of recruitment is dictated by sequence elements in and around the RNA polymerase loading zone. A combination of sequence elements and RNA binding proteins subsequently influence the ultimate stability of the resulting transcript. Some of these transcripts are capable of providing feedback on the process, influencing subsequent transcription. By monitoring RNA polymerase activity, nascent assays provide insights into every step of the regulated process of transcription.
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Affiliation(s)
| | - Gilson J Sanchez
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.,Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
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119
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Pallares RM, Thanh NTK, Su X. Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods. Chem Commun (Camb) 2019; 55:15041-15044. [PMID: 31696164 DOI: 10.1039/c9cc07511a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of transcription factors to DNA is one of the main mechanisms in gene regulation. While transcription factors frequently bind to unwrapped long DNA sequences known as open chromatin structures, most bioassays that study protein-DNA binding rely on short oligonucleotide probes. In this work, we develop a gold nanorod-based colorimetric assay for the binding of transcription factors to DNA in long open chromatin-like structures. After the determination of the binding affinity and stoichiometry, we explored the effect of the probe length on the assay performance and compared it to other established techniques.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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120
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Korkmaz G, Manber Z, Lopes R, Prekovic S, Schuurman K, Kim Y, Teunissen H, Flach K, Wit ED, Galli GG, Zwart W, Elkon R, Agami R. A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation. Nucleic Acids Res 2019; 47:9557-9572. [PMID: 31372638 PMCID: PMC6765117 DOI: 10.1093/nar/gkz675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/11/2019] [Accepted: 07/24/2019] [Indexed: 01/07/2023] Open
Abstract
Estrogen receptor α (ERα) is an enhancer activating transcription factor, a key driver of breast cancer and a main target for cancer therapy. ERα-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ERα-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ERα-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screen targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one of them in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ERα-dependency in cell lines, and is associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ERα- driven breast cancer cell proliferation.
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Affiliation(s)
- Gozde Korkmaz
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Zohar Manber
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rui Lopes
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Yongsoo Kim
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Koen Flach
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Giorgio G Galli
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands
| | - Ran Elkon
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Erasmus MC, Rotterdam University, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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121
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Payankaulam S, Raicu AM, Arnosti DN. Transcriptional Regulation of INSR, the Insulin Receptor Gene. Genes (Basel) 2019; 10:genes10120984. [PMID: 31795422 PMCID: PMC6947883 DOI: 10.3390/genes10120984] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/19/2019] [Accepted: 11/23/2019] [Indexed: 01/19/2023] Open
Abstract
The insulin receptor gene encodes an evolutionarily conserved signaling protein with a wide spectrum of functions in metazoan development. The insulin signaling pathway plays key roles in processes such as metabolic regulation, growth control, and neuronal function. Misregulation of the pathway features in diabetes, cancer, and neurodegenerative diseases, making it an important target for clinical interventions. While much attention has been focused on differential pathway activation through ligand availability, sensitization of overall signaling may also be mediated by differential expression of the insulin receptor itself. Although first characterized as a “housekeeping” gene with stable expression, comparative studies have shown that expression levels of the human INSR mRNA differ by tissue and in response to environmental signals. Our recent analysis of the transcriptional controls affecting expression of the Drosophila insulin receptor gene indicates that a remarkable amount of DNA is dedicated to encoding sophisticated feedback and feed forward signals. The human INSR gene is likely to contain a similar level of transcriptional complexity; here, we summarize over three decades of molecular biology and genetic research that points to a still incompletely understood regulatory control system. Further elucidation of transcriptional controls of INSR will provide the basis for understanding human genetic variation that underlies population-level physiological differences and disease.
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Affiliation(s)
- Sandhya Payankaulam
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd. 413 Biochemistry, East Lansing, MI 48824, USA;
| | - Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, 603 Wilson Rd. 413 Biochemistry, East Lansing, MI 48824, USA;
| | - David N. Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd. 413 Biochemistry, East Lansing, MI 48824, USA;
- Cell and Molecular Biology Program, Michigan State University, 603 Wilson Rd. 413 Biochemistry, East Lansing, MI 48824, USA;
- Correspondence: ; Tel.: +1-(517)-432-5504
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122
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Stengel KR, Bhaskara S, Wang J, Liu Q, Ellis JD, Sampathi S, Hiebert SW. Histone deacetylase 3 controls a transcriptional network required for B cell maturation. Nucleic Acids Res 2019; 47:10612-10627. [PMID: 31586401 PMCID: PMC6847391 DOI: 10.1093/nar/gkz816] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/03/2019] [Accepted: 09/26/2019] [Indexed: 11/15/2022] Open
Abstract
Histone deacetylase 3 (Hdac3) is a target of the FDA approved HDAC inhibitors, which are used for the treatment of lymphoid malignancies. Here, we used Cd19-Cre to conditionally delete Hdac3 to define its role in germinal center B cells, which represent the cell of origin for many B cell malignancies. Cd19-Cre-Hdac3-/- mice showed impaired germinal center formation along with a defect in plasmablast production. Analysis of Hdac3-/- germinal centers revealed a reduction in dark zone centroblasts and accumulation of light zone centrocytes. RNA-seq revealed a significant correlation between genes up-regulated upon Hdac3 loss and those up-regulated in Foxo1-deleted germinal center B cells, even though Foxo1 typically activates transcription. Therefore, to determine whether gene expression changes observed in Hdac3-/- germinal centers were a result of direct effects of Hdac3 deacetylase activity, we used an HDAC3 selective inhibitor and examined nascent transcription in germinal center-derived cell lines. Transcriptional changes upon HDAC3 inhibition were enriched for light zone gene signatures as observed in germinal centers. Further comparison of PRO-seq data with ChIP-seq/exo data for BCL6, SMRT, FOXO1 and H3K27ac identified direct targets of HDAC3 function including CD86, CD83 and CXCR5 that are likely responsible for driving the light zone phenotype observed in vivo.
