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Transcription at a Distance in the Budding Yeast Saccharomyces cerevisiae. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proper transcriptional regulation depends on the collaboration of multiple layers of control simultaneously. Cells tightly balance cellular resources and integrate various signaling inputs to maintain homeostasis during growth, development and stressors, among other signals. Many eukaryotes, including the budding yeast Saccharomyces cerevisiae, exhibit a non-random distribution of functionally related genes throughout their genomes. This arrangement coordinates the transcription of genes that are found in clusters, and can occur over long distances. In this work, we review the current literature pertaining to gene regulation at a distance in budding yeast.
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MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations. G3-GENES GENOMES GENETICS 2020; 10:3009-3014. [PMID: 32605926 PMCID: PMC7466961 DOI: 10.1534/g3.120.401396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from https://github.com/mae92/MutantHuntWGS.
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Functionally Related Genes Cluster into Genomic Regions That Coordinate Transcription at a Distance in Saccharomyces cerevisiae. mSphere 2019; 4:4/2/e00063-19. [PMID: 30867326 PMCID: PMC6416364 DOI: 10.1128/msphere.00063-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The two-dimensional, physical positioning of genes along a chromosome can impact proper transcriptional regulation throughout a genomic region. The transcription of neighboring genes is correlated in a genome-wide manner, which is a characteristic of eukaryotes. Many coregulated gene families can be found clustered with another member of the same set—which can result in adjacent gene coregulation of the pair. Due to the myriad gene families that exhibit a nonrandom genomic distribution, there are likely multiple mechanisms working in concert to properly regulate transcriptional coordination of functionally clustered genes. In this study, we utilized budding yeast in an attempt to elucidate mechanisms that underlie this coregulation: testing and empirically validating the enhancer-promoter hypothesis in this species and reporting that functionally related genes cluster to genomic regions that are more conducive to transcriptional regulation at a distance. These clusters rely, in part, on chromatin maintenance and remodelers to maintain proper transcriptional coordination. Our work provides insight into the mechanisms underlying adjacent gene coregulation. Balancing gene expression is a fundamental challenge of all cell types. To properly regulate transcription on a genome-wide level, there are myriad mechanisms employed by the cell. One layer to this regulation is through spatial positioning, with particular chromosomal loci exerting an influence on transcription throughout a region. Many coregulated gene families utilize spatial positioning to coordinate transcription, with functionally related genes clustering together which can allow coordinated expression via adjacent gene coregulation. The mechanisms underlying this process have not been elucidated, though there are many coregulated gene families that exhibit this genomic distribution. In the present study, we tested for a role for the enhancer-promoter (EP) hypothesis, which demonstrates that regulatory elements can exert transcriptional effects over a broad distance, in coordinating transcriptional coregulation using budding yeast, Saccharomyces cerevisiae. We empirically validated the EP model, finding that the genomic distance a promoter can affect varies by locus, which can profoundly affect levels of transcription, phenotype, and the extent of transcriptional disruption throughout a genomic region. Using the nitrogen metabolism, ribosomal protein, toxin response, and heat shock gene families as our test case, we report functionally clustered genes localize to genomic loci that are more conducive to transcriptional regulation at a distance compared to the unpaired members of the same families. Furthermore, we report that the coregulation of functional clusters is dependent, in part, on chromatin maintenance and remodeling, providing one mechanism underlying adjacent gene coregulation. IMPORTANCE The two-dimensional, physical positioning of genes along a chromosome can impact proper transcriptional regulation throughout a genomic region. The transcription of neighboring genes is correlated in a genome-wide manner, which is a characteristic of eukaryotes. Many coregulated gene families can be found clustered with another member of the same set—which can result in adjacent gene coregulation of the pair. Due to the myriad gene families that exhibit a nonrandom genomic distribution, there are likely multiple mechanisms working in concert to properly regulate transcriptional coordination of functionally clustered genes. In this study, we utilized budding yeast in an attempt to elucidate mechanisms that underlie this coregulation: testing and empirically validating the enhancer-promoter hypothesis in this species and reporting that functionally related genes cluster to genomic regions that are more conducive to transcriptional regulation at a distance. These clusters rely, in part, on chromatin maintenance and remodelers to maintain proper transcriptional coordination. Our work provides insight into the mechanisms underlying adjacent gene coregulation.
