1
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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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2
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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
Our understanding of how the DNA sequences of cis-regulatory elements encode transcription initiation patterns remains limited. Here we introduce CLIPNET, a deep learning model trained on population-scale PRO-cap data that accurately predicts the position and quantity of transcription initiation with single nucleotide resolution from DNA sequence. 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 different transcriptional activators. Transcriptional activator and core promoter motifs occupy different positions and play distinct roles in regulating 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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3
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Rosales-Vega M, Reséndez-Pérez D, Vázquez M. Antennapedia: The complexity of a master developmental transcription factor. Genesis 2024; 62:e23561. [PMID: 37830148 DOI: 10.1002/dvg.23561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023]
Abstract
Hox genes encode transcription factors that play an important role in establishing the basic body plan of animals. In Drosophila, Antennapedia is one of the five genes that make up the Antennapedia complex (ANT-C). Antennapedia determines the identity of the second thoracic segment, known as the mesothorax. Misexpression of Antennapedia at different developmental stages changes the identity of the mesothorax, including the muscles, nervous system, and cuticle. In Drosophila, Antennapedia has two distinct promoters highly regulated throughout development by several transcription factors. Antennapedia proteins are found with other transcription factors in different ANTENNAPEDIA transcriptional complexes to regulate multiple subsets of target genes. In this review, we describe the different mechanisms that regulate the expression and function of Antennapedia and the role of this Hox gene in the development of Drosophila.
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Affiliation(s)
- Marco Rosales-Vega
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Diana Reséndez-Pérez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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4
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Awazu A, Takemoto D, Watanabe K, Sakamoto N. Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data. Genes Cells 2023; 28:893-905. [PMID: 37864512 DOI: 10.1111/gtc.13076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the first intron of KIT by its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.
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Affiliation(s)
- Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
| | - Daigo Takemoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kaichi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Naoaki Sakamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
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5
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Nikumbh S, Lenhard B. Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation. PLoS Comput Biol 2023; 19:e1011491. [PMID: 37983292 PMCID: PMC10695386 DOI: 10.1371/journal.pcbi.1011491] [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: 04/13/2023] [Revised: 12/04/2023] [Accepted: 09/05/2023] [Indexed: 11/22/2023] Open
Abstract
Core promoters are stretches of DNA at the beginning of genes that contain information that facilitates the binding of transcription initiation complexes. Different functional subsets of genes have core promoters with distinct architectures and characteristic motifs. Some of these motifs inform the selection of transcription start sites (TSS). By discovering motifs with fixed distances from known TSS positions, we could in principle classify promoters into different functional groups. Due to the variability and overlap of architectures, promoter classification is a difficult task that requires new approaches. In this study, we present a new method based on non-negative matrix factorisation (NMF) and the associated software called seqArchR that clusters promoter sequences based on their motifs at near-fixed distances from a reference point, such as TSS. When combined with experimental data from CAGE, seqArchR can efficiently identify TSS-directing motifs, including known ones like TATA, DPE, and nucleosome positioning signal, as well as novel lineage-specific motifs and the function of genes associated with them. By using seqArchR on developmental time courses, we reveal how relative use of promoter architectures changes over time with stage-specific expression. seqArchR is a powerful tool for initial genome-wide classification and functional characterisation of promoters. Its use cases are more general: it can also be used to discover any motifs at near-fixed distances from a reference point, even if they are present in only a small subset of sequences.
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Affiliation(s)
- Sarvesh Nikumbh
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
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6
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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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7
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Hoffmann A. Designer genes courtesy of artificial intelligence. Genes Dev 2023; 37:351-353. [PMID: 37253615 PMCID: PMC10270197 DOI: 10.1101/gad.350783.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The core promoter determines not only where gene transcription initiates but also the transcriptional activity in both basal and enhancer-induced conditions. Multiple short sequence elements within the core promoter have been identified in different species, but how they function together and to what extent they are truly species-specific has remained unclear. In this issue of Genes & Development, Vo ngoc and colleagues (pp. 377-382) report undertaking massively parallel measurements of synthetic core promoters to generate a large data set of their activities that informs a statistical learning model to identify the sequence differences of human and Drosophila core promoters. This machine learning model was then applied to design gene core promoters that are particularly specific for the human transcriptional machinery.
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Affiliation(s)
- Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, Institute for Quantitative and Computational Biosciences, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90025, USA
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8
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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: 2] [Impact Index Per Article: 2.0] [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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9
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Takeuchi C, Yokoshi M, Kondo S, Shibuya A, Saito K, Fukaya T, Siomi H, Iwasaki Y. Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers. Nucleic Acids Res 2022; 50:11580-11599. [PMID: 36373634 PMCID: PMC9723646 DOI: 10.1093/nar/gkac1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.
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Affiliation(s)
- Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Moe Yokoshi
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shu Kondo
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | | | - Yuka W Iwasaki
- To whom correspondence should be addressed. Tel: +81 3 5363 3529; Fax: +81 3 5363 3266;
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10
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Bu L, Cripps RM. Promoter architecture of Drosophila genes regulated by Myocyte enhancer factor-2. PLoS One 2022; 17:e0271554. [PMID: 35862472 PMCID: PMC9302807 DOI: 10.1371/journal.pone.0271554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
To gain understanding into the mechanisms of transcriptional activation of muscle genes, we sought to determine if genes targeted by the myogenic transcription factor Myocyte enhancer factor-2 (MEF2) were enriched for specific core promoter elements. We identified 330 known MEF2 target promoters in Drosophila, and analyzed them for for the presence and location of 17 known consensus promoter sequences. As a control, we also searched all Drosophila RNA polymerase II-dependent promoters for the same sequences. We found that promoter motifs were readily detected in the MEF2 target dataset, and that many of them were slightly enriched in frequency compared to the control dataset. A prominent sequence over-represented in the MEF2 target genes was NDM2, that appeared in over 50% of MEF2 target genes and was 2.5-fold over-represented in MEF2 targets compared to background. To test the functional significance of NDM2, we identified two promoters containing a single copy of NDM2 plus an upstream MEF2 site, and tested the activity of these promoters in vivo. Both the sticks and stones and Kahuli fragments showed strong skeletal myoblast-specific expression of a lacZ reporter in embryos. However, the timing and level of reporter expression was unaffected when the NDM2 site in either element was mutated. These studies identify variations in promoter architecture for a set of regulated genes compared to all RNA polymerase II-dependent genes, and underline the potential redundancy in the activities of some core promoter elements.