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Affiliation(s)
- Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Srividya Bhaskara
- Department of Radiation Oncology and Oncological Sciences, Univ. of Utah School of Medicine and the Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt School of Medicine, Nashville, TN 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt School of Medicine, Nashville, TN 37203, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37027, USA
| | - Jacob D Ellis
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Shilpa Sampathi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37027, USA
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123
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Duttke SH, Chang MW, Heinz S, Benner C. Identification and dynamic quantification of regulatory elements using total RNA. Genome Res 2019; 29:1836-1846. [PMID: 31649059 PMCID: PMC6836739 DOI: 10.1101/gr.253492.119] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.
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Affiliation(s)
- Sascha H Duttke
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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124
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Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J. FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples. Genome Res 2019; 29:1826-1835. [PMID: 31649055 PMCID: PMC6836741 DOI: 10.1101/gr.249656.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/03/2019] [Indexed: 12/16/2022]
Abstract
The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5′ ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5′ capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5′ end RNA-seq libraries from FFPE-derived RNA.
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Affiliation(s)
- Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Kathryn Szczotka
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mark K Dodson
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Elke A Jarboe
- Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Andrew P Soisson
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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125
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Shuaib M, Parsi KM, Thimma M, Adroub SA, Kawaji H, Seridi L, Ghosheh Y, Fort A, Fallatah B, Ravasi T, Carninci P, Orlando V. Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells. Cell Syst 2019; 9:446-458.e6. [PMID: 31629687 DOI: 10.1016/j.cels.2019.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/29/2019] [Accepted: 09/12/2019] [Indexed: 12/21/2022]
Abstract
The impact of mammalian RNA interference components, particularly, Argonaute proteins, on chromatin organization is unexplored. Recent reports indicate that AGO1 association with chromatin appears to influence gene expression. To uncover the role of AGO1 in the nucleus, we used a combination of genome-wide approaches in control and AGO1-depleted HepG2 cells. We found that AGO1 strongly associates with active enhancers and RNA being produced at those sites. Hi-C analysis revealed AGO1 enrichment at the boundaries of topologically associated domains (TADs). By Hi-C in AGO1 knockdown cells, we observed changes in chromatin organization, including TADs and A/B compartment mixing, specifically in AGO1-bound regions. Distinct groups of genes and especially eRNA transcripts located within differentially interacting loci showed altered expression upon AGO1 depletion. Moreover, AGO1 association with enhancers is dependent on eRNA transcription. Collectively, our data suggest that enhancer-associated AGO1 contributes to the fine-tuning of chromatin architecture and gene expression in human cells.
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Affiliation(s)
- Muhammad Shuaib
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Krishna Mohan Parsi
- IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy
| | - Manjula Thimma
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Sabir Abdu Adroub
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Loqmane Seridi
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Yanal Ghosheh
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Bodor Fallatah
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia; IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy.
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126
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Zhang Z, Lee JH, Ruan H, Ye Y, Krakowiak J, Hu Q, Xiang Y, Gong J, Zhou B, Wang L, Lin C, Diao L, Mills GB, Li W, Han L. Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer. Nat Commun 2019; 10:4562. [PMID: 31594934 PMCID: PMC6783481 DOI: 10.1038/s41467-019-12543-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
Enhancer RNA (eRNA) is a type of noncoding RNA transcribed from the enhancer. Although critical roles of eRNA in gene transcription control have been increasingly realized, the systemic landscape and potential function of eRNAs in cancer remains largely unexplored. Here, we report the integration of multi-omics and pharmacogenomics data across large-scale patient samples and cancer cell lines. We observe a cancer-/lineage-specificity of eRNAs, which may be largely driven by tissue-specific TFs. eRNAs are involved in multiple cancer signaling pathways through putatively regulating their target genes, including clinically actionable genes and immune checkpoints. They may also affect drug response by within-pathway or cross-pathway means. We characterize the oncogenic potential and therapeutic liability of one eRNA, NET1e, supporting the clinical feasibility of eRNA-targeted therapy. We identify a panel of clinically relevant eRNAs and developed a user-friendly data portal. Our study reveals the transcriptional landscape and clinical utility of eRNAs in cancer.
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Affiliation(s)
- Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jing Gong
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bingying Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, PR China
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, PR China
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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127
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Ha SD, Cho W, DeKoter RP, Kim SO. The transcription factor PU.1 mediates enhancer-promoter looping that is required for IL-1β eRNA and mRNA transcription in mouse melanoma and macrophage cell lines. J Biol Chem 2019; 294:17487-17500. [PMID: 31586032 DOI: 10.1074/jbc.ra119.010149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/11/2019] [Indexed: 01/08/2023] Open
Abstract
The DNA-binding protein PU.1 is a myeloid lineage-determining and pioneering transcription factor due to its ability to bind "closed" genomic sites and maintain "open" chromatin state for myeloid lineage-specific genes. The precise mechanism of PU.1 in cell type-specific programming is yet to be elucidated. The melanoma cell line B16BL6, although it is nonmyeloid lineage, expressed Toll-like receptors and activated the transcription factor NF-κB upon stimulation by the bacterial cell wall component lipopolysaccharide. However, it did not produce cytokines, such as IL-1β mRNA. Ectopic PU.1 expression induced remodeling of a novel distal enhancer (located ∼10 kbp upstream of the IL-1β transcription start site), marked by nucleosome depletion, enhancer-promoter looping, and histone H3 lysine 27 acetylation (H3K27ac). PU.1 induced enhancer-promoter looping and H3K27ac through two distinct PU.1 regions. These PU.1-dependent events were independently required for subsequent signal-dependent and co-dependent events: NF-κB recruitment and further H3K27ac, both of which were required for enhancer RNA (eRNA) transcription. In murine macrophage RAW264.7 cells, these PU.1-dependent events were constitutively established and readily expressed eRNA and subsequently IL-1β mRNA by lipopolysaccharide stimulation. In summary, this study showed a sequence of epigenetic events in programming IL-1β transcription by the distal enhancer priming and eRNA production mediated by PU.1 and the signal-dependent transcription factor NF-κB.
