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Hajheidari M, Sunyaev S, de Meaux J. Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression. PLANT & CELL PHYSIOLOGY 2025; 66:444-460. [PMID: 39626022 PMCID: PMC12085094 DOI: 10.1093/pcp/pcae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 11/17/2024] [Accepted: 11/29/2024] [Indexed: 05/18/2025]
Abstract
Variation in complex traits is controlled by multiple genes. The prevailing assumption is that such polygenic complex traits are underpinned by variation in elementary molecular traits, such as gene expression, which themselves have a simple genetic basis. Here, we review recent advances that reveal the captivating complexity of gene regulation: the cell type, time point, and magnitude of gene expression are not merely dependent on a couple of regulators; rather, they result from a probabilistic process shaped by cis- and trans-regulatory elements collaboratively integrating internal and external cues with the tightly regulated dynamics of DNA. In addition, the finding that genetic variants linked to complex diseases in humans often do not co-localize with quantitative trait loci modulating gene expression, along with the role of nonfunctional transcription factor (TF) binding sites, suggests that some of the genetic effects influencing gene expression variation may be indirect. If the number of genomic positions responsible for TF binding, TF binding site search time, DNA conformation and accessibility as well as regulation of all trans-acting factors is indeed vast, is it plausible that the complexity of elementary molecular traits approaches the complexity of higher-level organismal traits? Although it is hard to know the answer to this question, we motivate it by reviewing the complexity of the molecular machinery further.
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Affiliation(s)
- Mohsen Hajheidari
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Juliette de Meaux
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany
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2
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Krchlikova V, Lu Y, Sauter D. Viral influencers: deciphering the role of endogenous retroviral LTR12 repeats in cellular gene expression. J Virol 2025; 99:e0135124. [PMID: 39887236 PMCID: PMC11853044 DOI: 10.1128/jvi.01351-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2025] Open
Abstract
The human genome is like a museum of ancient retroviral infections. It contains a large number of endogenous retroviruses (ERVs) that bear witness to past integration events. About 5,000 of them are so-called long terminal repeat 12 (LTR12) elements. Compared with 20,000 human genes, this is a remarkable number. Although LTR12 elements can act as promoters or enhancers of cellular genes, the function of most of these retroviral elements has remained unclear. In our mini-review, we show that different LTR12 elements share many similarities, including common transcription factor binding sites. Furthermore, we summarize novel insights into the epigenetic mechanisms governing their silencing and activation. Specific examples of genes and pathways that are regulated by LTR12 loci are used to illustrate the regulatory network built by these repetitive elements. A particular focus is on their role in the regulation of antiviral immune responses, tumor cell proliferation, and senescence. Finally, we describe how a targeted activation of this fascinating ERV family could be used for diagnostic or therapeutic purposes.
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Affiliation(s)
- Veronika Krchlikova
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Yueshuang Lu
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
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3
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Pavlu S, Nikumbh S, Kovacik M, An T, Lenhard B, Simkova H, Navratilova P. Core promoterome of barley embryo. Comput Struct Biotechnol J 2024; 23:264-277. [PMID: 38173877 PMCID: PMC10762323 DOI: 10.1016/j.csbj.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.
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Affiliation(s)
- Simon Pavlu
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Sarvesh Nikumbh
- Merck Sharp & Dohme (UK) Limited, 120 Moorgate, London EC2M 6UR, UK
| | - Martin Kovacik
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Tadaichi An
- DNAFORM Precision Gene Technologies, 230–0046 Yokohama, Kanagawa, Japan
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Hana Simkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
| | - Pavla Navratilova
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, 77900 Olomouc, Czech Republic
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4
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Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Shah SR, Yu H, Lis JT, Kundaje A. Dissecting the cis-regulatory syntax of transcription initiation with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596138. [PMID: 38853896 PMCID: PMC11160661 DOI: 10.1101/2024.05.28.596138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understood. We trained and interpreted a neural network called ProCapNet that accurately models base-resolution initiation profiles from PRO-cap experiments using local DNA sequence. ProCapNet learns sequence motifs with distinct effects on initiation rates and TSS positioning and uncovers context-specific cryptic initiator elements intertwined within other TF motifs. ProCapNet annotates predictive motifs in nearly all actively transcribed regulatory elements across multiple cell-lines, revealing a shared cis-regulatory logic across promoters and enhancers and a highly epistatic sequence syntax of cooperative and competitive motif interactions. ProCapNet models of steady-state RAMPAGE profiles distill initiation signals on par with models trained directly on PRO-cap profiles. ProCapNet learns a largely cell-type-agnostic cis-regulatory code of initiation complementing sequence drivers of cell-type-specific chromatin state critical for accurate prediction of cell-type-specific transcription initiation.
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Affiliation(s)
- Kelly Cochran
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Sagar R Shah
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Haiyuan Yu
- Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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5
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Chivu AG, Basso BA, Abuhashem A, Leger MM, Barshad G, Rice EJ, Vill AC, Wong W, Chou SP, Chovatiya G, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. Evolution of promoter-proximal pausing enabled a new layer of transcription control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.19.529146. [PMID: 39416036 PMCID: PMC11482795 DOI: 10.1101/2023.02.19.529146] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here we analyzed transcription in species across the tree of life. Unicellular eukaryotes display a slow acceleration of Pol II near transcription start sites that transitioned to a longer-lived, focused pause in metazoans. This event coincided with the evolution of new subunits in the NELF and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.
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Affiliation(s)
- Alexandra G. Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Brent A. Basso
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, NY 10065, USA
| | - Michelle M. Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward J. Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Albert C. Vill
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Tri-Institutional training Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Shao-Pei Chou
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Gopal Chovatiya
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Rebecca Brady
- Department of Biology, Ithaca College, Ithaca NY 14850, USA
| | - Jeramiah J. Smith
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | | | - César Arenas-Mena
- Department of Biology at the College of Staten Island and PhD Programs in Biology and Biochemistry at The Graduate Center, The City University of New York (CUNY), Staten Island, NY 10314, USA
| | - Ilana L. Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain., Barcelona, 08003, Spain
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, NY 10065, USA
| | - John T. Lis
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - James J. Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Genetics and Biochemistry, Clemson University, 105 Collings St, Clemson, SC 29634
| | - Charles G. Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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6
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He AY, Danko CG. Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.583868. [PMID: 38559255 PMCID: PMC10979970 DOI: 10.1101/2024.03.13.583868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
How the DNA sequence of cis-regulatory elements encode transcription initiation patterns remains poorly understood. Here we introduce CLIPNET, a deep learning model trained on population-scale PRO-cap data that predicts the position and quantity of transcription initiation with single nucleotide resolution from DNA sequence more accurately than existing approaches. Interpretation of CLIPNET revealed a complex regulatory syntax consisting of DNA-protein interactions in five major positions between -200 and +50 bp relative to the transcription start site, as well as more subtle positional preferences among transcriptional activators. Transcriptional activator and core promoter motifs work non-additively to encode distinct aspects of initiation, with the former driving initiation quantity and the latter initiation position. We identified core promoter motifs that explain initiation patterns in the majority of promoters and enhancers, including DPR motifs and AT-rich TBP binding sequences in TATA-less promoters. Our results provide insights into the sequence architecture governing transcription initiation.