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Affiliation(s)
- Lijing Bu
- Department of Biology and Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
| | - Richard M. Cripps
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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11
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Galouzis CC, Furlong EEM. Regulating specificity in enhancer-promoter communication. Curr Opin Cell Biol 2022; 75:102065. [PMID: 35240372 DOI: 10.1016/j.ceb.2022.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
Enhancers are cis-regulatory elements that can activate transcription remotely to regulate a specific pattern of a gene's expression. Genes typically have many enhancers that are often intermingled in the loci of other genes. To regulate expression, enhancers must therefore activate their correct promoter while ignoring others that may be in closer linear proximity. In this review, we discuss mechanisms by which enhancers engage with promoters, including recent findings on the role of cohesin and the Mediator complex, and how this specificity in enhancer-promoter communication is encoded. Genetic dissection of model loci, in addition to more recent findings using genome-wide approaches, highlight the core promoter sequence, its accessibility, cofactor-promoter preference, in addition to the surrounding genomic context, as key components.
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Affiliation(s)
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117, Heidelberg, Germany.
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12
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Vanaja A, Yella VR. Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes. ACS OMEGA 2022; 7:5657-5669. [PMID: 35224327 PMCID: PMC8867553 DOI: 10.1021/acsomega.1c04603] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/27/2022] [Indexed: 05/02/2023]
Abstract
The eukaryotic transcription is orchestrated from a chunk of the DNA region stated as the core promoter. Multifarious and punctilious core promoter signals, viz., TATA-box, Inr, BREs, and Pause Button, are associated with a subset of genes and regulate their spatiotemporal expression. However, the core promoter architecture linked with these signals has not been investigated exhaustively for several species. In this study, we attempted to envisage the adaptive binding landscape of the transcription initiation machinery as a function of DNA structure. To this end, we deployed a set of k-mer based DNA structural estimates and regular expression models derived from experiments, molecular dynamic simulations, and theoretical frameworks, and high-throughout promoter data sets retrieved from the eukaryotic promoter database. We categorized protein-coding gene core promoters based on characteristic motifs at precise locations and analyzed the B-DNA structural properties and non-B-DNA structural motifs for 15 different eukaryotic genomes. We observed that Inr, BREd, and no-motif classes display common patterns of DNA sequence and structural environment. TATA-containing, BREu, and Pause Button classes show a deviant behavior with the TATA class displaying varied axial and twisting flexibility while BREu and Pause Button leaned toward G-quadruplex motif enrichment. Intriguingly, DNA meltability and shape signals are conserved irrespective of the presence or absence of distinct core promoter motifs in the majority of species. Altogether, here we delineated the conserved DNA structural signals associated with several promoter classes that may contribute to the chromatin configuration, orchestration of transcription machinery, and DNA duplex melting during the transcription process.
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Affiliation(s)
- Akkinepally Vanaja
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
- KL
College of Pharmacy, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
| | - Venkata Rajesh Yella
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
- . Tel: +91-863-2399999, Extn-1021. Website: https://www.kluniversity.in/bt/faculty-list.aspx
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13
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Genome-Wide Prediction of Transcription Start Sites in Conifers. Int J Mol Sci 2022; 23:ijms23031735. [PMID: 35163661 PMCID: PMC8836283 DOI: 10.3390/ijms23031735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 02/04/2023] Open
Abstract
The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms.
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14
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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: 7] [Impact Index Per Article: 3.5] [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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15
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Yokoshi M, Kawasaki K, Cambón M, Fukaya T. Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryos. Nucleic Acids Res 2021; 50:92-107. [PMID: 34897508 PMCID: PMC8754644 DOI: 10.1093/nar/gkab1177] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/12/2022] Open
Abstract
Regulatory interactions between enhancers and core promoters are fundamental for the temporal and spatial specificity of gene expression in development. The central role of core promoters is to initiate productive transcription in response to enhancer's activation cues. However, it has not been systematically assessed how individual core promoter elements affect the induction of transcriptional bursting by enhancers. Here, we provide evidence that each core promoter element differentially modulates functional parameters of transcriptional bursting in developing Drosophila embryos. Quantitative live imaging analysis revealed that the timing and the continuity of burst induction are common regulatory steps on which core promoter elements impact. We further show that the upstream TATA also affects the burst amplitude. On the other hand, Inr, MTE and DPE mainly contribute to the regulation of the burst frequency. Genome editing analysis of the pair-rule gene fushi tarazu revealed that the endogenous TATA and DPE are both essential for its correct expression and function during the establishment of body segments in early embryos. We suggest that core promoter elements serve as a key regulatory module in converting enhancer activity into transcription dynamics during animal development.
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Affiliation(s)
- Moe Yokoshi
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Koji Kawasaki
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Manuel Cambón
- Applied Mathematics Department, University of Granada, Granada, Spain
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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16
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Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics 2021; 219:6372693. [PMID: 34849867 DOI: 10.1093/genetics/iyab154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene's overall expression pattern.
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Affiliation(s)
- Lily Li
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.,Department of Biology, Boston University, Boston, MA 02215, USA
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17
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Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Mol Cell 2021; 81:4398-4412.e7. [PMID: 34520723 DOI: 10.1016/j.molcel.2021.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/19/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022]
Abstract
Despite the critical regulatory function of promoter-proximal pausing, the influence of pausing kinetics on transcriptional control remains an active area of investigation. Here, we present Start-TimeLapse-seq (STL-seq), a method that captures the genome-wide kinetics of short, capped RNA turnover and reveals principles of regulation at the pause site. By measuring the rates of release into elongation and premature termination through the inhibition of pause release, we determine that pause-release rates are highly variable, and most promoter-proximal paused RNA polymerase II molecules prematurely terminate (∼80%). The preferred regulatory mechanism upon a hormonal stimulus (20-hydroxyecdysone) is to influence pause-release rather than termination rates. Transcriptional shutdown occurs concurrently with the induction of promoter-proximal termination under hyperosmotic stress, but paused transcripts from TATA box-containing promoters remain stable, demonstrating an important role for cis-acting DNA elements in pausing. STL-seq dissects the kinetics of pause release and termination, providing an opportunity to identify mechanisms of transcriptional regulation.