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Affiliation(s)
- Soon-Duck Ha
- Department of Microbiology and Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, University of Western Ontario, London, Ontario N6G 2V4, Canada
| | - Woohyun Cho
- Department of Microbiology and Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, University of Western Ontario, London, Ontario N6G 2V4, Canada
| | - Rodney P DeKoter
- Department of Microbiology and Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, University of Western Ontario, London, Ontario N6G 2V4, Canada
| | - Sung Ouk Kim
- Department of Microbiology and Immunology and Infectious Diseases Research Group, Siebens-Drake Research Institute, University of Western Ontario, London, Ontario N6G 2V4, Canada
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128
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Esse R, Gushchanskaia ES, Lord A, Grishok A. DOT1L complex suppresses transcription from enhancer elements and ectopic RNAi in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2019; 25:1259-1273. [PMID: 31300558 PMCID: PMC6800474 DOI: 10.1261/rna.070292.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/10/2019] [Indexed: 05/14/2023]
Abstract
Methylation of histone H3 on lysine 79 (H3K79) by DOT1L is associated with actively transcribed genes. Earlier, we described that DOT-1.1, the Caenorhabditis elegans homolog of mammalian DOT1L, cooperates with the chromatin-binding protein ZFP-1 (AF10 homolog) to negatively modulate transcription of highly and widely expressed target genes. Also, the reduction of ZFP-1 levels has consistently been associated with lower efficiency of RNA interference (RNAi) triggered by exogenous double-stranded RNA (dsRNA), but the reason for this is not clear. Here, we demonstrate that the DOT1L complex suppresses transcription originating from enhancer elements and antisense transcription, thus potentiating the expression of enhancer-regulated genes. We also show that worms lacking H3K79 methylation do not survive, and this lethality is suppressed by a loss of caspase-3 or Dicer complex components that initiate gene silencing response to exogenous dsRNA. Our results suggest that ectopic elevation of endogenous dsRNA directly or indirectly resulting from global misregulation of transcription in DOT1L complex mutants may engage the Dicer complex and, therefore, limit the efficiency of exogenous RNAi.
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Affiliation(s)
- Ruben Esse
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | | | - Avery Lord
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Alla Grishok
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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129
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Murakami S, Li R, Nagari A, Chae M, Camacho CV, Kraus WL. Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells. Mol Cancer Res 2019; 17:2356-2368. [PMID: 31551256 DOI: 10.1158/1541-7786.mcr-19-0393] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/28/2019] [Accepted: 09/17/2019] [Indexed: 01/23/2023]
Abstract
The bromodomain family member proteins (BRD; BET proteins) are key coregulators for estrogen receptor alpha (ERα)-mediated transcriptional enhancers. The use of BRD-selective inhibitors has gained much attention as a potential treatment for various solid tumors, including ER-positive breast cancers. However, the roles of individual BET family members have largely remained unexplored. Here, we describe the role of BRDs in estrogen (E2)-dependent gene expression in ERα-positive breast cancer cells. We observed that chemical inhibition of BET family proteins with JQ1 impairs E2-regulated gene expression and growth in breast cancer cells. In addition, RNAi-mediated depletion of each BET family member (BRDs 2, 3, and 4) revealed partially redundant roles at ERα enhancers and for target gene transcription. Furthermore, we found a unique role of BRD3 as a molecular sensor of total BET family protein levels and activity through compensatory control of its own protein levels. Finally, we observed that BRD3 is recruited to a subset of ERα-binding sites (ERBS) that are enriched for active enhancer features, located in clusters of ERBSs likely functioning as "super enhancers," and associated with highly E2-responsive genes. Collectively, our results illustrate a critical and specific role for BET family members in ERα-dependent gene transcription. IMPLICATIONS: BRD3 is recruited to and controls the activity of a subset ERα transcriptional enhancers, providing a therapeutic opportunity to target BRD3 with BET inhibitors in ERα-positive breast cancers.
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Affiliation(s)
- Shino Murakami
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas.,Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rui Li
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas.,Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anusha Nagari
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Minho Chae
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Cristel V Camacho
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas. .,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas.,Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
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130
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Abstract
Mammalian genomes are extensively transcribed, which produces a large number of both coding and non-coding transcripts. Various RNAs are physically associated with chromatin, through being either retained in cis at their site of transcription or recruited in trans to other genomic regions. Driven by recent technological innovations for detecting chromatin-associated RNAs, diverse roles are being revealed for these RNAs and associated RNA-binding proteins (RBPs) in gene regulation and genome function. Such functions include locus-specific roles in gene activation and silencing, as well as emerging roles in higher-order genome organization, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions.
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Affiliation(s)
- Xiao Li
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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131
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Sathyan KM, McKenna BD, Anderson WD, Duarte FM, Core L, Guertin MJ. An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. Genes Dev 2019; 33:1441-1455. [PMID: 31467088 PMCID: PMC6771385 DOI: 10.1101/gad.328237.119] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]
Abstract
Rapid perturbation of protein function permits the ability to define primary molecular responses while avoiding downstream cumulative effects of protein dysregulation. The auxin-inducible degron (AID) system was developed as a tool to achieve rapid and inducible protein degradation in nonplant systems. However, tagging proteins at their endogenous loci results in chronic auxin-independent degradation by the proteasome. To correct this deficiency, we expressed the auxin response transcription factor (ARF) in an improved inducible degron system. ARF is absent from previously engineered AID systems but is a critical component of native auxin signaling. In plants, ARF directly interacts with AID in the absence of auxin, and we found that expression of the ARF PB1 (Phox and Bem1) domain suppresses constitutive degradation of AID-tagged proteins. Moreover, the rate of auxin-induced AID degradation is substantially faster in the ARF-AID system. To test the ARF-AID system in a quantitative and sensitive manner, we measured genome-wide changes in nascent transcription after rapidly depleting the ZNF143 transcription factor. Transcriptional profiling indicates that ZNF143 activates transcription in cis and regulates promoter-proximal paused RNA polymerase density. Rapidly inducible degradation systems that preserve the target protein's native expression levels and patterns will revolutionize the study of biological systems by enabling specific and temporally defined protein dysregulation.