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Affiliation(s)
- Adam Y. He
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Graduate Field of Computational Biology, Cornell University
| | - Charles G. Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University
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7
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Liu LL, Song CC, Abu-Elala N, Tan XY, Zhao T, Zheng H, Yang H, Luo Z. Transcriptional regulation of Znt family members znt4, znt5 and znt10 and their function in zinc transport in yellow catfish (Pelteobagrus fulvidraco). BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195041. [PMID: 38740364 DOI: 10.1016/j.bbagrm.2024.195041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
The study characterized the transcriptionally regulatory mechanism and functions of three zinc (Zn) transporters (znt4, znt5 and znt10) in Zn2+ metabolism in yellow catfish (Pelteobagrus fulvidraco), commonly freshwater fish in China and other countries. We cloned the sequences of znt4 promoter, spanning from -1217 bp to +80 bp relative to TSS (1297 bp); znt5, spanning from -1783 bp to +49 bp relative to TSS (1832 bp) and znt10, spanning from -1923 bp to +190 bp relative to TSS (2113 bp). In addition, after conducting the experiments of sequential deletion of promoter region and mutation of potential binding site, we found that the Nrf2 binding site (-607/-621 bp) and Klf4 binding site (-5/-14 bp) were required on znt4 promoter, the Mtf-1 binding site (-1674/-1687 bp) and Atf4 binding site (-444/-456 bp) were required on znt5 promoter and the Atf4 binding site (-905/-918 bp) was required on znt10 promoter. Then, according to EMSA and ChIP, we found that Zn2+ incubation increased DNA affinity of Atf4 to znt5 or znt10 promoter, but decreased DNA affinity of Nrf2 to znt4 promoter, Klf4 to znt4 promoter and Mtf-1 to znt5 promoter. Using fluorescent microscopy, it was revealed that Znt4 and Znt10 were located in the lysosome and Golgi, and Znt5 was located in the Golgi. Finally, we found that znt4 knockdown reduced the zinc content of lysosome and Golgi in the control and zinc-treated group; znt5 knockdown reduced the zinc content of Golgi in the control and zinc-treated group and znt10 knockdown reduced the zinc content of Golgi in the zinc-treated group. High dietary zinc supplement up-regulated Znt4 and Znt5 protein expression. Above all, for the first time, we revealed that Klf4 and Nrf2 transcriptionally regulated the activities of znt4 promoter; Mtf-1 and Atf4 transcriptionally regulated the activities of znt5 promoter and Atf4 transcriptionally regulated the activities of znt10 promoter, which provided innovative regulatory mechanism of zinc transporting in yellow catfish. Our study also elucidated their subcellular location, and regulatory role of zinc homeostasis in yellow catfish.
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Affiliation(s)
- Lu-Lu Liu
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Chang-Chun Song
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Nermeen Abu-Elala
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Egypt; Faculty of Veterinary Medicine, King Salman International University, South Saini, Egypt
| | - Xiao-Ying Tan
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Zhao
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Hua Zheng
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Yang
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Luo
- Hubei Hongshan Laboratory, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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8
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Sloutskin A, Itzhak D, Vogler G, Pozeilov H, Ideses D, Alter H, Adato O, Shachar H, Doniger T, Shohat-Ophir G, Frasch M, Bodmer R, Duttke SH, Juven-Gershon T. From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function in vivo. Development 2024; 151:dev202355. [PMID: 38958007 DOI: 10.1242/dev.202355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Transcription initiates at the core promoter, which contains distinct core promoter elements. Here, we highlight the complexity of transcriptional regulation by outlining the effect of core promoter-dependent regulation on embryonic development and the proper function of an organism. We demonstrate in vivo the importance of the downstream core promoter element (DPE) in complex heart formation in Drosophila. Pioneering a novel approach using both CRISPR and nascent transcriptomics, we show the effects of mutating a single core promoter element within the natural context. Specifically, we targeted the downstream core promoter element (DPE) of the endogenous tin gene, encoding the Tinman transcription factor, a homologue of human NKX2-5 associated with congenital heart diseases. The 7 bp substitution mutation results in massive perturbation of the Tinman regulatory network that orchestrates dorsal musculature, which is manifested as physiological and anatomical changes in the cardiac system, impaired specific activity features, and significantly compromised viability of adult flies. Thus, a single motif can have a critical impact on embryogenesis and, in the case of DPE, functional heart formation.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dekel Itzhak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Hadar Pozeilov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadar Alter
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Orit Adato
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hadar Shachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Galit Shohat-Ophir
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Manfred Frasch
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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9
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Villani RM, McKenzie ME, Davidson AL, Spurdle AB. Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease. Am J Hum Genet 2024; 111:1301-1315. [PMID: 38815586 PMCID: PMC11267523 DOI: 10.1016/j.ajhg.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024] Open
Abstract
To date, clinical genetic testing for Mendelian disease variants has focused heavily on exonic coding and intronic gene regions. This multi-step study was undertaken to provide an evidence base for selecting and applying computational approaches for use in clinical classification of 5' cis-regulatory region variants. Curated datasets of clinically reported disease-causing 5' cis-regulatory region variants and variants from matched genomic regions in population controls were used to calibrate six bioinformatic tools as predictors of variant pathogenicity. Likelihood ratio estimates were aligned to code weights following ClinGen recommendations for application of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) classification scheme. Considering code assignment across all reference dataset variants, performance was best for CADD (81.2%) and REMM (81.5%). Optimized thresholds provided moderate evidence toward pathogenicity (CADD, REMM) and moderate (CADD) or supporting (REMM) evidence against pathogenicity. Both sensitivity and specificity of prediction were improved when further categorizing variants based on location in an EPDnew-defined promoter region. Combining predictions (CADD, REMM, and location in a promoter region) increased specificity at the expense of sensitivity. Importantly, the optimal CADD thresholds for assigning ACMG/AMP codes PP3 (≥10) and BP4 (≤8) were vastly different from recommendations for protein-coding variants (PP3 ≥25.3; BP4 ≤22.7); CADD <22.7 would incorrectly assign BP4 for >90% of reported disease-causing cis-regulatory region variants. Our results demonstrate the need to consider a tiered approach and tailored score thresholds to optimize bioinformatic impact prediction for clinical classification of 5' cis-regulatory region variants.
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Affiliation(s)
- Rehan M Villani
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Maddison E McKenzie
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Aimee L Davidson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; University of Queensland, Brisbane, Queensland, Australia.
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10
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Duttke SH, Guzman C, Chang M, Delos Santos NP, McDonald BR, Xie J, Carlin AF, Heinz S, Benner C. Position-dependent function of human sequence-specific transcription factors. Nature 2024; 631:891-898. [PMID: 39020164 PMCID: PMC11269187 DOI: 10.1038/s41586-024-07662-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/04/2024] [Indexed: 07/19/2024]
Abstract
Patterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, contain similar assortments of sequence-specific transcription factor (TF) binding sites1-3. Knowledge of how these sequence motifs encode multiple, often overlapping, gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease4,5. Here, by studying gene regulation from the perspective of individual transcription start sites (TSSs), using natural genetic variation, perturbation of endogenous TF protein levels and massively parallel analysis of natural and synthetic regulatory elements, we show that the effect of TF binding on transcription initiation is position dependent. Analysing TF-binding-site occurrences relative to the TSS, we identified several motifs with highly preferential positioning. We show that these patterns are a combination of a TF's distinct functional profiles-many TFs, including canonical activators such as NRF1, NFY and Sp1, activate or repress transcription initiation depending on their precise position relative to the TSS. As such, TFs and their spacing collectively guide the site and frequency of transcription initiation. More broadly, these findings reveal how similar assortments of TF binding sites can generate distinct gene regulatory outcomes depending on their spatial configuration and how DNA sequence polymorphisms may contribute to transcription variation and disease and underscore a critical role for TSS data in decoding the regulatory information of our genome.
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Affiliation(s)
- Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.
| | - Carlos Guzman
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA, USA
| | - Max Chang
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA, USA
| | - Nathaniel P Delos Santos
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA, USA
| | - Bayley R McDonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Jialei Xie
- Department of Pathology and Medicine, U.C. San Diego School of Medicine, La Jolla, CA, USA
| | - Aaron F Carlin
- Department of Pathology and Medicine, U.C. San Diego School of Medicine, La Jolla, CA, USA
| | - Sven Heinz
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA, USA.
| | - Christopher Benner
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA, USA.
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11
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Adato O, Sloutskin A, Komemi H, Brabb I, Duttke S, Bucher P, Unger R, Juven-Gershon T. ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements. Bioinformatics 2024; 40:btae110. [PMID: 38407414 PMCID: PMC10950481 DOI: 10.1093/bioinformatics/btae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 02/27/2024] Open
Abstract
MOTIVATION Prediction and identification of core promoter elements and transcription factor binding sites is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus. Thus, there is a need for an up-to-date tool to detect and curate core promoter elements/motifs in any provided nucleotide sequences. RESULTS Here, we introduce ElemeNT 2023-a new and enhanced version of the Elements Navigation Tool, which provides novel capabilities for assessing evolutionary conservation and for readily evaluating the quality of high-throughput transcription start site (TSS) datasets, leveraging preferential motif positioning. ElemeNT 2023 is accessible both as a fast web-based tool and via command line (no coding skills are required to run the tool). While this tool is focused on core promoter elements, it can also be used for searching any user-defined motif, including sequence-specific DNA binding sites. Furthermore, ElemeNT's CORE database, which contains predicted core promoter elements around annotated TSSs, is now expanded to cover 10 species, ranging from worms to human. In this applications note, we describe the new workflow and demonstrate a case study using ElemeNT 2023 for core promoter composition analysis of diverse species, revealing motif prevalence and highlighting evolutionary insights. We discuss how this tool facilitates the exploration of uncharted transcriptomic data, appraises TSS quality, and aids in designing synthetic promoters for gene expression optimization. Taken together, ElemeNT 2023 empowers researchers with comprehensive tools for meticulous analysis of sequence elements and gene expression strategies. AVAILABILITY AND IMPLEMENTATION ElemeNT 2023 is freely available at https://www.juven-gershonlab.org/resources/element-v2023/. The source code and command line version of ElemeNT 2023 are available at https://github.com/OritAdato/ElemeNT. No coding skills are required to run the tool.