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Affiliation(s)
- Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Daniele Canzio
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA.
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18
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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: 3] [Impact Index Per Article: 1.0] [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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19
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Dreos R, Sloutskin A, Malachi N, Ideses D, Bucher P, Juven-Gershon T. Computational identification and experimental characterization of preferred downstream positions in human core promoters. PLoS Comput Biol 2021; 17:e1009256. [PMID: 34383743 PMCID: PMC8384218 DOI: 10.1371/journal.pcbi.1009256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 08/24/2021] [Accepted: 07/07/2021] [Indexed: 12/02/2022] Open
Abstract
Metazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements/motifs (e.g. the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in Drosophila, where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the Drosophila DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the Drosophila DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the Drosophila DPE. Available chromatin accessibility footprints revealed that Drosophila and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters. Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properties to it. Interestingly, core promoter motifs can be located both upstream and downstream of the transcription start site. Variable compositions of core promoter elements were identified. The initiator (Inr) motif and the downstream core promoter element (DPE) is a combination of elements that has been identified and extensively characterized in fruit flies. Although a few Inr+DPE -containing human promoters were identified, the presence of transcriptionally important downstream core promoter positions within human promoters has been a matter of controversy in the literature. Here, using a newly-designed motif discovery strategy, we discovered preferred downstream positions in human promoters that resemble fruit fly DPE. Clustering of the corresponding sequence motifs in eight additional species indicated that such promoters could be common to multicellular non-plant organisms. Importantly, functional characterization of the newly discovered preferred downstream positions supports the existence of Inr+DPE-containing promoters in human genes.
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Affiliation(s)
- René Dreos
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nati Malachi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Philipp Bucher
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
- * E-mail: (PB); (TJG)
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail: (PB); (TJG)
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20
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Jores T, Tonnies J, Wrightsman T, Buckler ES, Cuperus JT, Fields S, Queitsch C. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. NATURE PLANTS 2021; 7:842-855. [PMID: 34083762 PMCID: PMC10246763 DOI: 10.1038/s41477-021-00932-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 05/24/2023]
Abstract
Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements-notably the TATA box-as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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21
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Linzer N, Trumbull A, Nar R, Gibbons MD, Yu DT, Strouboulis J, Bungert J. Regulation of RNA Polymerase II Transcription Initiation and Elongation by Transcription Factor TFII-I. Front Mol Biosci 2021; 8:681550. [PMID: 34055891 PMCID: PMC8155576 DOI: 10.3389/fmolb.2021.681550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription by RNA polymerase II (Pol II) is regulated by different processes, including alterations in chromatin structure, interactions between distal regulatory elements and promoters, formation of transcription domains enriched for Pol II and co-regulators, and mechanisms involved in the initiation, elongation, and termination steps of transcription. Transcription factor TFII-I, originally identified as an initiator (INR)-binding protein, contains multiple protein–protein interaction domains and plays diverse roles in the regulation of transcription. Genome-wide analysis revealed that TFII-I associates with expressed as well as repressed genes. Consistently, TFII-I interacts with co-regulators that either positively or negatively regulate the transcription. Furthermore, TFII-I has been shown to regulate transcription pausing by interacting with proteins that promote or inhibit the elongation step of transcription. Changes in TFII-I expression in humans are associated with neurological and immunological diseases as well as cancer. Furthermore, TFII-I is essential for the development of mice and represents a barrier for the induction of pluripotency. Here, we review the known functions of TFII-I related to the regulation of Pol II transcription at the stages of initiation and elongation.
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Affiliation(s)
- Niko Linzer
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - Alexis Trumbull
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - Rukiye Nar
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - Matthew D Gibbons
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - David T Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - John Strouboulis
- Comprehensive Cancer Center, School of Cancer and Pharmaceutical Sciences, King's College London, United Kingdom
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
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22
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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: 86] [Impact Index Per Article: 28.7] [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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23
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Korotkov EV, Suvorova YM, Kostenko DO, Korotkova MA. Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome. Genes (Basel) 2021; 12:135. [PMID: 33494278 PMCID: PMC7909805 DOI: 10.3390/genes12020135] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee, Kalign, and Muscle to these sets. The results indicated that most of the existing methods could produce statistically significant alignments only for the sets with x < 2.5, whereas MAHDS could operate on sequences with x = 4.4. We also used MAHDS to analyze a set of promoter sequences from the Arabidopsis thaliana genome and discovered many conserved regions upstream of the transcription initiation site (from -499 to +1 bp); a part of the downstream region (from +1 to +70 bp) also significantly contributed to the obtained alignments. The possibilities of applying the newly developed method for the identification of promoter sequences in any genome are discussed. A server for multiple alignment of nucleotide sequences has been created.
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Affiliation(s)
- Eugene V. Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia;
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoye Shosse, 115409 Moscow, Russia; (D.O.K.); (M.A.K.)
| | - Yulia M. Suvorova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia;
| | - Dmitrii O. Kostenko
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoye Shosse, 115409 Moscow, Russia; (D.O.K.); (M.A.K.)
| | - Maria A. Korotkova
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoye Shosse, 115409 Moscow, Russia; (D.O.K.); (M.A.K.)