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Affiliation(s)
- Kizhakke Mattada Sathyan
- Biochemistry and Molecular Genetics Department, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Brian D McKenna
- Biochemistry and Molecular Genetics Department, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Warren D Anderson
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Leighton Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Michael J Guertin
- Biochemistry and Molecular Genetics Department, University of Virginia, Charlottesville, Virginia 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA.,Cancer Center, University of Virginia, Charlottesville, Virginia 22908, USA
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132
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A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia. Noncoding RNA Res 2019; 4:96-108. [PMID: 31891018 PMCID: PMC6926186 DOI: 10.1016/j.ncrna.2019.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/09/2019] [Accepted: 08/01/2019] [Indexed: 11/16/2022] Open
Abstract
Noncoding RNAs are increasingly being accredited with key roles in gene regulation during development and disease. Here we report the discovery and characterization of a novel long noncoding RNA, Hmrhl, which shares synteny and partial sequence similarity with the mouse lncRNA, Mrhl. The human homolog, Hmrhl, transcribed from intron 14 of phkb gene, is 5.5 kb in size, expressed in all tissues examined and is associated with chromatin. Analysis of Hmrhl locus using ENCODE database revealed that it exhibits hallmarks of enhancers like the open chromatin configuration, binding of transcription factors, enhancer specific histone signature etc. in the K562 Chronic Myelogenous Leukemia (CML) cells. We compared the expression of Hmrhl in the normal lymphoblast cell line, GM12878, with that of K562 cells and lymphoma samples and show that it is highly upregulated in leukemia as well as several cases of lymphoma. Further, we validated the enhancer properties of Hmrhl locus in K562 cells with the help of ChIP-qPCR and Luciferase assay. Moreover, siRNA mediated down-regulation of Hmrhl in K562 cells leads to a concomitant down regulation of its parent gene, phkb, showing that Hmrhl functions as an enhancer RNA and positively regulates its host gene, phkb, in chronic myelogenous leukemia. This study is significant in view of the fact that a better understanding of mechanism of gene regulation under normal conditions and its perturbation in cancer could in turn help in its therapeutic intervention through molecular medicine/RNA based drug discovery.
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133
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Lewis MW, Li S, Franco HL. Transcriptional control by enhancers and enhancer RNAs. Transcription 2019; 10:171-186. [PMID: 31791217 PMCID: PMC6948965 DOI: 10.1080/21541264.2019.1695492] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/02/2022] Open
Abstract
The regulation of gene expression is a fundamental cellular process and its misregulation is a key component of disease. Enhancers are one of the most salient regulatory elements in the genome and help orchestrate proper spatiotemporal gene expression during development, in homeostasis, and in response to signaling. Notably, molecular aberrations at enhancers, such as translocations and single nucleotide polymorphisms, are emerging as an important source of human variation and susceptibility to disease. Herein we discuss emerging paradigms addressing how genes are regulated by enhancers, common features of active enhancers, and how non-coding enhancer RNAs (eRNAs) can direct gene expression programs that underlie cellular phenotypes. We survey the current evidence, which suggests that eRNAs can bind to transcription factors, mediate enhancer-promoter interactions, influence RNA Pol II elongation, and act as decoys for repressive cofactors. Furthermore, we discuss current methodologies for the identification of eRNAs and novel approaches to elucidate their functions.
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Affiliation(s)
- Michael W. Lewis
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Shen Li
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hector L. Franco
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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134
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Perenthaler E, Yousefi S, Niggl E, Barakat TS. Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development. Front Cell Neurosci 2019; 13:352. [PMID: 31417368 PMCID: PMC6685065 DOI: 10.3389/fncel.2019.00352] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022] Open
Abstract
The development of the human cerebral cortex is a complex and dynamic process, in which neural stem cell proliferation, neuronal migration, and post-migratory neuronal organization need to occur in a well-organized fashion. Alterations at any of these crucial stages can result in malformations of cortical development (MCDs), a group of genetically heterogeneous neurodevelopmental disorders that present with developmental delay, intellectual disability and epilepsy. Recent progress in genetic technologies, such as next generation sequencing, most often focusing on all protein-coding exons (e.g., whole exome sequencing), allowed the discovery of more than a 100 genes associated with various types of MCDs. Although this has considerably increased the diagnostic yield, most MCD cases remain unexplained. As Whole Exome Sequencing investigates only a minor part of the human genome (1-2%), it is likely that patients, in which no disease-causing mutation has been identified, could harbor mutations in genomic regions beyond the exome. Even though functional annotation of non-coding regions is still lagging behind that of protein-coding genes, tremendous progress has been made in the field of gene regulation. One group of non-coding regulatory regions are enhancers, which can be distantly located upstream or downstream of genes and which can mediate temporal and tissue-specific transcriptional control via long-distance interactions with promoter regions. Although some examples exist in literature that link alterations of enhancers to genetic disorders, a widespread appreciation of the putative roles of these sequences in MCDs is still lacking. Here, we summarize the current state of knowledge on cis-regulatory regions and discuss novel technologies such as massively-parallel reporter assay systems, CRISPR-Cas9-based screens and computational approaches that help to further elucidate the emerging role of the non-coding genome in disease. Moreover, we discuss existing literature on mutations or copy number alterations of regulatory regions involved in brain development. We foresee that the future implementation of the knowledge obtained through ongoing gene regulation studies will benefit patients and will provide an explanation to part of the missing heritability of MCDs and other genetic disorders.