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Affiliation(s)
- Orit Adato
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Hodaya Komemi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Ian Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, United States
| | - Sascha Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, United States
| | - Philipp Bucher
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
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12
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Archuleta SR, Goodrich JA, Kugel JF. Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules 2024; 14:176. [PMID: 38397413 PMCID: PMC10886972 DOI: 10.3390/biom14020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.
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Affiliation(s)
| | - James A. Goodrich
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
| | - Jennifer F. Kugel
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
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13
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Uemura K, Ohyama T. Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function. Int J Mol Sci 2024; 25:1487. [PMID: 38338773 PMCID: PMC10855393 DOI: 10.3390/ijms25031487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Since the discovery of physical peculiarities around transcription start sites (TSSs) and a site corresponding to the TATA box, research has revealed only the average features of these sites. Unsettled enigmas include the individual genes with these features and whether they relate to gene function. Herein, using 10 physical properties of DNA, including duplex DNA free energy, base stacking energy, protein-induced deformability, and stabilizing energy of Z-DNA, we clarified for the first time that approximately 97% of the promoters of 21,056 human protein-coding genes have distinctive physical properties around the TSS and/or position -27; of these, nearly 65% exhibited such properties at both sites. Furthermore, about 55% of the 21,056 genes had a minimum value of regional duplex DNA free energy within TSS-centered ±300 bp regions. Notably, distinctive physical properties within the promoters and free energies of the surrounding regions separated human protein-coding genes into five groups; each contained specific gene ontology (GO) terms. The group represented by immune response genes differed distinctly from the other four regarding the parameter of the free energies of the surrounding regions. A vital suggestion from this study is that physical-feature-based analyses of genomes may reveal new aspects of the organization and regulation of genes.
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Affiliation(s)
- Kohei Uemura
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan;
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan;
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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14
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Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y. Structural visualization of transcription initiation in action. Science 2023; 382:eadi5120. [PMID: 38127763 DOI: 10.1126/science.adi5120] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
Abstract
Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuechun Qu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
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15
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Kharytonchyk S, Burnett C, GC K, Telesnitsky A. Transcription start site heterogeneity and its role in RNA fate determination distinguish HIV-1 from other retroviruses and are mediated by core promoter elements. J Virol 2023; 97:e0081823. [PMID: 37681957 PMCID: PMC10537674 DOI: 10.1128/jvi.00818-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 09/09/2023] Open
Abstract
HIV-1 uses heterogeneous transcription start sites (TSSs) to generate two RNA 5´ isoforms that adopt radically different structures and perform distinct replication functions. Although these RNAs differ in length by only two bases, exclusively, the shorter RNA is encapsidated while the longer RNA is excluded from virions and provides intracellular functions. The current study examined TSS usage and packaging selectivity for a broad range of retroviruses and found that heterogeneous TSS usage was a conserved feature of all tested HIV-1 strains, but all other retroviruses examined displayed unique TSSs. Phylogenetic comparisons and chimeric viruses' properties provided evidence that this mechanism of RNA fate determination was an innovation of the HIV-1 lineage, with determinants mapping to core promoter elements. Fine-tuning differences between HIV-1 and HIV-2, which uses a unique TSS, implicated purine residue positioning plus a specific TSS-adjacent dinucleotide in specifying multiplicity of TSS usage. Based on these findings, HIV-1 expression constructs were generated that differed from the parental strain by only two point mutations yet each expressed only one of HIV-1's two RNAs. Replication defects of the variant with only the presumptive founder TSS were less severe than those for the virus with only the secondary start site. IMPORTANCE Retroviruses use RNA both to encode their proteins and to serve in place of DNA as their genomes. A recent surprising discovery was that the genomic RNAs and messenger RNAs of HIV-1 are not identical but instead differ subtly on one of their ends. These differences enable the functional separation of HIV-1 RNAs into genome and messenger roles. In this report, we examined a broad collection of HIV-1-related viruses and discovered that each produced only one end class of RNA, and thus must differ from HIV-1 in how they specify RNA fates. By comparing regulatory signals, we generated virus variants that pinpointed the determinants of HIV-1 RNA fates, as well as HIV-1 variants that produced only one or the other functional class of RNA. Competition and replication assays confirmed that HIV-1 has evolved to rely on the coordinated actions of both its RNA forms.
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Affiliation(s)
- Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Keshav GC
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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16
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Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559415. [PMID: 37808859 PMCID: PMC10557634 DOI: 10.1101/2023.09.25.559415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating ("nascent") transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many "distal" elements in plants initiate tissue-specific stable transcripts and are likely bone fide promoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer "enhancers" or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.
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Affiliation(s)
- Bayley R. Mcdonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Colette Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M. Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Marina I. Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | | | - Steven E. Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H. Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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17
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Fisher MJ, Luse DS. Promoter-proximal nucleosomes attenuate RNA polymerase II transcription through TFIID. J Biol Chem 2023; 299:104928. [PMID: 37330174 PMCID: PMC10404688 DOI: 10.1016/j.jbc.2023.104928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023] Open
Abstract
A nucleosome is typically positioned with its proximal edge (NPE) ∼50 bp downstream from the transcription start site of metazoan RNA polymerase II promoters. This +1 nucleosome has distinctive characteristics, including the presence of variant histone types and trimethylation of histone H3 at lysine 4. To address the role of these features in transcription complex assembly, we generated templates with four different promoters and nucleosomes located at a variety of downstream positions, which were transcribed in vitro using HeLa nuclear extracts. Two promoters lacked TATA elements, but all supported strong initiation from a single transcription start site. In contrast to results with minimal in vitro systems based on the TATA-binding protein (TBP), TATA promoter templates with a +51 NPE were transcriptionally inhibited in extracts; activity continuously increased as the nucleosome was moved downstream to +100. Inhibition was much more pronounced for the TATA-less promoters: +51 NPE templates were inactive, and substantial activity was only seen with the +100 NPE templates. Substituting the histone variants H2A.Z, H3.3, or both did not eliminate the inhibition. However, addition of excess TBP restored activity on nucleosomal templates with TATA promoters, even with an NPE at +20. Remarkably, nucleosomal templates with histone H3 trimethylated at lysine 4 are active with an NPE at +51 for both TATA and TATA-less promoters. Our results strongly suggest that the +1 nucleosome interferes with promoter recognition by TFIID. This inhibition can be overcome with TBP alone at TATA promoters or through positive interactions with histone modifications and TFIID.
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Affiliation(s)
- Michael J Fisher
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.