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24
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Mornico D, Hon CC, Koutero M, Weber C, Coppee JY, Dillies MA, Guillen N. Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica. Sci Rep 2020; 10:20190. [PMID: 33214622 PMCID: PMC7677554 DOI: 10.1038/s41598-020-77010-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/02/2020] [Indexed: 01/27/2023] Open
Abstract
Natural antisense transcripts (NAT) have been reported in prokaryotes and eukaryotes. While the functions of most reported NATs remain unknown, their potentials in regulating the transcription of their counterparts have been speculated. Entamoeba histolytica, which is a unicellular eukaryotic parasite, has a compact protein-coding genome with very short intronic and intergenic regions. The regulatory mechanisms of gene expression in this compact genome are under-described. In this study, by genome-wide mapping of RNA-Seq data in the genome of E. histolytica, we show that a substantial fraction of its protein-coding genes (28%) has significant transcription on their opposite strand (i.e. NAT). Intriguingly, we found the location of transcription start sites or polyadenylation sites of NAT are determined by the specific motifs encoded on the opposite strand of the gene coding sequences, thereby providing a compact regulatory system for gene transcription. Moreover, we demonstrated that NATs are globally up-regulated under various environmental conditions including temperature stress and pathogenicity. While NATs do not appear to be consequences of spurious transcription, they may play a role in regulating gene expression in E. histolytica, a hypothesis which needs to be tested.
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Affiliation(s)
- Damien Mornico
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France.
| | - Chung-Chau Hon
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France.,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France.,Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho. Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikael Koutero
- Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Christian Weber
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France.,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France
| | - Jean-Yves Coppee
- Plate-forme Transcriptome et Epigénome, Institut Pasteur, Paris, France
| | - Marie-Agnes Dillies
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Nancy Guillen
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France. .,Institut National de La Santé Et de La Recherche Médicale, INSERM U786, Paris, France. .,Centre National de La Recherche Scientifique, CNRS ERL9195, Paris, France.
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25
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Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis. Int J Mol Sci 2020; 21:ijms21228460. [PMID: 33187090 PMCID: PMC7696854 DOI: 10.3390/ijms21228460] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.
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26
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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: 28] [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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27
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Steinhaus R, Gonzalez T, Seelow D, Robinson PN. Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers. Nucleic Acids Res 2020; 48:5306-5317. [PMID: 32338759 PMCID: PMC7261191 DOI: 10.1093/nar/gkaa223] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022] Open
Abstract
The temporal and spatial expression of genes is controlled by promoters and enhancers. Findings obtained over the last decade that not only promoters but also enhancers are characterized by bidirectional, divergent transcription have challenged the traditional notion that promoters and enhancers represent distinct classes of regulatory elements. Over half of human promoters are associated with CpG islands (CGIs), relatively CpG-rich stretches of generally several hundred nucleotides that are often associated with housekeeping genes. Only about 6% of transcribed enhancers defined by CAGE-tag analysis are associated with CGIs. Here, we present an analysis of enhancer and promoter characteristics and relate them to the presence or absence of CGIs. We show that transcribed enhancers share a number of CGI-dependent characteristics with promoters, including statistically significant local overrepresentation of core promoter elements. CGI-associated enhancers are longer, display higher directionality of transcription, greater expression, a lesser degree of tissue specificity, and a higher frequency of transcription-factor binding events than non-CGI-associated enhancers. Genes putatively regulated by CGI-associated enhancers are enriched for transcription regulator activity. Our findings show that CGI-associated transcribed enhancers display a series of characteristics related to sequence, expression and function that distinguish them from enhancers not associated with CGIs.
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Affiliation(s)
- Robin Steinhaus
- Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tonatiuh Gonzalez
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.,Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA
| | - Dominik Seelow
- Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.,Institute for Systems Genomics, University of Connecticut, 263 Farmington Avenue, Farmington, CT 06030, USA
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28
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The RNA Polymerase II Core Promoter in Drosophila. Genetics 2019; 212:13-24. [PMID: 31053615 DOI: 10.1534/genetics.119.302021] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/05/2019] [Indexed: 11/18/2022] Open
Abstract
Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression.
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29
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Xia LQ, Chen JL, Zhang HL, Cai J, Zhou S, Lu YS. Identification of virion-associated transcriptional transactivator (VATT) of SGIV ICP46 promoter and their binding site on promoter. Virol J 2019; 16:110. [PMID: 31481132 PMCID: PMC6724233 DOI: 10.1186/s12985-019-1210-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/05/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Iridoviruses are large DNA viruses that cause diseases in fish, amphibians and insects. Singapore grouper iridovirus (SGIV) is isolated from cultured grouper and characterized as a ranavirus. ICP46 is defined to be a core gene of the family Iridoviridae and SGIV ICP46 was demonstrated to be an immediate-early (IE) gene associated with cell growth control and could contribute to virus replication in previous research. METHODS The transcription start site (TSS) and 5'-untranslated region (5'-UTR) of SGIV ICP46 were determined using 5' RACE. The core promoter elements of ICP46s were analyzed by bioinformatics analysis. The core promoter region and the regulation model of SGIV ICP46 promoter were revealed by the construction of serially deleted promoter plasmids, transfections, drug treat and luciferase reporter assays. The identification of virion-associated transcriptional transactivator (VATT) that interact with SGIV ICP46 promoter and their binding site on promoter were performed by electrophoretic mobility shift assays (EMSA), DNA pull-down assays and mass spectrometry (MS). RESULTS SGIV ICP46 was found to have short 5'-UTR and a presumptive downstream promoter element (DPE), AGACA, which locates at + 36 to + 39 nt downstream of the TSS. The core promoter region of SGIV ICP46 located from - 22 to + 42 nt relative to the TSS. VATTs were involved in the promoter activation of SGIV ICP46 and further identified to be VP12, VP39, VP57 and MCP. A 10-base DNA sequence "ATGGCTTTCG" between the TSS and presumptive DPE was determined to be the binding site of the VATTs. CONCLUSION Our study showed that four VAATs (VP12, VP39, VP57 and MCP) might bind with the SGIV ICP46 promoter and be involved in the promoter activation. Further, the binding site of the VATTs on promoter was a 10-base DNA sequence between the TSS and presumptive DPE.