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Affiliation(s)
| | | | | | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC – University Medical Center, Rotterdam, Netherlands
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135
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Insights into active intragenic enhancers. Biochem Biophys Res Commun 2019; 515:423-428. [PMID: 31160092 DOI: 10.1016/j.bbrc.2019.05.160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/26/2019] [Indexed: 01/22/2023]
Abstract
Enhancers can regulate gene transcription from afar. Many enhancers are located in genes. Although the regulatory roles of several individual intragenic enhancers have been elaborated, a genome-wide insight into intragenic enhancers remains to be elucidated. We found that active intragenic enhancers have a preference for being located in expressed genes. Unlike intergenic enhancers, active intragenic enhancers are enriched of H3K79me2 epigenetic signal, and depleted of variant histone H2A.Z. Moreover, eRNAs of active intragenic enhancers show lower degradation rates than those of the other enhancers. Our findings will have implications in understanding functions of intragenic enhancers.
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136
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Jia Y, Chng WJ, Zhou J. Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. J Hematol Oncol 2019; 12:77. [PMID: 31311566 PMCID: PMC6636097 DOI: 10.1186/s13045-019-0757-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Super-enhancers (SEs) in a broad range of human cell types are large clusters of enhancers with aberrant high levels of transcription factor binding, which are central to drive expression of genes in controlling cell identity and stimulating oncogenic transcription. Cancer cells acquire super-enhancers at oncogene and cancerous phenotype relies on these abnormal transcription propelled by SEs. Furthermore, specific inhibitors targeting SEs assembly and activation have offered potential targets for treating various tumors including hematological malignancies. Here, we first review the identification, functional significance of SEs. Next, we summarize recent findings of SEs and SE-driven gene regulation in normal hematopoiesis and hematologic malignancies. The importance and various modes of SE-mediated MYC oncogene amplification are illustrated. Finally, we highlight the progress of SEs as selective therapeutic targets in basic research and clinical trials. Some open questions regarding functional significance and future directions of targeting SEs in the clinic will be discussed too.
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Affiliation(s)
- Yunlu Jia
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
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137
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Zhang P, Wu W, Chen Q, Chen M. Non-Coding RNAs and their Integrated Networks. J Integr Bioinform 2019; 16:/j/jib.2019.16.issue-3/jib-2019-0027/jib-2019-0027.xml. [PMID: 31301674 PMCID: PMC6798851 DOI: 10.1515/jib-2019-0027] [Citation(s) in RCA: 358] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/02/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs' essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.
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Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenyi Wu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
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138
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Zhu C, Li L, Zhang Z, Bi M, Wang H, Su W, Hernandez K, Liu P, Chen J, Chen M, Huang THM, Chen L, Liu Z. A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer. Mol Cell 2019; 75:791-806.e8. [PMID: 31303470 DOI: 10.1016/j.molcel.2019.06.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/06/2019] [Accepted: 06/05/2019] [Indexed: 12/26/2022]
Abstract
YAP/TEAD are nuclear effectors of the Hippo pathway, regulating organ size and tumorigenesis largely through promoter-associated function. However, their function as enhancer regulators remains poorly understood. Through an in vivo proximity-dependent labeling (BioID) technique, we identified YAP1 and TEAD4 protein as co-regulators of ERα on enhancers. The binding of YAP1/TEAD4 to ERα-bound enhancers is augmented upon E2 stimulation and is required for the induction of E2/ERα target genes and E2-induced oncogenic cell growth. Furthermore, their enhancer binding is a prerequisite for enhancer activation marked by eRNA transcription and for the recruitment of the enhancer activation machinery component MED1. The binding of TEAD4 on active ERE-containing enhancers is independent of its DNA-binding behavior, and instead, occurs through protein-tethering trans-binding. Our data reveal a non-canonical function of YAP1 and TEAD4 as ERα cofactors in regulating cancer growth, highlighting the potential of YAP/TEAD as possible actionable drug targets for ERα+ breast cancer.
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Affiliation(s)
- Chi Zhu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Li Li
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Oncology, The Second People's Hospital of Jiaozuo, Jiaozuo City, Henan 454001, China
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Mingjun Bi
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Hu Wang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenyue Su
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karen Hernandez
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Pingping Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Junqiang Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Mingqiu Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lizhen Chen
- Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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139
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Anderson AP, Jones AG. erefinder: Genome-wide detection of oestrogen response elements. Mol Ecol Resour 2019; 19:1366-1373. [PMID: 31177626 DOI: 10.1111/1755-0998.13046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 11/28/2022]
Abstract
Oestrogen response elements (EREs) are specific DNA sequences to which ligand-bound oestrogen receptors (ERs) physically bind, allowing them to act as transcription factors for target genes. Locating EREs and ER responsive regions is therefore a potentially important component of the study of oestrogen-regulated pathways. Here, we report the development of a novel software tool, erefinder, which conducts a genome-wide, sliding-window analysis of oestrogen receptor binding affinity. We demonstrate the effects of adjusting window size and highlight the program's general agreement with ChIP studies. We further provide two examples of how erefinder can be used for comparative approaches. erefinder can handle large input files, has settings to allow for broad and narrow searches, and provides the full output to allow for greater data manipulation. These features facilitate a wide range of hypothesis testing for researchers and make erefinder an excellent tool to aid in oestrogen-related research.
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Affiliation(s)
- Andrew P Anderson
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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140
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Lu Y, Li Q, Zheng K, Fu C, Jiang C, Zhou D, Xia C, Ma S. Development of a high efficient promoter finding method based on transient transfection. Gene 2019; 2:100008. [PMID: 32550544 PMCID: PMC7286058 DOI: 10.1016/j.gene.2019.100008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/23/2019] [Accepted: 02/08/2019] [Indexed: 01/19/2023]
Abstract
In metazoan genome, the mechanism of gene expression regulation between transcriptional regulatory elements and their target gene is spatiotemporal. Active promoters possess many specific chromosomal features, such as hypersensitive to DNaseI and enrichment of specific histone modifications. In this article, we proposed a novel method which possesses a high efficiency to find promoters in vitro. A promoter-trap library was constructed with totally 706 random mouse genomic DNA fragment clones, and 260 promoter-active fragments of the library were screened by transient transfection into 4T1 cells. To demonstrate the accuracy of this promoter finding method, 13 fragments with promoter activities were randomly selected for published DNase-seq and ChIP-seq data analysis, downstream transcripts prediction and expression confirmation. qRT-PCR results showed that six predicted transcription units were successfully amplified in different mouse tissues/cells or in reconstituted mouse mammary tumors. Our results indicate that this promoter finding method can successfully detect the promoter-active fragments and their downstream transcripts.