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18
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Sloutskin A, Itzhak D, Vogler G, Ideses D, Alter H, Shachar H, Doniger T, Frasch M, Bodmer R, Duttke SH, Juven-Gershon T. A single DPE core promoter motif contributes to in vivo transcriptional regulation and affects cardiac function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544490. [PMID: 37398300 PMCID: PMC10312617 DOI: 10.1101/2023.06.11.544490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Transcription is initiated at the core promoter, which confers specific functions depending on the unique combination of core promoter elements. The downstream core promoter element (DPE) is found in many genes related to heart and mesodermal development. However, the function of these core promoter elements has thus far been studied primarily in isolated, in vitro or reporter gene settings. tinman (tin) encodes a key transcription factor that regulates the formation of the dorsal musculature and heart. Pioneering a novel approach utilizing both CRISPR and nascent transcriptomics, we show that a substitution mutation of the functional tin DPE motif within the natural context of the core promoter results in a massive perturbation of Tinman's regulatory network orchestrating dorsal musculature and heart formation. Mutation of endogenous tin DPE reduced the expression of tin and distinct target genes, resulting in significantly reduced viability and an overall decrease in adult heart function. We demonstrate the feasibility and importance of characterizing DNA sequence elements in vivo in their natural context, and accentuate the critical impact a single DPE motif has during Drosophila embryogenesis and functional heart formation.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Dekel Itzhak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hadar Alter
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hadar Shachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Manfred Frasch
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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19
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Volkening JD, Spatz SJ, Ponnuraj N, Akbar H, Arrington JV, Vega-Rodriguez W, Jarosinski KW. Viral proteogenomic and expression profiling during productive replication of a skin-tropic herpesvirus in the natural host. PLoS Pathog 2023; 19:e1011204. [PMID: 37289833 PMCID: PMC10284419 DOI: 10.1371/journal.ppat.1011204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/21/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023] Open
Abstract
Efficient transmission of herpesviruses is essential for dissemination in host populations; however, little is known about the viral genes that mediate transmission, mostly due to a lack of natural virus-host model systems. Marek's disease is a devastating herpesviral disease of chickens caused by Marek's disease virus (MDV) and an excellent natural model to study skin-tropic herpesviruses and transmission. Like varicella zoster virus that causes chicken pox in humans, the only site where infectious cell-free MD virions are efficiently produced is in epithelial skin cells, a requirement for host-to-host transmission. Here, we enriched for heavily infected feather follicle epithelial skin cells of live chickens to measure both viral transcription and protein expression using combined short- and long-read RNA sequencing and LC/MS-MS bottom-up proteomics. Enrichment produced a previously unseen breadth and depth of viral peptide sequencing. We confirmed protein translation for 84 viral genes at high confidence (1% FDR) and correlated relative protein abundance with RNA expression levels. Using a proteogenomic approach, we confirmed translation of most well-characterized spliced viral transcripts and identified a novel, abundant isoform of the 14 kDa transcript family via IsoSeq transcripts, short-read intron-spanning sequencing reads, and a high-quality junction-spanning peptide identification. We identified peptides representing alternative start codon usage in several genes and putative novel microORFs at the 5' ends of two core herpesviral genes, pUL47 and ICP4, along with strong evidence of independent transcription and translation of the capsid scaffold protein pUL26.5. Using a natural animal host model system to examine viral gene expression provides a robust, efficient, and meaningful way of validating results gathered from cell culture systems.
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Affiliation(s)
| | - Stephen J. Spatz
- US National Poultry Research Laboratory, ARS, USDA, Athens, Georgia, United States of America
| | - Nagendraprabhu Ponnuraj
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Haji Akbar
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Justine V. Arrington
- Protein Sciences Facility, Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Widaliz Vega-Rodriguez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Keith W. Jarosinski
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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20
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Kharytonchyk S, Burnett C, Gc K, Telesnitsky A. Transcription start site heterogeneity and its role in RNA fate determination distinguish HIV-1 from other retroviruses and are mediated by core promoter elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541776. [PMID: 37292892 PMCID: PMC10245945 DOI: 10.1101/2023.05.22.541776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
HIV-1 uses heterogeneous transcription start sites (TSSs) to generate two RNA 5' isoforms that adopt radically different structures and perform distinct replication functions. Although these RNAs differ in length by only two bases, exclusively the shorter RNA is encapsidated while the longer RNA is excluded from virions and provides intracellular functions. The current study examined TSS usage and packaging selectivity for a broad range of retroviruses and found that heterogenous TSS usage was a conserved feature of all tested HIV-1 strains, but all other retroviruses examined displayed unique TSSs. Phylogenetic csomparisons and chimeric viruses' properties provided evidence that this mechanism of RNA fate determination was an innovation of the HIV-1 lineage, with determinants mapping to core promoter elements. Fine-tuning differences between HIV-1 and HIV-2, which uses a unique TSS, implicated purine residue positioning plus a specific TSS-adjacent dinucleotide in specifying multiplicity of TSS usage. Based on these findings, HIV-1 expression constructs were generated that differed from the parental strain by only two point mutations yet each expressed only one of HIV-1's two RNAs. Replication defects of the variant with only the presumptive founder TSS were less severe than those for the virus with only the secondary start site.
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Affiliation(s)
- Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA
| | - Keshav Gc
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA
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21
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Vo Ngoc L, Rhyne TE, Kadonaga JT. Analysis of the Drosophila and human DPR elements reveals a distinct human variant whose specificity can be enhanced by machine learning. Genes Dev 2023; 37:377-382. [PMID: 37163335 PMCID: PMC10270198 DOI: 10.1101/gad.350572.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023]
Abstract
The RNA polymerase II core promoter is the site of convergence of the signals that lead to the initiation of transcription. Here, we performed a comparative analysis of the downstream core promoter region (DPR) in Drosophila and humans by using machine learning. These studies revealed a distinct human-specific version of the DPR and led to the use of machine learning models for the identification of synthetic extreme DPR motifs with specificity for human transcription factors relative to Drosophila factors and vice versa. More generally, machine learning models could similarly be used to design synthetic DNA elements with customized functional properties.
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Affiliation(s)
- Long Vo Ngoc
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, USA
| | - Torrey E Rhyne
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, USA
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22
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van den Elzen AMG, Watson MJ, Thoreen CC. mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay. PLoS Genet 2022; 18:e1010532. [PMID: 36441824 PMCID: PMC9731452 DOI: 10.1371/journal.pgen.1010532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/08/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022] Open
Abstract
mRNA regulatory sequences control gene expression at multiple levels including translation initiation and mRNA decay. The 5' terminal sequences of mRNAs have unique regulatory potential because of their proximity to key post-transcriptional regulators. Here we have systematically probed the function of 5' terminal sequences in gene expression in human cells. Using a library of reporter mRNAs initiating with all possible 7-mer sequences at their 5' ends, we find an unexpected impact on transcription that underlies 200-fold differences in mRNA expression. Library sequences that promote high levels of transcription mirrored those found in native mRNAs and define two basic classes with similarities to classic Initiator (Inr) and TCT core promoter motifs. By comparing transcription, translation and decay rates, we identify sequences that are optimized for both efficient transcription and growth-regulated translation and stability, including variants of terminal oligopyrimidine (TOP) motifs. We further show that 5' sequences of endogenous mRNAs are enriched for multi-functional TCT/TOP hybrid sequences. Together, our results reveal how 5' sequences define two general classes of mRNAs with distinct growth-responsive profiles of expression across synthesis, translation and decay.
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Affiliation(s)
- Antonia M. G. van den Elzen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Maegan J. Watson
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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23
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Chou SP, Alexander AK, Rice EJ, Choate LA, Danko CG. Genetic dissection of the RNA polymerase II transcription cycle. eLife 2022; 11:e78458. [PMID: 35775732 PMCID: PMC9286732 DOI: 10.7554/elife.78458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during transcription remains poorly understood. Here, we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, allowing us to redefine molecular models of core transcriptional processes. Our results implicate DNA sequence, including both known and novel DNA sequence motifs, as key determinants of the position of Pol II initiation and pause. We report evidence that initiation site selection follows a stochastic process similar to Brownian motion along the DNA template. We found widespread differences in the position of transcription termination, which impact the primary structure and stability of mature mRNA. Finally, we report evidence that allelic changes in transcription often affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.
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Affiliation(s)
- Shao-Pei Chou
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Adriana K Alexander
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
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24
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Hou TY, Kraus WL. Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Rep 2022; 39:110944. [PMID: 35705040 PMCID: PMC9246336 DOI: 10.1016/j.celrep.2022.110944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/12/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022] Open
Abstract
To better understand the functions of non-coding enhancer RNAs (eRNAs), we annotated the estrogen-regulated eRNA transcriptome in estrogen receptor α (ERα)-positive breast cancer cells using PRO-cap and RNA sequencing. We then cloned a subset of the eRNAs identified, fused them to single guide RNAs, and targeted them to their ERα enhancers of origin using CRISPR/dCas9. Some of the eRNAs tested modulated the expression of cognate, but not heterologous, target genes after estrogen treatment by increasing ERα recruitment and stimulating p300-catalyzed H3K27 acetylation at the enhancer. We identified a ∼40 nucleotide functional eRNA regulatory motif (FERM) present in many eRNAs that was necessary and sufficient to modulate gene expression, but not the specificity of activation, after estrogen treatment. The FERM interacted with BCAS2, an RNA-binding protein amplified in breast cancers. The ectopic expression of a targeted eRNA controlling the expression of an oncogene resulted in increased cell proliferation, demonstrating the regulatory potential of eRNAs in breast cancer.