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Affiliation(s)
- Li-Qun Xia
- Shenzhen Institute of Guangdong Ocean University, Shenzhen City, Guangdong, China
- College of Fisheries, Guangdong Ocean University, Zhanjiang City, Guangdong, China
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen City, Guangdong, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Guangdong Ocean University, Zhanjiang City, Guangdong, China
| | - Jian-Lin Chen
- Shenzhen Institute of Guangdong Ocean University, Shenzhen City, Guangdong, China
- College of Fisheries, Guangdong Ocean University, Zhanjiang City, Guangdong, China
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen City, Guangdong, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Guangdong Ocean University, Zhanjiang City, Guangdong, China
| | - Hong-Lian Zhang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen City, Guangdong, China
- College of Fisheries, Guangdong Ocean University, Zhanjiang City, Guangdong, China
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen City, Guangdong, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Guangdong Ocean University, Zhanjiang City, Guangdong, China
| | - Jia Cai
- Shenzhen Institute of Guangdong Ocean University, Shenzhen City, Guangdong, China
- College of Fisheries, Guangdong Ocean University, Zhanjiang City, Guangdong, China
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen City, Guangdong, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Guangdong Ocean University, Zhanjiang City, Guangdong, China
| | - Sheng Zhou
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Guangdong Ocean University, Zhanjiang City, Guangdong, China
- College of Marine Sciences, South China Agricultural University, Guangzhou City, Guangdong, China
| | - Yi-Shan Lu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen City, Guangdong, China.
- College of Fisheries, Guangdong Ocean University, Zhanjiang City, Guangdong, China.
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen City, Guangdong, China.
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Guangdong Ocean University, Zhanjiang City, Guangdong, China.
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30
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Haberle V, Arnold CD, Pagani M, Rath M, Schernhuber K, Stark A. Transcriptional cofactors display specificity for distinct types of core promoters. Nature 2019; 570:122-126. [PMID: 31092928 PMCID: PMC7613045 DOI: 10.1038/s41586-019-1210-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 04/15/2019] [Indexed: 12/24/2022]
Abstract
Transcriptional cofactors (COFs) communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression1. Although some COFs have been shown to prefer certain promoter types2-5 over others (for example, see refs 6,7), the extent to which different COFs display intrinsic specificities for distinct promoters is unclear. Here we use a high-throughput promoter-activity assay in Drosophila melanogaster S2 cells to screen 23 COFs for their ability to activate 72,000 candidate core promoters (CPs). We observe differential activation of CPs, indicating distinct regulatory preferences or 'compatibilities'8,9 between COFs and specific types of CPs. These functionally distinct CP types are differentially enriched for known sequence elements2,4, such as the TATA box, downstream promoter element (DPE) or TCT motif, and display distinct chromatin properties at endogenous loci. Notably, the CP types differ in their relative abundance of H3K4me3 and H3K4me1 marks (see also refs 10-12), suggesting that these histone modifications might distinguish trans-regulatory factors rather than promoter- versus enhancer-type cis-regulatory elements. We confirm the existence of distinct COF-CP compatibilities in two additional Drosophila cell lines and in human cells, for which we find COFs that prefer TATA-box or CpG-island promoters, respectively. Distinct compatibilities between COFs and promoters can explain how different enhancers specifically activate distinct sets of genes9, alternative promoters within the same genes, and distinct transcription start sites within the same promoter13. Thus, COF-promoter compatibilities may underlie distinct transcriptional programs in species as divergent as flies and humans.
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Affiliation(s)
- Vanja Haberle
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Cosmas D. Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Martina Rath
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Katharina Schernhuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria,Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria,Correspondence and requests for materials should be addressed to A.S. ()
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31
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Abstract
In this review, Core et al. discuss the recent advances in our understanding of the early steps in Pol II transcription, highlighting the events and factors involved in the establishment and release of paused Pol II. They also discuss a number of unanswered questions about the regulation and function of Pol II pausing. Precise spatio–temporal control of gene activity is essential for organismal development, growth, and survival in a changing environment. Decisive steps in gene regulation involve the pausing of RNA polymerase II (Pol II) in early elongation, and the controlled release of paused polymerase into productive RNA synthesis. Here we describe the factors that enable pausing and the events that trigger Pol II release into the gene. We also discuss open questions in the field concerning the stability of paused Pol II, nucleosomes as obstacles to elongation, and potential roles of pausing in defining the precision and dynamics of gene expression.
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Affiliation(s)
- Leighton Core
- Department of Molecular and Cell Biology, Institute of Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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32
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Shao W, Alcantara SGM, Zeitlinger J. Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing. eLife 2019; 8:41461. [PMID: 31021316 PMCID: PMC6483594 DOI: 10.7554/elife.41461] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/04/2019] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase II (Pol II) pausing is a general regulatory step in transcription, yet the stability of paused Pol II varies widely between genes. Although paused Pol II stability correlates with core promoter elements, the contribution of individual sequences remains unclear, in part because no rapid assay is available for measuring the changes in Pol II pausing as a result of altered promoter sequences. Here, we overcome this hurdle by showing that ChIP-nexus captures the endogenous Pol II pausing on transfected plasmids. Using this reporter-ChIP-nexus assay in Drosophila cells, we show that the pausing stability is influenced by downstream promoter sequences, but that the strongest contribution to Pol II pausing comes from the initiator sequence, in which a single nucleotide, a G at the +2 position, is critical for stable Pol II pausing. These results establish reporter-ChIP-nexus as a valuable tool to analyze Pol II pausing.