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Key Words
- ATAC-seq, Assay for transposase-accessible chromatin using sequencing
- Bioinformatics
- CAGE, cap analysis of gene expression
- CMV, Cytomegalovirus
- Cancer-specific promoter
- ChIP-seq, Chromatin immunoprecipitation followed by massively parallel DNA sequencing
- Ct, threshold
- DHS, DNaseI hypersensitive sites
- DNase-seq, DNase I hypersensitive sites sequencing
- EF1a1, eukaryotic translation elongation factor 1 alpha 1
- FBS, fetal bovine serum
- GRO-seq, global run-on sequencing
- Gene expression regulation
- Gene finding
- H3K4me3, histone H3 lysine 4 trimethylation
- Itpr2, inositol 1, 4, 5-triphosphate receptor 2
- LSINCT5, long stress-induced non-coding transcript 5
- MCS, multiple cloning site
- MPRA, Massively parallel reporter assays
- Mouse breast cancer
- PBS, phosphate buffered solution
- Promoter trap
- RNA-seq, RNA sequencing
- SD, standard deviation
- STARR-seq, Self-transcribing active regulatory region sequencing
- TFs, transcription factors
- TSS, transcription start sites
- dNTPs, deoxy-ribonucleoside triphosphate
- eRNAs, enhancer RNAs
- mSEAP, mouse synthetic secreted embryonic alkaline phosphatase
- pNPP, p-nitropheny-phosate
- qRT-PCR, quantitative RT-PCR
- tpk1, thiamine pyrophosphokinase
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Affiliation(s)
- Yao Lu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Qilong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Kexin Zheng
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Chenghao Fu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Chunying Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Dayu Zhou
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Chao Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
| | - Shiliang Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, PR China
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141
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Man HSJ, Marsden PA. LncRNAs and epigenetic regulation of vascular endothelium: genome positioning system and regulators of chromatin modifiers. Curr Opin Pharmacol 2019; 45:72-80. [PMID: 31125866 DOI: 10.1016/j.coph.2019.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic mechanisms regulate the cell type-specific expression of endothelial-enriched genes. A major question has been how chromatin modifiers without inherent sequence specificity can be targeted to genomic coordinates. Recently, long noncoding RNAs (lncRNAs) have emerged as candidates for specifying genomic positioning for chromatin modifiers. However, lncRNAs function by a number of mechanisms in both the nucleus and the cytoplasm. Recent studies indicate the existence of endothelial-enriched lncRNAs. This review discusses lncRNA regulation in endothelial cells with a focus on four recently described nuclear-enriched lncRNAs: MANTIS, LEENE, STEEL, and GATA6-AS. This emerging work on these lncRNAs contributes to our understanding of epigenetic regulation in the vascular endothelium with links to important themes in endothelial biology, including angiogenesis and shear stress.
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Affiliation(s)
- Hon-Sum Jeffrey Man
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Philip A Marsden
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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142
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Holding AN, Giorgi FM, Donnelly A, Cullen AE, Nagarajan S, Selth LA, Markowetz F. VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer. Genome Biol 2019; 20:91. [PMID: 31084623 PMCID: PMC6515683 DOI: 10.1186/s13059-019-1698-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND VirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We apply our method to dissect the regulation of estrogen receptor-alpha activation in breast cancer to identify potential co-regulators of the estrogen receptor's transcriptional response. RESULTS VULCAN analysis of estrogen receptor activation in breast cancer highlights the key components of the estrogen receptor complex alongside a novel interaction with GRHL2. We demonstrate that GRHL2 is recruited to a subset of estrogen receptor binding sites and regulates transcriptional output, as evidenced by changes in estrogen receptor-associated eRNA expression and stronger estrogen receptor binding at active enhancers after GRHL2 knockdown. CONCLUSIONS Our findings provide new insight into the role of GRHL2 in regulating eRNA transcription as part of estrogen receptor signaling. These results demonstrate VULCAN, available from Bioconductor, as a powerful predictive tool.
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Affiliation(s)
- Andrew N Holding
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- The Alan Turing Institute, 96 Euston Road, Kings Cross, London, NW1 2DB, UK.
| | - Federico M Giorgi
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, Bologna, Italy
| | - Amanda Donnelly
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amy E Cullen
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Florian Markowetz
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
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143
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Azébi S, Batsché E, Michel F, Kornobis E, Muchardt C. Expression of endogenous retroviruses reflects increased usage of atypical enhancers in T cells. EMBO J 2019; 38:embj.2018101107. [PMID: 31068361 DOI: 10.15252/embj.2018101107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/20/2019] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Several autoimmune diseases including multiple sclerosis (MS) cause increased transcription of endogenous retroviruses (HERVs) normally repressed by heterochromatin. In parallel, HERV-derived sequences were reported to drive gene expression. Here, we have examined a possible link between promoter and enhancer divergent transcription and the production of HERV transcripts. We find that HERV-derived sequences are in general counter-selected at regulatory regions, a counter-selection that is strongest in brain tissues while very moderate in stem cells. By exposing T cells to the pesticide dieldrin, we further found that a series of HERV-driven enhancers otherwise active only at stem cell stages can be reactivated by stress. This in part relies on peptidylarginine deiminase activity, possibly participating in the reawakening of silenced enhancers. Likewise, usage of HERV-driven enhancers was increased in myelin-reactive T cells from patients with MS, correlating with activation of nearby genes at several sites. Altogether, we propose that HERV-driven enhancers constitute a reservoir of auxiliary enhancers transiently induced by stress while chronically active in diseases like MS.