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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, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, 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, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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25
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Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases. Nat Rev Mol Cell Biol 2022; 23:603-622. [PMID: 35505252 DOI: 10.1038/s41580-022-00476-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
Abstract
The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules. The labour of nuclear gene transcription is, therefore, divided among multiple DNA-dependent RNA polymerases. RNA polymerase I (Pol I) transcribes ribosomal RNA, Pol II synthesizes messenger RNAs and various non-coding RNAs (including long non-coding RNAs, microRNAs and small nuclear RNAs) and Pol III produces transfer RNAs and other short RNA molecules. Pol I, Pol II and Pol III are large, multisubunit protein complexes that associate with a multitude of additional factors to synthesize transcripts that largely differ in size, structure and abundance. The three transcription machineries share common characteristics, but differ widely in various aspects, such as numbers of RNA polymerase subunits, regulatory elements and accessory factors, which allows them to specialize in transcribing their specific RNAs. Common to the three RNA polymerases is that the transcription process consists of three major steps: transcription initiation, transcript elongation and transcription termination. In this Review, we outline the common principles and differences between the Pol I, Pol II and Pol III transcription machineries and discuss key structural and functional insights obtained into the three stages of their transcription processes.
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26
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Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, Hardy M, Hunt T, Jackson J, Joardar VS, Kay M, Kodali VK, McGarvey KM, McMahon A, Mudge JM, Murphy DN, Murphy MR, Rajput B, Rangwala SH, Riddick LD, Thibaud-Nissen F, Threadgold G, Vatsan AR, Wallin C, Webb D, Flicek P, Birney E, Pruitt KD, Frankish A, Cunningham F, Murphy TD. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature 2022; 604:310-315. [PMID: 35388217 PMCID: PMC9007741 DOI: 10.1038/s41586-022-04558-8] [Citation(s) in RCA: 268] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/07/2022] [Indexed: 12/25/2022]
Abstract
Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alex Astashyn
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Olga Ermolaeva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tamara Goldfarb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jose M Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - John Jackson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kelly M McGarvey
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lillian D Riddick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Glen Threadgold
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anjana R Vatsan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David Webb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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27
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Duttke SH, Beyhan S, Singh R, Neal S, Viriyakosol S, Fierer J, Kirkland TN, Stajich JE, Benner C, Carlin AF. Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA. mSystems 2022; 7:e0140421. [PMID: 35076277 PMCID: PMC8788335 DOI: 10.1128/msystems.01404-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 01/07/2023] Open
Abstract
New or emerging infectious diseases are commonly caused by pathogens that cannot be readily manipulated or studied under common laboratory conditions. These limitations hinder standard experimental approaches and our abilities to define the fundamental molecular mechanisms underlying pathogenesis. The advance of capped small RNA sequencing (csRNA-seq) now enables genome-wide mapping of actively initiated transcripts from genes and other regulatory transcribed start regions (TSRs) such as enhancers at a precise moment from total RNA. As RNA is nonpathogenic and can be readily isolated from inactivated infectious samples, csRNA-seq can detect acute changes in gene regulation within or in response to a pathogen with remarkable sensitivity under common laboratory conditions. Studying valley fever (coccidioidomycosis), an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health, we show how csRNA-seq can unravel transcriptional programs driving pathogenesis. Performing csRNA-seq on RNA isolated from different stages of the valley fever pathogen Coccidioides immitis revealed alternative promoter usage, connected cis-regulatory domains, and a WOPR family transcription factor, which are known regulators of virulence in other fungi, as being critical for pathogenic growth. We further demonstrate that a C. immitis WOPR homologue, CIMG_02671, activates transcription in a WOPR motif-dependent manner. Collectively, these findings provide novel insights into valley fever pathogenesis and provide a proof of principle for csRNA-seq as a powerful means to determine the genes, regulatory mechanisms, and transcription factors that control the pathogenesis of highly infectious agents. IMPORTANCE Infectious pathogens like airborne viruses or fungal spores are difficult to study; they require high-containment facilities, special equipment, and expertise. As such, establishing approaches such as genome editing or other means to identify the factors and mechanisms underlying caused diseases, and, thus, promising drug targets, is costly and time-intensive. These obstacles particularly hinder the analysis of new, emerging, or rare infectious diseases. We recently developed a method termed capped small RNA sequencing (csRNA-seq) that enables capturing acute changes in active gene expression from total RNA. Prior to csRNA-seq, such an analysis was possible only by using living cells or nuclei, in which pathogens are highly infectious. The process of RNA purification, however, inactivates pathogens and thus enables the analysis of gene expression during disease progression under standard laboratory conditions. As a proof of principle, here, we use csRNA-seq to unravel the gene regulatory programs and factors likely critical for the pathogenesis of valley fever, an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health.
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Affiliation(s)
- Sascha H. Duttke
- Department of Medicine, Division of Endocrinology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sinem Beyhan
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- J. Craig Venter Institute, Department of Infectious Diseases, La Jolla, California, USA
| | - Rajendra Singh
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sonya Neal
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Suganya Viriyakosol
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| | - Joshua Fierer
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- Infectious Diseases Section, VA Healthcare San Diego, San Diego, California, USA
- Department of Pathology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Theo N. Kirkland
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- Department of Pathology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, California, USA
| | - Christopher Benner
- Department of Medicine, Division of Endocrinology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
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28
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Rojas DA, Urbina F, Valenzuela-Pérez L, Leiva L, Miralles VJ, Maldonado E. Initiator-Directed Transcription: Fission Yeast Nmtl Initiator Directs Preinitiation Complex Formation and Transcriptional Initiation. Genes (Basel) 2022; 13:genes13020256. [PMID: 35205301 PMCID: PMC8871863 DOI: 10.3390/genes13020256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
The initiator element is a core promoter element encompassing the transcription start site, which is found in yeast, Drosophila, and human promoters. This element is observed in TATA-less promoters. Several studies have defined transcription factor requirements and additional cofactors that are needed for transcription initiation of initiator-containing promoters. However, those studies have been performed with additional core promoters in addition to the initiator. In this work, we have defined the pathway of preinitiation complex formation on the fission yeast nmt1 gene promoter, which contains a functional initiator with striking similarity to the initiator of the human dihydrofolate reductase (hDHFR) gene and to the factor requirement for transcription initiation of the nmt1 gene promoter. The results show that the nmt1 gene promoter possesses an initiator encompassing the transcription start site, and several conserved base positions are required for initiator function. A preinitiation complex formation on the nmt1 initiator can be started by TBP/TFIIA or TBP/TFIIB, but not TBP alone, and afterwards follows the same pathway as preinitiation complex formation on TATA-containing promoters. Transcription initiation is dependent on the general transcription factors TBP, TFIIB, TFIIE, TFIIF, TFIIH, RNA polymerase II, Mediator, and a cofactor identified as transcription cofactor for initiator function (TCIF), which is a high-molecular-weight protein complex of around 500 kDa. However, the TAF subunits of TFIID were not required for the nmt1 initiator transcription, as far as we tested. We also demonstrate that other initiators of the nmt1/hDHFR family can be transcribed in fission yeast whole-cell extracts.
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Affiliation(s)
- Diego A. Rojas
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile
- Correspondence: address: (D.A.R.); (E.M.)
| | - Fabiola Urbina
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
| | - Lucía Valenzuela-Pérez
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
| | - Lorenzo Leiva
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
| | - Vicente J. Miralles
- Departamento Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Valencia, 46010 Valencia, Spain;
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile; (F.U.); (L.V.-P.); (L.L.)
- Correspondence: address: (D.A.R.); (E.M.)