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Affiliation(s)
- Wanqing Shao
- Stowers Institute for Medical Research, Kansas City, United States
| | | | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, United States
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33
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Shir-Shapira H, Sloutskin A, Adato O, Ovadia-Shochat A, Ideses D, Zehavi Y, Kassavetis G, Kadonaga JT, Unger R, Juven-Gershon T. Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PLoS One 2019; 14:e0215695. [PMID: 30998799 PMCID: PMC6472829 DOI: 10.1371/journal.pone.0215695] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/07/2019] [Indexed: 12/21/2022] Open
Abstract
The regulation of transcription initiation is critical for developmental and cellular processes. RNA polymerase II (Pol II) is recruited by the basal transcription machinery to the core promoter where Pol II initiates transcription. The core promoter encompasses the region from -40 to +40 bp relative to the +1 transcription start site (TSS). Core promoters may contain one or more core promoter motifs that confer specific properties to the core promoter, such as the TATA box, initiator (Inr) and motifs that are located downstream of the TSS, namely, motif 10 element (MTE), the downstream core promoter element (DPE) and the Bridge, a bipartite core promoter element. We had previously shown that Caudal, an enhancer-binding homeodomain transcription factor and a key regulator of the Hox gene network, is a DPE-specific activator. Interestingly, pair-rule proteins have been implicated in enhancer-promoter communication at the engrailed locus. Fushi tarazu (Ftz) is an enhancer-binding homeodomain transcription factor encoded by the ftz pair-rule gene. Ftz works in concert with its co-factor, Ftz-F1, to activate transcription. Here, we examined whether Ftz and Ftz-F1 activate transcription with a preference for a specific core promoter motif. Our analysis revealed that similarly to Caudal, Ftz and Ftz-F1 activate the promoter containing a TATA box mutation to significantly higher levels than the promoter containing a DPE mutation, thus demonstrating a preference for the DPE motif. We further discovered that Ftz target genes are enriched for a combination of functional downstream core promoter elements that are conserved among Drosophila species. Thus, the unique combination (Inr, Bridge and DPE) of functional downstream core promoter elements within Ftz target genes highlights the complexity of transcriptional regulation via the core promoter in the transcription of different developmental gene regulatory networks.
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Affiliation(s)
- Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orit Adato
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avital Ovadia-Shochat
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yonathan Zehavi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - George Kassavetis
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - James T. Kadonaga
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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35
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Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol 2018; 19:621-637. [PMID: 29946135 PMCID: PMC6205604 DOI: 10.1038/s41580-018-0028-8] [Citation(s) in RCA: 373] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA polymerase II (Pol II) core promoters are specialized DNA sequences at transcription start sites of protein-coding and non-coding genes that support the assembly of the transcription machinery and transcription initiation. They enable the highly regulated transcription of genes by selectively integrating regulatory cues from distal enhancers and their associated regulatory proteins. In this Review, we discuss the defining properties of gene core promoters, including their sequence features, chromatin architecture and transcription initiation patterns. We provide an overview of molecular mechanisms underlying the function and regulation of core promoters and their emerging functional diversity, which defines distinct transcription programmes. On the basis of the established properties of gene core promoters, we discuss transcription start sites within enhancers and integrate recent results obtained from dedicated functional assays to propose a functional model of transcription initiation. This model can explain the nature and function of transcription initiation at gene starts and at enhancers and can explain the different roles of core promoters, of Pol II and its associated factors and of the activating cues provided by enhancers and the transcription factors and cofactors they recruit.
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Affiliation(s)
- Vanja Haberle
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
- Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
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36
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Three newly identified Immediate Early Genes of Bovine herpesvirus 1 lack the characteristic Octamer binding motif- 1. Sci Rep 2018; 8:11441. [PMID: 30061689 PMCID: PMC6065388 DOI: 10.1038/s41598-018-29490-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 07/11/2018] [Indexed: 02/06/2023] Open
Abstract
Only three immediate early genes (IE) BICP0, BICP4 and BICP22 of Bovine herpesvirus 1 (BoHV-1) are known. These genes are expressed coordinately and their promoters are well characterized. We provide evidence for expression of three additional IE genes of BoHV-1 i.e. UL21, UL33 and UL34. These genes are expressed in the presence of cycloheximide (CH) at the same time as known IE genes. Surprisingly, the promoters of newly identified IE genes (UL21, UL33, UL34) lack the OCT-1 binding site, a considered site of transactivation of the BoHV-1 IE genes. The other difference in the promoters of the newly identified IE genes is the presence of TATA box at near optimal site. However, all the IE genes have similar spatial placements of C/EBPα, DPE and INR elements.
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Dahiya R, Natarajan K. Mutational analysis of TAF6 revealed the essential requirement of the histone-fold domain and the HEAT repeat domain for transcriptional activation. FEBS J 2018; 285:1491-1510. [PMID: 29485702 DOI: 10.1111/febs.14423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 12/31/2022]
Abstract
TAF6, bearing the histone H4-like histone-fold domain (HFD), is a subunit of the core TAF module in TFIID and SAGA transcriptional regulatory complexes. We isolated and characterized several yeast TAF6 mutants bearing amino acid substitutions in the HFD, the middle region or the HEAT repeat domain. The TAF6 mutants were highly defective for transcriptional activation by the Gcn4 and Gal4 activators. CHIP assays showed that the TAF6-HFD and the TAF6-HEAT domain mutations independently abrogated the promoter occupancy of TFIID and SAGA complex in vivo. We employed genetic and biochemical assays to identify the relative contributions of the TAF6 HFD and HEAT domains. First, the temperature-sensitive phenotype of the HEAT domain mutant was suppressed by overexpression of the core TAF subunits TAF9 and TAF12, as well as TBP. The HFD mutant defect, however, was suppressed by TAF5 but not by TAF9, TAF12 or TBP. Second, the HEAT mutant but not the HFD mutant was defective for growth in the presence of transcription elongation inhibitors. Third, coimmunoprecipitation assays using yeast cell extracts indicated that the specific TAF6 HEAT domain residues are critical for the interaction of core TAF subunits with the SAGA complex but not with TFIID. The specific HFD residues in TAF6, although required for heterodimerization between TAF6 and TAF9 recombinant proteins, were dispensable for association of the core TAF subunits with TFIID and SAGA in yeast cell extracts. Taken together, the results of our studies have uncovered the non-overlapping requirement of the evolutionarily conserved HEAT domain and the HFD in TAF6 for transcriptional activation.