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Affiliation(s)
- Saliha Azébi
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France.,Unit of Cytokine Signaling, Department of Immunology, Institut Pasteur, Paris, France
| | - Eric Batsché
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France
| | - Frédérique Michel
- Ecole Doctorale "Complexité du Vivant" (ED515), Sorbonne Université, Paris, France
| | - Etienne Kornobis
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France
| | - Christian Muchardt
- Unité de Régulation Epigénétique, UMR3738, CNRS, Institut Pasteur, Paris, France
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144
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Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023] Open
Abstract
Tight regulation of gene transcription is essential for normal development, tissue homeostasis, and disease-free survival. Enhancers are distal regulatory elements in the genome that provide specificity to gene expression programs and are frequently misregulated in cancer. Recent studies examined various enhancer-driven malignant dependencies and identified different approaches to specifically target these programs. In this review, we describe numerous features that make enhancers good transcriptional targets in cancer therapy and discuss different approaches to overcome enhancer perturbation. Interestingly, a number of approved therapeutic agents, such as cyclosporine, steroid hormones, and thiazolidinediones, actually function by affecting enhancer landscapes by directly targeting very specific transcription factor programs. More recently, a broader approach to targeting deregulated enhancer programs has been achieved via Bromodomain and Extraterminal (BET) inhibition or perturbation of transcription-related cyclin-dependent kinases (CDK). One challenge to enhancer-targeted therapy is proper patient stratification. We suggest that monitoring of enhancer RNA (eRNA) expression may serve as a unique biomarker of enhancer activity that can help to predict and monitor responsiveness to enhancer-targeted therapies. A more thorough investigation of cancer-specific enhancers and the underlying mechanisms of deregulation will pave the road for an effective utilization of enhancer modulators in a precision oncology approach to cancer treatment.
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Affiliation(s)
- Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
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145
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Being in a loop: how long non-coding RNAs organise genome architecture. Essays Biochem 2019; 63:177-186. [DOI: 10.1042/ebc20180057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
Chromatin architecture has a significant impact on gene expression. Evidence in the last two decades support RNA as an important component of chromatin structure [Genes Dev. (2005) 19, 1635–1655; PLoS ONE (2007) 2, e1182; Nat. Genet. (2002) 30, 329–334]. Long non-coding RNAs (lncRNAs) are able to control chromatin structure through nucleosome positioning, interaction with chromatin re-modellers and chromosome looping. These functions are carried out in cis at the site of lncRNAs transcription or in trans at distant loci. While the evidence for a role in lncRNAs in regulating gene expression through chromatin interactions is increasing, there is still very little conclusive evidence for a potential role in looping organisation. Here, we review models for the involvement of lncRNAs in genome architecture and the experimental evidence to support them.
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146
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Meinsohn MC, Smith OE, Bertolin K, Murphy BD. The Orphan Nuclear Receptors Steroidogenic Factor-1 and Liver Receptor Homolog-1: Structure, Regulation, and Essential Roles in Mammalian Reproduction. Physiol Rev 2019; 99:1249-1279. [DOI: 10.1152/physrev.00019.2018] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nuclear receptors are intracellular proteins that act as transcription factors. Proteins with classic nuclear receptor domain structure lacking identified signaling ligands are designated orphan nuclear receptors. Two of these, steroidogenic factor-1 (NR5A1, also known as SF-1) and liver receptor homolog-1 (NR5A2, also known as LRH-1), bind to the same DNA sequences, with different and nonoverlapping effects on targets. Endogenous regulation of both is achieved predominantly by cofactor interactions. SF-1 is expressed primarily in steroidogenic tissues, LRH-1 in tissues of endodermal origin and the gonads. Both receptors modulate cholesterol homeostasis, steroidogenesis, tissue-specific cell proliferation, and stem cell pluripotency. LRH-1 is essential for development beyond gastrulation and SF-1 for genesis of the adrenal, sexual differentiation, and Leydig cell function. Ovary-specific depletion of SF-1 disrupts follicle development, while LRH-1 depletion prevents ovulation, cumulus expansion, and luteinization. Uterine depletion of LRH-1 compromises decidualization and pregnancy. In humans, SF-1 is present in endometriotic tissue, where it regulates estrogen synthesis. SF-1 is underexpressed in ovarian cancer cells and overexpressed in Leydig cell tumors. In breast cancer cells, proliferation, migration and invasion, and chemotherapy resistance are regulated by LRH-1. In conclusion, the NR5A orphan nuclear receptors are nonredundant factors that are crucial regulators of a panoply of biological processes, across multiple reproductive tissues.
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Affiliation(s)
- Marie-Charlotte Meinsohn
- Centre de Recherche en Reproduction et Fertilité, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Olivia E. Smith
- Centre de Recherche en Reproduction et Fertilité, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Kalyne Bertolin
- Centre de Recherche en Reproduction et Fertilité, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Bruce D. Murphy
- Centre de Recherche en Reproduction et Fertilité, Université de Montréal, St-Hyacinthe, Québec, Canada
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147
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Tecalco-Cruz AC, Ramírez-Jarquín JO, Cruz-Ramos E. Estrogen Receptor Alpha and its Ubiquitination in Breast Cancer Cells. Curr Drug Targets 2019; 20:690-704. [DOI: 10.2174/1389450119666181015114041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 12/23/2022]
Abstract
More than 70% of all breast cancer cases are estrogen receptor alpha-positive (ERα). ERα is a member of the nuclear receptor family, and its activity is implicated in the gene transcription linked to the proliferation of breast cancer cells, as well as in extranuclear signaling pathways related to the development of resistance to endocrine therapy. Protein-protein interactions and posttranslational modifications of ERα underlie critical mechanisms that modulate its activity. In this review, the relationship between ERα and ubiquitin protein (Ub), was investigated in the context of breast cancer cells. Interestingly, Ub can bind covalently or non-covalently to ERα resulting in either a proteolytic or non-proteolytic fate for this receptor. Thereby, Ub-dependent molecular pathways that modulate ERα signaling may play a central role in breast cancer progression, and consequently, present critical targets for treatment of this disease.