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29
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Fiszbein A, McGurk M, Calvo-Roitberg E, Kim G, Burge CB, Pai AA. Widespread occurrence of hybrid internal-terminal exons in human transcriptomes. SCIENCE ADVANCES 2022; 8:eabk1752. [PMID: 35044812 PMCID: PMC8769537 DOI: 10.1126/sciadv.abk1752] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/23/2021] [Indexed: 06/12/2023]
Abstract
Messenger RNA isoform differences are predominantly driven by alternative first, internal, and last exons. Despite the importance of classifying exons to understand isoform structure, few tools examine isoform-specific exon usage. We recently observed that alternative transcription start sites often arise near internal exons, often creating “hybrid” first/internal exons. To systematically detect hybrid exons, we built the hybrid-internal-terminal (HIT) pipeline to classify exons depending on their isoform-specific usage. On the basis of splice junction reads in RNA sequencing data and probabilistic modeling, the HIT index identified thousands of previously misclassified hybrid first-internal and internal-last exons. Hybrid exons are enriched in long genes and genes involved in RNA splicing and have longer flanking introns and strong splice sites. Their usage varies considerably across human tissues. By developing the first method to classify exons according to isoform contexts, our findings document the occurrence of hybrid exons, a common quirk of the human transcriptome.
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Affiliation(s)
- Ana Fiszbein
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Michael McGurk
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - GyeungYun Kim
- Department of Biology, Boston University, Boston, MA, USA
| | - Christopher B. Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Athma A. Pai
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
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30
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Identification and characterization of the promoter and transcription factors regulating the expression of cerebral sodium/calcium exchanger 2 (NCX2) gene. Cell Calcium 2022; 102:102542. [DOI: 10.1016/j.ceca.2022.102542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/30/2021] [Accepted: 01/22/2022] [Indexed: 11/22/2022]
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31
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Sloutskin A, Shir-Shapira H, Freiman RN, Juven-Gershon T. The Core Promoter Is a Regulatory Hub for Developmental Gene Expression. Front Cell Dev Biol 2021; 9:666508. [PMID: 34568311 PMCID: PMC8461331 DOI: 10.3389/fcell.2021.666508] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
The development of multicellular organisms and the uniqueness of each cell are achieved by distinct transcriptional programs. Multiple processes that regulate gene expression converge at the core promoter region, an 80 bp region that directs accurate transcription initiation by RNA polymerase II (Pol II). In recent years, it has become apparent that the core promoter region is not a passive DNA component, but rather an active regulatory module of transcriptional programs. Distinct core promoter compositions were demonstrated to result in different transcriptional outputs. In this mini-review, we focus on the role of the core promoter, particularly its downstream region, as the regulatory hub for developmental genes. The downstream core promoter element (DPE) was implicated in the control of evolutionarily conserved developmental gene regulatory networks (GRNs) governing body plan in both the anterior-posterior and dorsal-ventral axes. Notably, the composition of the basal transcription machinery is not universal, but rather promoter-dependent, highlighting the importance of specialized transcription complexes and their core promoter target sequences as key hubs that drive embryonic development, differentiation and morphogenesis across metazoan species. The extent of transcriptional activation by a specific enhancer is dependent on its compatibility with the relevant core promoter. The core promoter content also regulates transcription burst size. Overall, while for many years it was thought that the specificity of gene expression is primarily determined by enhancers, it is now clear that the core promoter region comprises an important regulatory module in the intricate networks of developmental gene expression.
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Affiliation(s)
- Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Richard N. Freiman
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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32
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Zinghirino F, Pappalardo XG, Messina A, Nicosia G, De Pinto V, Guarino F. VDAC Genes Expression and Regulation in Mammals. Front Physiol 2021; 12:708695. [PMID: 34421651 PMCID: PMC8374620 DOI: 10.3389/fphys.2021.708695] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
VDACs are pore-forming proteins, coating the mitochondrial outer membrane, and playing the role of main regulators for metabolites exchange between cytosol and mitochondria. In mammals, three isoforms have evolutionary originated, VDAC1, VDAC2, and VDAC3. Despite similarity in sequence and structure, evidence suggests different biological roles in normal and pathological conditions for each isoform. We compared Homo sapiens and Mus musculus VDAC genes and their regulatory elements. RNA-seq transcriptome analysis shows that VDAC isoforms are expressed in human and mouse tissues at different levels with a predominance of VDAC1 and VDAC2 over VDAC3, with the exception of reproductive system. Numerous transcript variants for each isoform suggest specific context-dependent regulatory mechanisms. Analysis of VDAC core promoters has highlighted that, both in a human and a mouse, VDAC genes show features of TATA-less ones. The level of CG methylation of the human VDAC genes revealed that VDAC1 promoter is less methylated than other two isoforms. We found that expression of VDAC genes is mainly regulated by transcription factors involved in controlling cell growth, proliferation and differentiation, apoptosis, and bioenergetic metabolism. A non-canonical initiation site termed "the TCT/TOP motif," the target for translation regulation by the mTOR pathway, was identified in human VDAC2 and VDAC3 and in every murine VDACs promoter. In addition, specific TFBSs have been identified in each VDAC promoter, supporting the hypothesis that there is a partial functional divergence. These data corroborate our experimental results and reinforce the idea that gene regulation could be the key to understanding the evolutionary specialization of VDAC isoforms.
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Affiliation(s)
- Federica Zinghirino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
| | - Giuseppe Nicosia
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
- Section of Catania, National Institute of Biostructures and Biosystems, Catania, Italy
| | - Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
- Section of Catania, National Institute of Biostructures and Biosystems, Catania, Italy
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Shamie I, Duttke SH, Karottki KJLC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 2021; 3:lqab061. [PMID: 34268494 PMCID: PMC8276764 DOI: 10.1093/nargab/lqab061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
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Affiliation(s)
- Isaac Shamie
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego 92093, USA
| | - Karen J la Cour Karottki
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Anders H Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Hooman Hefzi
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Shangzhong Li
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Samuel J Roth
- Department of Medicine, University of California, San Diego 92093, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | | | | | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
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Grencewicz DJ, Romigh T, Thacker S, Abbas A, Jaini R, Luse D, Eng C. Redefining the PTEN promoter: Identification of novel upstream transcription start regions. Hum Mol Genet 2021; 30:2135-2148. [PMID: 34218272 DOI: 10.1093/hmg/ddab175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022] Open
Abstract
Germline mutation of PTEN is causally observed in Cowden syndrome (CS) and is one of the most common, penetrant risk genes for autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are PTEN-mutation negative. Reassessment of PTEN promoter regulation may help explain abnormal PTEN dosage, as only the minimal promoter and coding regions are currently included in diagnostic PTEN mutation analysis. Therefore, we reanalyzed the architecture of the PTEN promoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional transcription start regions (TSRs) at -2053 and - 1906 basepairs from the canonical start of PTEN, thus extending the PTEN 5'UTR and redefining the PTEN promoter. We show that these novel upstream TSRs are active in cancer cell lines, human cancer, and normal tissue. Further, these TSRs can produce novel PTEN transcripts due to the introduction of new splice donors at -2041, -1826, and - 1355, which may allow for splicing out of the PTEN 5'UTR or the first and second exon in upstream-initiated transcripts. Combining ENCODE ChIP-seq and pertinent literature, we also compile and analyze all transcription factors (TFs) binding at the redefined PTEN locus. Enrichment analyses suggest that TFs bind specifically to the upstream TSRs may be implicated in inflammatory processes. Together, these data redefine the architecture of the PTEN promoter, an important step toward a comprehensive model of PTEN transcription regulation, a basis for future investigations into the new promoters' role in disease pathogenesis.
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Affiliation(s)
- Dennis J Grencewicz
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Todd Romigh
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ata Abbas
- Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Developmental Therapeutics Program, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Developmental Therapeutics Program, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Donal Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Center for Personalized Genetic Healthcare, Cleveland Clinic Community Care and Population Health, Cleveland, OH 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Zhang M, Chaney HL, Current JZ, Yao J. Identification of the core promoter of ZNFO, an oocyte-specific maternal effect gene in cattle. Gene 2021; 791:145717. [PMID: 33991649 DOI: 10.1016/j.gene.2021.145717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/26/2023]
Abstract
ZNFO is a Krüppel-associated box (KRAB) containing zinc finger transcription factor, which is exclusively expressed in bovine oocytes. Previous studies have demonstrated that ZNFO possesses an intrinsic transcriptional repressive activity and is essential for early embryonic development in cattle. However, the mechanisms regulating ZNFO transcription remain elusive. In the present study, the core promoter that controls the ZNFO basal transcription was identified. A 1.7 kb 5' regulatory region of the ZNFO gene was cloned and its promoter activity was confirmed by a luciferase reporter assay. A series of 5' deletion in the ZNFO promoter followed by luciferase reporter assays indicated that the core promoter region has to include the sequence located within 57 bp to 31 bp upstream of the transcription start site. Sequence analysis revealed that a putative USF1/USF2 binding site (GGTCACGTGACC) containing an E-box motif (CACGTG) is located within the essential region. Depletion of USF1/USF2 by RNAi and E-box mutation analysis demonstrated that the USF1/USF2 binding site is required for the ZNFO basal transcription. Furthermore, EMSA and super-shift assays indicated that the observed effects are dependent on the specific interactions between USF proteins and the ZNFO core promoter. From these results, it is concluded that USF1 and USF2 are essential for the basal transcription of the ZNFO gene.