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Affiliation(s)
- Rashmi Dahiya
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Krishnamurthy Natarajan
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Scruggs BS, Adelman K. The Importance of Controlling Transcription Elongation at Coding and Noncoding RNA Loci. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:33-44. [PMID: 27325707 DOI: 10.1101/sqb.2015.80.027235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Here we discuss current paradigms for how transcription initiation and elongation control are achieved in mammalian cells, and how they differ at protein-coding mRNA genes versus noncoding RNA (ncRNA) loci. We present a model for the function of ncRNAs wherein the act of transcription is regulatory, rather than the ncRNA products themselves. We further describe how the establishment of transcriptionally engaged, but paused, RNA polymerase II impacts chromatin structure around divergent transcription start sites, and how this can influence transcription factor binding and mRNA gene activity in the region.
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Affiliation(s)
- Benjamin S Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
This review by Vo ngoc et al. expands the view of the RNA polymerase II core promoter, which is comprised of classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.
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Affiliation(s)
- Long Vo Ngoc
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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41
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Jian W, Yan B, Huang S, Qiu Y. Histone deacetylase 1 activates PU.1 gene transcription through regulating TAF9 deacetylation and transcription factor IID assembly. FASEB J 2017; 31:4104-4116. [PMID: 28572446 DOI: 10.1096/fj.201700022r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/15/2017] [Indexed: 11/11/2022]
Abstract
Histone acetyltransferases and histone deacetylases (HDACs) are important epigenetic coregulators. It has been thought that HDACs associate with corepressor complexes and repress gene transcription; however, in this study, we have found that PU.1-a key master regulator for hematopoietic self-renewal and lineage specification-requires HDAC activity for gene activation. Deregulated PU.1 gene expression is linked to dysregulated hematopoiesis and the development of leukemia. In this study, we used erythroid differentiation as a model to analyze how the PU.1 gene is regulated. We found that active HDAC1 is directly recruited to active PU.1 promoter in progenitor cells, whereas acetylated HDAC1, which is inactive, is on the silenced PU.1 promoter in differentiated erythroid cells. We then studied the mechanism of HDAC1-mediated activation. We discovered that HDAC1 activates PU.1 gene transcription via deacetylation of TATA-binding protein-associated factor 9 (TAF9), a component in the transcription factor IID (TFIID) complex. Treatment with HDAC inhibitor results in an increase in TAF9 acetylation. Acetylated TAF9 does not bind to the PU.1 gene promoter and subsequently leads to the disassociation of the TFIID complex and transcription repression. Thus, these results demonstrate a key role for HDAC1 in PU.1 gene transcription and, more importantly, uncover a novel mechanism of TFIID recruitment and gene activation.-Jian, W., Yan, B., Huang, S., Qiu, Y. Histone deacetylase 1 activates PU.1 gene transcription through regulating TAF9 deacetylation and transcription factor IID assembly.
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Affiliation(s)
- Wei Jian
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Bowen Yan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Suming Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA; and.,Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau
| | - Yi Qiu
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, USA;
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42
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Monribot-Villanueva J, Zurita M, Vázquez M. Developmental transcriptional regulation by SUMOylation, an evolving field. Genesis 2017; 55. [PMID: 27935206 DOI: 10.1002/dvg.23009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 02/05/2023]
Abstract
SUMOylation is a reversible post-translational protein modification that affects the intracellular localization, stability, activity, and interactions of its protein targets. The SUMOylation pathway influences several nuclear and cytoplasmic processes. The expression of many genes, in particular those involved in development is finely tuned in space and time by several groups of proteins. There is growing evidence that transcriptional regulation mechanisms involve direct SUMOylation of transcriptional-related proteins such as initiation and elongation factors, and subunits of chromatin modifier and remodeling complexes originally described as members of the trithorax and Polycomb groups in Drosophila. Therefore, it is being unveiled that SUMOylation has a role in both, gene silencing and gene activation mechanisms. The goal of this review is to discuss the information on how SUMO modification in components of these multi-subunit complexes may have an effect in genome architecture and function and, therefore, in the regulation of gene expression in time and space.
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Affiliation(s)
- Juan Monribot-Villanueva
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Vázquez
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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43
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Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Nat Biotechnol 2016; 35:136-144. [PMID: 28024147 DOI: 10.1038/nbt.3739] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/08/2016] [Indexed: 01/13/2023]
Abstract
Gene expression is controlled by enhancers that activate transcription from the core promoters of their target genes. Although a key function of core promoters is to convert enhancer activities into gene transcription, whether and how strongly they activate transcription in response to enhancers has not been systematically assessed on a genome-wide level. Here we describe self-transcribing active core promoter sequencing (STAP-seq), a method to determine the responsiveness of genomic sequences to enhancers, and apply it to the Drosophila melanogaster genome. We cloned candidate fragments at the position of the core promoter (also called minimal promoter) in reporter plasmids with or without a strong enhancer, transfected the resulting library into cells, and quantified the transcripts that initiated from each candidate for each setup by deep sequencing. In the presence of a single strong enhancer, the enhancer responsiveness of different sequences differs by several orders of magnitude, and different levels of responsiveness are associated with genes of different functions. We also identify sequence features that predict enhancer responsiveness and discuss how different core promoters are employed for the regulation of gene expression.
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Zabidi MA, Stark A. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet 2016; 32:801-814. [PMID: 27816209 DOI: 10.1016/j.tig.2016.10.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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45
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Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T. ElemeNT: a computational tool for detecting core promoter elements. Transcription 2016. [PMID: 26226151 PMCID: PMC4581360 DOI: 10.1080/21541264.2015.1067286] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.
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Affiliation(s)
- Anna Sloutskin
- a The Mina and Everard Goodman Faculty of Life Sciences ; Bar-Ilan University ; Ramat Gan , Israel
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46
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Sedwick C. Jim Kadonaga: Exploring transcription and chromatin. ACTA ACUST UNITED AC 2016; 212:608-9. [PMID: 26975847 DOI: 10.1083/jcb.2126pi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kadonaga studies the RNA polymerase II core promoter and chromatin assembly.