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Affiliation(s)
- Angeles C. Tecalco-Cruz
- Instituto de Investigaciones Biomedicas. Universidad Nacional Autonoma de Mexico. Mexico City, 04510, Mexico
| | - Josué O. Ramírez-Jarquín
- Instituto de Fisiologia Celular. Universidad Nacional Autonoma de Mexico. Mexico City, 04510, Mexico
| | - Eduardo Cruz-Ramos
- Instituto de Investigaciones Biomedicas. Universidad Nacional Autonoma de Mexico. Mexico City, 04510, Mexico
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148
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Aho ER, Wang J, Gogliotti RD, Howard GC, Phan J, Acharya P, Macdonald JD, Cheng K, Lorey SL, Lu B, Wenzel S, Foshage AM, Alvarado J, Wang F, Shaw JG, Zhao B, Weissmiller AM, Thomas LR, Vakoc CR, Hall MD, Hiebert SW, Liu Q, Stauffer SR, Fesik SW, Tansey WP. Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. Cell Rep 2019; 26:2916-2928.e13. [PMID: 30865883 PMCID: PMC6448596 DOI: 10.1016/j.celrep.2019.02.047] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023] Open
Abstract
The chromatin-associated protein WDR5 is a promising target for pharmacological inhibition in cancer. Drug discovery efforts center on the blockade of the "WIN site" of WDR5, a well-defined pocket that is amenable to small molecule inhibition. Various cancer contexts have been proposed to be targets for WIN site inhibitors, but a lack of understanding of WDR5 target genes and of the primary effects of WIN site inhibitors hampers their utility. Here, by the discovery of potent WIN site inhibitors, we demonstrate that the WIN site links WDR5 to chromatin at a small cohort of loci, including a specific subset of ribosome protein genes. WIN site inhibitors rapidly displace WDR5 from chromatin and decrease the expression of associated genes, causing translational inhibition, nucleolar stress, and p53 induction. Our studies define a mode by which WDR5 engages chromatin and forecast that WIN site blockade could have utility against multiple cancer types.
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Affiliation(s)
- Erin R Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rocco D Gogliotti
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jonathan D Macdonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ken Cheng
- National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sabine Wenzel
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Audra M Foshage
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Joseph Alvarado
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Feng Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - J Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | | | - Matthew D Hall
- National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shaun R Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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149
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Nair SJ, Yang L, Meluzzi D, Oh S, Yang F, Friedman MJ, Wang S, Suter T, Alshareedah I, Gamliel A, Ma Q, Zhang J, Hu Y, Tan Y, Ohgi KA, Jayani RS, Banerjee PR, Aggarwal AK, Rosenfeld MG. Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. Nat Struct Mol Biol 2019; 26:193-203. [PMID: 30833784 PMCID: PMC6709854 DOI: 10.1038/s41594-019-0190-5] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022]
Abstract
A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. The potential contributions of physicochemical properties of enhancer assembly in signaling events remain poorly understood. Here we report that in human breast cancer cells, the acute 17β-estradiol-dependent activation of functional enhancers requires assembly of an enhancer RNA-dependent ribonucleoprotein (eRNP) complex exhibiting properties of phase-separated condensates. Unexpectedly, while acute ligand-dependent assembly of eRNPs resulted in enhancer activation sensitive to chemical disruption of phase separation, chronically activated enhancers proved resistant to such disruption, with progressive maturation of eRNPs to a more gel-like state. Acute, but not chronic, stimulation resulted in ligand-induced, condensin-dependent changes in spatial chromatin conformation based on homotypic enhancer association, resulting in cooperative enhancer-activation events. Thus, distinct physicochemical properties of eRNP condensates on enhancers serve as determinants of rapid ligand-dependent alterations in chromosomal architecture and cooperative enhancer activation.
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Affiliation(s)
- Sreejith J Nair
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dario Meluzzi
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Soohwan Oh
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Meyer J Friedman
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Amir Gamliel
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qi Ma
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jie Zhang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yiren Hu
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Yuliang Tan
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kenneth A Ohgi
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ranveer Singh Jayani
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Priya R Banerjee
- Department of Physics, University at Buffalo-SUNY, Buffalo, NY, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
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150
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Pang B, Sui S, Wang Q, Wu J, Yin Y, Xu S. Upregulation of DLEU1 expression by epigenetic modification promotes tumorigenesis in human cancer. J Cell Physiol 2019; 234:17420-17432. [PMID: 30793303 DOI: 10.1002/jcp.28364] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
The function of DLEU1 in human cancer is largely unknown. The Cancer Genome Atlas data were applied to identify the landscape of differential genes between tumor tissues and normal tissues, which was further validated by our cohort data and pan-cancer data including 33 cancer types with 11,060 patients. Next, DLEU1 was selected to validate the novel finding and result showed that it promoted tumorigenesis in vitro and in vivo. Mechanistically, DLEU1 promotes SRP4 expression via increasing H3K27ac enrichment to SRP4 locus epigenetically. Moreover, epigenetic modification leads to upregulation of DLEU1 expression via decreased DNA methylation and increased H3K27ac and H3K4me3 histone modification in its locus. Finally, high expression of DLEU1 correlates with worse prognosis not only in specific cancer type patients but also in patients in the pan-cancer cohort. In summary, the work broadens the function landscape of known long noncoding RNAs in human cancer and provides novel insights into their roles in tumorigenesis.
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Affiliation(s)
- Boran Pang
- Department of Surgery, Rui Jin Hospital, Shanghai Key Laboratory of Gastric Neoplasm, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyao Sui
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Junqiang Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanling Yin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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