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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 DOI: 10.1038/s41580-024-00710-6] [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] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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2
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Zaytsev K, Fedorov A, Korotkov E. Classification of Promoter Sequences from Human Genome. Int J Mol Sci 2023; 24:12561. [PMID: 37628742 PMCID: PMC10454140 DOI: 10.3390/ijms241612561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
We have developed a new method for promoter sequence classification based on a genetic algorithm and the MAHDS sequence alignment method. We have created four classes of human promoters, combining 17,310 sequences out of the 29,598 present in the EPD database. We searched the human genome for potential promoter sequences (PPSs) using dynamic programming and position weight matrices representing each of the promoter sequence classes. A total of 3,065,317 potential promoter sequences were found. Only 1,241,206 of them were located in unannotated parts of the human genome. Every other PPS found intersected with either true promoters, transposable elements, or interspersed repeats. We found a strong intersection between PPSs and Alu elements as well as transcript start sites. The number of false positive PPSs is estimated to be 3 × 10-8 per nucleotide, which is several orders of magnitude lower than for any other promoter prediction method. The developed method can be used to search for PPSs in various eukaryotic genomes.
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Affiliation(s)
- Konstantin Zaytsev
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey Fedorov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Eugene Korotkov
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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3
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Database of Potential Promoter Sequences in the Capsicum annuum Genome. BIOLOGY 2022; 11:biology11081117. [PMID: 35892972 PMCID: PMC9332048 DOI: 10.3390/biology11081117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
In this study, we used a mathematical method for the multiple alignment of highly divergent sequences (MAHDS) to create a database of potential promoter sequences (PPSs) in the Capsicum annuum genome. To search for PPSs, 20 statistically significant classes of sequences located in the range from −499 to +100 nucleotides near the annotated genes were calculated. For each class, a position–weight matrix (PWM) was computed and then used to identify PPSs in the C. annuum genome. In total, 825,136 PPSs were detected, with a false positive rate of 0.13%. The PPSs obtained with the MAHDS method were tested using TSSFinder, which detects transcription start sites. The databank of the found PPSs provides their coordinates in chromosomes, the alignment of each PPS with the PWM, and the level of statistical significance as a normal distribution argument, and can be used in genetic engineering and biotechnology.
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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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5
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Cordon-Obras C, Gomez-Liñan C, Torres-Rusillo S, Vidal-Cobo I, Lopez-Farfan D, Barroso-Del Jesus A, Rojas-Barros D, Carrington M, Navarro M. Identification of sequence-specific promoters driving polycistronic transcription initiation by RNA polymerase II in trypanosomes. Cell Rep 2022; 38:110221. [PMID: 35021094 DOI: 10.1016/j.celrep.2021.110221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 11/20/2022] Open
Abstract
Protein-coding genes in trypanosomes occur in polycistronic transcription units (PTUs). How RNA polymerase II (Pol II) initiates transcription of PTUs has not been resolved; the current model favors chromatin modifications inducing transcription rather than sequence-specific promoters. Here, we uncover core promoters by functional characterization of Pol II peaks identified by chromatin immunoprecipitation sequencing (ChIP-seq). Two distinct promoters are located between divergent PTUs, each driving unidirectional transcription. Detailed analysis identifies a 75-bp promoter that is necessary and sufficient to drive full reporter expression and contains functional motifs. Analysis of further promoters suggests transcription initiation is regulated and promoters are either focused or dispersed. In contrast to the previous model of unregulated and promoter-independent transcription initiation, we find that sequence-specific promoters determine the initiation of Pol II transcription of protein-coding genes PTUs. These findings in Trypanosoma brucei suggest that in addition of chromatin modifications, promoter motifs-based regulation of gene expression is deeply conserved among eukaryotes.
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Affiliation(s)
- Carlos Cordon-Obras
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Claudia Gomez-Liñan
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Sara Torres-Rusillo
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Isabel Vidal-Cobo
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Diana Lopez-Farfan
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Alicia Barroso-Del Jesus
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Domingo Rojas-Barros
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain.
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6
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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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7
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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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8
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Brázda V, Bartas M, Bowater RP. Evolution of Diverse Strategies for Promoter Regulation. Trends Genet 2021; 37:730-744. [PMID: 33931265 DOI: 10.1016/j.tig.2021.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]
Abstract
DNA is fundamentally important for all cellular organisms due to its role as a store of hereditary genetic information. The precise and accurate regulation of gene transcription depends primarily on promoters, which vary significantly within and between genomes. Some promoters are rich in specific types of bases, while others have more varied, complex sequence characteristics. However, it is not only base sequence but also epigenetic modifications and altered DNA structure that regulate promoter activity. Significantly, many promoters across all organisms contain sequences that can form intrastrand hairpins (cruciforms) or four-stranded structures (G-quadruplex or i-motif). In this review we integrate recent studies on promoter regulation that highlight the importance of DNA structure in the evolutionary adaptation of promoter sequences.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Richard P Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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Tokumoto S, Miyata Y, Usui K, Deviatiiarov R, Ohkawa T, Kondratieva S, Shagimardanova E, Gusev O, Cornette R, Itoh M, Hayashizaki Y, Kikawada T. Development of a Tet-On Inducible Expression System for the Anhydrobiotic Cell Line, Pv11. INSECTS 2020; 11:E781. [PMID: 33187095 PMCID: PMC7696976 DOI: 10.3390/insects11110781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022]
Abstract
The Pv11 cell line established from an African chironomid, Polypedilum vanderplanki, is the only cell line tolerant to complete desiccation. In Pv11 cells, a constitutive expression system for Pv11 cells was previously exploited and several reporter genes were successfully expressed. Here we report the identification of an effective minimal promoter for Pv11 cells and its application to the Tet-On inducible expression system. First, using a luciferase reporter assay, we showed that a 202 bp deletion fragment derived from the constitutively active 121-promoter functions in Pv11 cells as an appropriate minimal promoter with the Tet-On inducible expression system. The AcGFP1 (Aequorea coerulescens green fluorescent protein) was also successfully expressed in Pv11 cells using the inducible system. In addition to these reporter genes, the avian myeloblastosis virus reverse transcriptase α subunit (AMV RTα), which is one of the most widely commercially available RNA-dependent DNA polymerases, was successfully expressed through the inducible expression system and its catalytic activity was verified. These results demonstrate the establishment of an inducible expression system in cells that can be preserved in the dry state and highlight a possible application to the production of large and complex proteins.
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Affiliation(s)
- Shoko Tokumoto
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan; (S.T.); (R.C.)
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Institute of Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan;
| | - Kengo Usui
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan; (K.U.); (T.O.)
| | - Ruslan Deviatiiarov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
| | - Takahiro Ohkawa
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan; (K.U.); (T.O.)
| | - Sabina Kondratieva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; (M.I.); (Y.H.)
| | - Richard Cornette
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan; (S.T.); (R.C.)
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; (M.I.); (Y.H.)
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; (M.I.); (Y.H.)
| | - Takahiro Kikawada
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan; (S.T.); (R.C.)
- Institute of Agrobiological Sciences, National Institute of Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan;
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