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47
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Even DY, Kedmi A, Basch-Barzilay S, Ideses D, Tikotzki R, Shir-Shapira H, Shefi O, Juven-Gershon T. Engineered Promoters for Potent Transient Overexpression. PLoS One 2016; 11:e0148918. [PMID: 26872062 PMCID: PMC4752495 DOI: 10.1371/journal.pone.0148918] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 01/23/2016] [Indexed: 12/25/2022] Open
Abstract
The core promoter, which is generally defined as the region to which RNA Polymerase II is recruited to initiate transcription, plays a pivotal role in the regulation of gene expression. The core promoter consists of different combinations of several short DNA sequences, termed core promoter elements or motifs, which confer specific functional properties to each promoter. Earlier studies that examined the ability to modulate gene expression levels via the core promoter, led to the design of strong synthetic core promoters, which combine different core elements into a single core promoter. Here, we designed a new core promoter, termed super core promoter 3 (SCP3), which combines four core promoter elements (the TATA box, Inr, MTE and DPE) into a single promoter that drives prolonged and potent gene expression. We analyzed the effect of core promoter architecture on the temporal dynamics of reporter gene expression by engineering EGFP expression vectors that are driven by distinct core promoters. We used live cell imaging and flow cytometric analyses in different human cell lines to demonstrate that SCPs, particularly the novel SCP3, drive unusually strong long-term EGFP expression. Importantly, this is the first demonstration of long-term expression in transiently transfected mammalian cells, indicating that engineered core promoters can provide a novel non-viral strategy for biotechnological as well as gene-therapy-related applications that require potent expression for extended time periods.
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Affiliation(s)
- Dan Y. Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Adi Kedmi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shani Basch-Barzilay
- 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
| | - Ravid Tikotzki
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Orit Shefi
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnologies and Advanced Materials, 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
- * E-mail:
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48
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Macías F, López MC, Thomas MC. The Trypanosomatid Pr77-hallmark contains a downstream core promoter element essential for transcription activity of the Trypanosoma cruzi L1Tc retrotransposon. BMC Genomics 2016; 17:105. [PMID: 26861854 PMCID: PMC4748587 DOI: 10.1186/s12864-016-2427-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/01/2016] [Indexed: 01/11/2023] Open
Abstract
Background Trypanosomatid genomes are highly colonized by non-LTR retroelements that make up to 5 % of the nuclear genome. These elements are mainly accumulated in the strand switch regions (SSRs) where polycistronic transcription is initiated and have a 77 nt-long sequence - Pr77 - at their 5′ ends. L1Tc is the best represented retrotransposon in the Trypanosoma cruzi genome and is a potentially functional autonomous element that encodes its own retrotransposition machinery. The Pr77 of the T. cruzi L1Tc element activates gene transcription via RNA polymerase II, generating abundant, unspliced transcripts which are translated. Results The present manuscript describes the identification of a downstream core promoter element (DPE) in the L1Tc Pr77 sequence. Just four nucleotides long (CGTG), it covers in Pr77 positions +25 to +28 of the described L1Tc transcription start site. The Pr77-DPE motif is conserved in terms of sequence composition and position in the Pr77 of most trypanosomatid non-LTR retrotransposons, independent of the coding or non-coding capacity of these retroelements. Transcription assays in T. cruzi stable transfectants with vector containing point mutations at 17 locations of the Pr77 nucleotide sequence evidence that the DPE motif is essential for the promoter function of Pr77. Furthermore, the obtained data show that other nucleotides also contributed to the promoter function of Pr77. In addition, the presented results indicate that parasite nuclear proteins specifically bind to different regions of the Pr77 sequence although the strongest binding is to the DPE motif. Moreover, it is shown that the DPE sense single-stranded sequence is being required in DNA-protein recognition of nuclear factors. Conclusions The Pr77 sequence present in most of non-LTR retrotransposons of trypanosomatids contains a downstream core promoter element (DPE) which is conserved in terms of nucleotide composition and location. The Pr77-DPE motif is essential for the transcriptional activity of Pr77 although other nucleotides are also involved. DPE has a high affinity binding for nuclear proteins in T. cruzi. The wide retroelement-mediated distribution of Pr77 suggests that it may represent an important tool for regulating gene expression in trypanosomatids. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2427-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francisco Macías
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento S/N, 18016, Granada, Spain.
| | - Manuel Carlos López
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento S/N, 18016, Granada, Spain.
| | - M Carmen Thomas
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, Avda. del Conocimiento S/N, 18016, Granada, Spain.
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Ravarani CNJ, Chalancon G, Breker M, de Groot NS, Babu MM. Affinity and competition for TBP are molecular determinants of gene expression noise. Nat Commun 2016; 7:10417. [PMID: 26832815 PMCID: PMC4740812 DOI: 10.1038/ncomms10417] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
Cell-to-cell variation in gene expression levels (noise) generates phenotypic diversity and is an important phenomenon in evolution, development and disease. TATA-box binding protein (TBP) is an essential factor that is required at virtually every eukaryotic promoter to initiate transcription. While the presence of a TATA-box motif in the promoter has been strongly linked with noise, the molecular mechanism driving this relationship is less well understood. Through an integrated analysis of multiple large-scale data sets, computer simulation and experimental validation in yeast, we provide molecular insights into how noise arises as an emergent property of variable binding affinity of TBP for different promoter sequences, competition between interaction partners to bind the same surface on TBP (to either promote or disrupt transcription initiation) and variable residence times of TBP complexes at a promoter. These determinants may be fine-tuned under different conditions and during evolution to modulate eukaryotic gene expression noise.
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Affiliation(s)
- Charles N J Ravarani
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guilhem Chalancon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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50
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Haberle V, Lenhard B. Promoter architectures and developmental gene regulation. Semin Cell Dev Biol 2016; 57:11-23. [PMID: 26783721 DOI: 10.1016/j.semcdb.2016.01.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 01/03/2023]
Abstract
Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation. Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development. This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.
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Affiliation(s)
- Vanja Haberle
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Department of Biology, University of Bergen, Thormøhlensgate 53A, N-5008 Bergen, Norway
| | - Boris Lenhard
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.
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