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Affiliation(s)
- Mingxiang Zhang
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Heather L Chaney
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jaelyn Z Current
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jianbo Yao
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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36
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Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y. Structural insights into preinitiation complex assembly on core promoters. Science 2021; 372:science.aba8490. [PMID: 33795473 DOI: 10.1126/science.aba8490] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 02/01/2021] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
Abstract
Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yilun Qi
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Dan Zhao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Haifeng Hou
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yan Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Mo Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Ze Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Huirong Yang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China. .,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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Conservation of the HBV RNA element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription. Proc Natl Acad Sci U S A 2021; 118:2022373118. [PMID: 33753499 DOI: 10.1073/pnas.2022373118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepadnaviruses, with the human hepatitis B virus as prototype, are small, enveloped hepatotropic DNA viruses which replicate by reverse transcription of an RNA intermediate. Replication is initiated by a unique protein-priming mechanism whereby a hydroxy amino acid side chain of the terminal protein (TP) domain of the viral polymerase (P) is extended into a short DNA oligonucleotide, which subsequently serves as primer for first-strand synthesis. A key component in the priming of reverse transcription is the viral RNA element epsilon, which contains the replication origin and serves as a template for DNA primer synthesis. Here, we show that recently discovered non-enveloped fish viruses, termed nackednaviruses [C. Lauber et al., Cell Host Microbe 22, 387-399 (2017)], employ a fundamentally similar replication mechanism despite their huge phylogenetic distance and major differences in genome organization and viral lifestyle. In vitro cross-priming studies revealed that few strategic nucleotide substitutions in epsilon enable site-specific protein priming by heterologous P proteins, demonstrating that epsilon is functionally conserved since the two virus families diverged more than 400 Mya. In addition, other cis elements crucial for the hepadnavirus-typical replication of pregenomic RNA into relaxed circular double-stranded DNA were identified at conserved positions in the nackednavirus genomes. Hence, the replication mode of both hepadnaviruses and nackednaviruses was already established in their Paleozoic common ancestor, making it a truly ancient and evolutionary robust principle of genome replication that is more widespread than previously thought.
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38
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Skopenkova VV, Egorova TV, Bardina MV. Muscle-Specific Promoters for Gene Therapy. Acta Naturae 2021; 13:47-58. [PMID: 33959386 PMCID: PMC8084301 DOI: 10.32607/actanaturae.11063] [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: 06/06/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Many genetic diseases that are responsible for muscular disorders have been described to date. Gene replacement therapy is a state-of-the-art strategy used to treat such diseases. In this approach, the functional copy of a gene is delivered to the affected tissues using viral vectors. There is an urgent need for the design of short, regulatory sequences that would drive a high and robust expression of a therapeutic transgene in skeletal muscles, the diaphragm, and the heart, while exhibiting limited activity in non-target tissues. This review focuses on the development and improvement of muscle-specific promoters based on skeletal muscle α-actin, muscle creatine kinase, and desmin genes, as well as other genes expressed in muscles. The current approaches used to engineer synthetic muscle-specific promoters are described. Other elements of the viral vectors that contribute to tissue-specific expression are also discussed. A special feature of this review is the presence of up-to-date information on the clinical and preclinical trials of gene therapy drug candidates that utilize muscle-specific promoters.
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Affiliation(s)
- V. V. Skopenkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - T. V. Egorova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
| | - M. V. Bardina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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39
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Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Nat Commun 2020; 11:5963. [PMID: 33235186 PMCID: PMC7687912 DOI: 10.1038/s41467-020-19829-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancer RNAs (eRNA) are unstable non-coding RNAs, transcribed bidirectionally from active regulatory sequences, whose expression levels correlate with enhancer activity. We use capped-nascent-RNA sequencing to efficiently capture bidirectional transcription initiation across several human lymphoblastoid cell lines (Yoruba population) and detect ~75,000 eRNA transcription sites with high sensitivity and specificity. The use of nascent-RNA sequencing sidesteps the confounding effect of eRNA instability. We identify quantitative trait loci (QTLs) associated with the level and directionality of eRNA expression. High-resolution analyses of these two types of QTLs reveal distinct positions of enrichment at the central transcription factor (TF) binding regions and at the flanking eRNA initiation regions, both of which are associated with mRNA expression QTLs. These two regions-the central TF-binding footprint and the eRNA initiation cores-define a bipartite architecture of enhancers, inform enhancer function, and can be used as an indicator of the significance of non-coding regulatory variants.
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40
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Srinivasachar Badarinarayan S, Shcherbakova I, Langer S, Koepke L, Preising A, Hotter D, Kirchhoff F, Sparrer KMJ, Schotta G, Sauter D. HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression. Nucleic Acids Res 2020; 48:10890-10908. [PMID: 33021676 PMCID: PMC7641743 DOI: 10.1093/nar/gkaa832] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Although endogenous retroviruses (ERVs) are known to harbor cis-regulatory elements, their role in modulating cellular immune responses remains poorly understood. Using an RNA-seq approach, we show that several members of the ERV9 lineage, particularly LTR12C elements, are activated upon HIV-1 infection of primary CD4+ T cells. Intriguingly, HIV-1-induced ERVs harboring transcription start sites are primarily found in the vicinity of immunity genes. For example, HIV-1 infection activates LTR12C elements upstream of the interferon-inducible genes GBP2 and GBP5 that encode for broad-spectrum antiviral factors. Reporter assays demonstrated that these LTR12C elements drive gene expression in primary CD4+ T cells. In line with this, HIV-1 infection triggered the expression of a unique GBP2 transcript variant by activating a cryptic transcription start site within LTR12C. Furthermore, stimulation with HIV-1-induced cytokines increased GBP2 and GBP5 expression in human cells, but not in macaque cells that naturally lack the GBP5 gene and the LTR12C element upstream of GBP2. Finally, our findings suggest that GBP2 and GBP5 have already been active against ancient viral pathogens as they suppress the maturation of the extinct retrovirus HERV-K (HML-2). In summary, our findings uncover how human cells can exploit remnants of once-infectious retroviruses to regulate antiviral gene expression.
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Affiliation(s)
| | - Irina Shcherbakova
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Simon Langer
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Andrea Preising
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Gunnar Schotta
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
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41
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Luse DS, Parida M, Spector BM, Nilson KA, Price DH. A unified view of the sequence and functional organization of the human RNA polymerase II promoter. Nucleic Acids Res 2020; 48:7767-7785. [PMID: 32597978 PMCID: PMC7641323 DOI: 10.1093/nar/gkaa531] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location.
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Affiliation(s)
- Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Benjamin M Spector
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Kyle A Nilson
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
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42
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Identification of the human DPR core promoter element using machine learning. Nature 2020; 585:459-463. [PMID: 32908305 PMCID: PMC7501168 DOI: 10.1038/s41586-020-2689-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/16/2020] [Indexed: 01/31/2023]
Abstract
The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to transcription initiation1-5, but the downstream core promoter in humans has been difficult to decipher1-3. Here, we analyze the human Pol II core promoter and use machine learning to generate predictive models for the downstream core promoter region (DPR) and the TATA box. We developed a method termed HARPE (high-throughput analysis of randomized promoter elements) to create hundreds of thousands of DPR (or TATA box) variants that are each of known transcriptional strength. We then analyzed the HARPE data by support vector regression (SVR) to provide comprehensive models for the sequence motifs, and found that the SVR-based approach is more effective than a consensus-based method for predicting transcriptional activity. These studies revealed that the DPR is a functionally important core promoter element that is widely used in human promoters. Importantly, there appears to be a duality between the DPR and TATA box, as many promoters contain one or the other element. More broadly, these findings show that functional DNA motifs can be identified by machine learning analysis of a comprehensive set of sequence variants.
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, Pugh BF, Nickels BE, Kaplan CD. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol 2020; 21:132. [PMID: 32487207 PMCID: PMC7265651 DOI: 10.1186/s13059-020-02040-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. RESULTS To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. CONCLUSIONS Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
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Affiliation(s)
- Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Huiyan Jin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Irina Vvedenskaya
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jordi Abante Llenas
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3128, USA
- Present Address: Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tingting Zhao
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Indranil Malik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alex M Visbisky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Scott L Schwartz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Ping Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Pavel Čabart
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: First Faculty of Medicine, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kang Hoo Han
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
| | - William K M Lai
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843-3127, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Bryce E Nickels
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Dubaisi S, Fang H, Caruso JA, Gaedigk R, Vyhlidal CA, Kocarek TA, Runge-Morris M. Developmental Expression of SULT1C4 Transcript Variants in Human Liver: Implications for Discordance Between SULT1C4 mRNA and Protein Levels. Drug Metab Dispos 2020; 48:515-520. [PMID: 32303576 PMCID: PMC7250359 DOI: 10.1124/dmd.120.090829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/20/2020] [Indexed: 01/11/2023] Open
Abstract
The cytosolic sulfotransferases (SULTs) metabolize a variety of xenobiotic and endogenous substrates. Several SULTs are expressed in the fetus, implying that these enzymes have important functions during human development. We recently reported that while SULT1C4 mRNA is abundant in prenatal human liver specimens, SULT1C4 protein is barely detectable. Two coding transcript variants (TVs) of SULT1C4 are indexed in GenBank, TV1 (full-length) and TV2 (lacking exons 3 and 4). The purpose of this study was to evaluate expression of the individual TVs as a clue for understanding the discordance between mRNA and protein levels. Reverse-transcription polymerase chain reaction was initially performed to identify TVs expressed in intestinal and hepatic cell lines. This analysis generated fragments corresponding to TV1, TV2, and a third variant that lacked exon 3 (E3DEL). Using reverse-transcription quantitative polymerase chain reaction assays designed to quantify TV1, TV2, or E3DEL individually, all three TVs were more highly expressed in prenatal than postnatal specimens. TV2 levels were ∼fivefold greater than TV1, while E3DEL levels were minimal. RNA sequencing (RNA-seq) analysis of another set of liver specimens confirmed that TV1 and TV2 levels were highest in prenatal liver, with TV2 higher than TV1. RNA-seq also detected a noncoding RNA, which was also more abundant in prenatal liver. Transfection of HEK293T cells with plasmids expressing individual Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys-tagged SULT1C4 isoforms demonstrated that TV1 produced much more protein than did TV2. These data suggest that the lack of correspondence between SULT1C4 mRNA and protein levels in human liver is likely attributable to the inability of the more abundant TV2 to produce stable protein. SIGNIFICANCE STATEMENT: Cytosolic sulfotransferases (SULTs) metabolize a variety of xenobiotic and endogenous substrates, and several SULTs are highly expressed in the fetus, implying that they have important functions during human development. SULT1C4 is highly expressed in prenatal liver at the mRNA level but not the protein level. This study provides an explanation for this discordance by demonstrating that the predominant SULT1C4 transcript is a variant that produces relatively little protein.
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Affiliation(s)
- Sarah Dubaisi
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Hailin Fang
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Joseph A Caruso
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Roger Gaedigk
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Carrie A Vyhlidal
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Thomas A Kocarek
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Melissa Runge-Morris
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
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46
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020; 30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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Affiliation(s)
| | | | - Volker P Brendel
- Department of Biology
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Gabriel E Zentner
- Department of Biology
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, USA
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47
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Catizone AN, Uzunbas GK, Celadova P, Kuang S, Bose D, Sammons MA. Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Res 2020; 48:4195-4213. [PMID: 32133495 PMCID: PMC7192610 DOI: 10.1093/nar/gkaa147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/27/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
The master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CREs), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors. Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. Our data suggest p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that global p53 activity is guarded against loss of any one regulatory partner, allowing for dynamic and redundant control of p53-mediated transcription.
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Affiliation(s)
- Allison N Catizone
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Gizem Karsli Uzunbas
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Petra Celadova
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Sylvia Kuang
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Daniel Bose
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Morgan A Sammons
- Department of Biological Sciences and the RNA Institute, University at Albany, State University of New York, Albany, NY, USA
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48
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Lee Q, Padula MP, Pinello N, Williams SH, O'Rourke MB, Fumagalli MJ, Orkin JD, Song R, Shaban B, Brenner O, Pimanda JE, Weninger W, de Souza WM, Melin AD, Wong JJL, Crim MJ, Monette S, Roediger B, Jolly CJ. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLoS Pathog 2020; 16:e1008262. [PMID: 31971979 PMCID: PMC6999912 DOI: 10.1371/journal.ppat.1008262] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/04/2020] [Accepted: 12/08/2019] [Indexed: 12/21/2022] Open
Abstract
Mouse kidney parvovirus (MKPV) is a member of the provisional genus Chapparvovirus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four major MKPV transcripts, created by alternative splicing, to a common initiator region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and the splicing-dependent putative accessory protein NS2 are conserved in all near-complete amniote chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that many mammal chapparvoviruses are likely to be nephrotropic. Parvoviruses are small, genetically simple single-strand DNA viruses that remain viable outside their hosts for very long periods of time. They cause disease in several domesticated species and in humans. Mouse kidney parvovirus (MKPV) is a causative agent of kidney failure in immune-compromised mice and is the only member of the provisional Chapparvovirus genus for which the complete genome including telomeres is known. Here, we show that MKPV propagates almost exclusively in the kidneys of mice infected naturally, wherein it produces novel accessory proteins whose coding regions are conserved in amniote-associated chapparvovirus sequences. We assemble a closely related complete viral genome present in DNA extracted from the kidney of a wild Cebus imitator monkey, and show that another related chapparvovirus is preferentially found in kidneys of the vampire bat Desmodus rotundus. We conclude that many mammal-hosted chapparvovirus are adapted to the kidney niche and may therefore cause disease following kidney stress in multiple species.
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Affiliation(s)
- Quintin Lee
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney, Sydney, NSW, Australia
| | - Natalia Pinello
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Simon H. Williams
- Center for Infection & Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Matthew B. O'Rourke
- Kolling Institute of Medical Research, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcilio Jorge Fumagalli
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Joseph D. Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Renhua Song
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Babak Shaban
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - John E. Pimanda
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Wolfgang Weninger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - William Marciel de Souza
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Amanda D. Melin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Justin J.-L. Wong
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcus J. Crim
- Microbiology and Aquatic Diagnostics, IDEXX BioAnalytics, Discovery Drive, Columbia, MO, United States of America
| | - Sébastien Monette
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, United States of America
| | - Ben Roediger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Autoimmunity, Transplantation, Inflammation (ATI) Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (BR); (CJJ)
| | - Christopher J. Jolly
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
- * E-mail: (BR); (CJJ)
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49
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Atlas of quantitative single-base-resolution N 6-methyl-adenine methylomes. Nat Commun 2019; 10:5636. [PMID: 31822664 PMCID: PMC6904561 DOI: 10.1038/s41467-019-13561-z] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/12/2019] [Indexed: 01/14/2023] Open
Abstract
Various methyltransferases and demethylases catalyse methylation and demethylation of N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) but precise methylomes uniquely mediated by each methyltransferase/demethylase are still lacking. Here, we develop m6A-Crosslinking-Exonuclease-sequencing (m6ACE-seq) to map transcriptome-wide m6A and m6Am at quantitative single-base-resolution. This allows for the generation of a comprehensive atlas of distinct methylomes uniquely mediated by every individual known methyltransferase or demethylase. Our atlas reveals METTL16 to indirectly impact manifold methylation targets beyond its consensus target motif and highlights the importance of precision in mapping PCIF1-dependent m6Am. Rather than reverse RNA methylation, we find that both ALKBH5 and FTO instead maintain their regulated sites in an unmethylated steady-state. In FTO's absence, anomalous m6Am disrupts snRNA interaction with nuclear export machinery, potentially causing aberrant pre-mRNA splicing events.
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50
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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: 111] [Impact Index Per Article: 18.5] [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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