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Abstract
The Mediator-associated kinases CDK8 and CDK19 function in the context of three additional proteins: CCNC and MED12, which activate CDK8/CDK19 kinase function, and MED13, which enables their association with the Mediator complex. The Mediator kinases affect RNA polymerase II (pol II) transcription indirectly, through phosphorylation of transcription factors and by controlling Mediator structure and function. In this review, we discuss cellular roles of the Mediator kinases and mechanisms that enable their biological functions. We focus on sequence-specific, DNA-binding transcription factors and other Mediator kinase substrates, and how CDK8 or CDK19 may enable metabolic and transcriptional reprogramming through enhancers and chromatin looping. We also summarize Mediator kinase inhibitors and their therapeutic potential. Throughout, we note conserved and divergent functions between yeast and mammalian CDK8, and highlight many aspects of kinase module function that remain enigmatic, ranging from potential roles in pol II promoter-proximal pausing to liquid-liquid phase separation.
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Affiliation(s)
- Charli B Fant
- a Department of Biochemistry , University of Colorado , Boulder , CO , USA
| | - Dylan J Taatjes
- a Department of Biochemistry , University of Colorado , Boulder , CO , USA
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Tourigny JP, Saleh MM, Schumacher K, Devys D, Zentner GE. Mediator Is Essential for Small Nuclear and Nucleolar RNA Transcription in Yeast. Mol Cell Biol 2018; 38:e00296-18. [PMID: 30275344 PMCID: PMC6275182 DOI: 10.1128/mcb.00296-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/13/2018] [Accepted: 09/21/2018] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein-coding RNA (ncRNA) genes, including those encoding small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA and mRNA expression relies on a set of common factors, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in sn/snoRNA gene transcription. We found that Mediator maps to sn/snoRNA gene regulatory regions and that rapid depletion of the essential structural subunit Med14 strongly reduces RNAPII and TFIIB occupancy as well as nascent transcription of sn/snoRNA genes. Deletion of Med3 and Med15, subunits of the activator-interacting Mediator tail module, does not affect Mediator recruitment to or RNAPII and TFIIB occupancy of sn/snoRNA genes. Our analyses suggest that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.
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Affiliation(s)
- Jason P Tourigny
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Moustafa M Saleh
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kenny Schumacher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- UMR7104, Centre National de la Recherche Scientifique, Illkirch, France
- U964, Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, USA
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Knoll ER, Zhu ZI, Sarkar D, Landsman D, Morse RH. Role of the pre-initiation complex in Mediator recruitment and dynamics. eLife 2018; 7:39633. [PMID: 30540252 PMCID: PMC6322861 DOI: 10.7554/elife.39633] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022] Open
Abstract
The Mediator complex stimulates the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that yeast lacking Med2-Med3-Med15 are viable and that Mediator and PolII are recruited to promoters genome-wide in these cells, albeit at reduced levels. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.
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Affiliation(s)
- Elisabeth R Knoll
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Z Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, United States
| | - Debasish Sarkar
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, United States
| | - Randall H Morse
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States.,Wadsworth Center, New York State Department of Health, Albany, United States
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Systematic Identification, Characterization, and Conservation of Adjacent-Gene Coregulation in the Budding Yeast Saccharomyces cerevisiae. mSphere 2018; 3:3/3/e00220-18. [PMID: 29898982 PMCID: PMC6001612 DOI: 10.1128/msphere.00220-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/23/2018] [Indexed: 12/28/2022] Open
Abstract
The spatial positioning of genes throughout the genome arrangement can alter their expression in many eukaryotic organisms. Often this results in a genomic context-specific effect on transcription. One example of this is through the clustering of functionally related genes, which results in adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiae. In the present study, we set out to systematically characterize the prevalence of this phenomenon, finding the genomic organization of functionally related genes into clusters is a characteristic of myriad gene families. These arrangements are found in many evolutionarily divergent fungi and thus represent a widespread, yet underappreciated, layer of transcriptional regulation. It is essential that cells orchestrate gene expression for the specific niche that they occupy, and this often requires coordination of the expression of large sets of genes. There are multiple regulatory systems that exist for modulation of gene expression, including the adjacent-gene coregulation of the rRNA and ribosome biogenesis and ribosomal protein families. Both gene families exhibit a nonrandom genomic distribution, often clustered directly adjacent to another member of the same family, which results in a tighter transcriptional coordination among adjacent paired genes than that of the unpaired genes within each regulon and can result in a shared promoter that coordinates expression of the pairs. This nonrandom genomic distribution has been seen in a few functionally related gene families, and many of these functional pairings are conserved across divergent fungal lineages. To date, the significance of these observations has not been extended in a systematic way to characterize how prevalent the role of adjacent-gene coregulation is in transcriptional regulation. In the present study, we systematically analyzed the transcriptional coherence of the functional pairs compared to the singletons within all gene families defined by the Gene Ontology Slim designation, using Saccharomyces cerevisiae as a model system, finding that clusters exhibit a tighter transcriptional correlation under specific contexts. We found that the longer a functional pairing is conserved the tighter its response to broad stress and nutritional responses, that roughly 25% of gene families exhibit a nonrandom genomic distribution, and that many of these clusters are conserved. This suggests that adjacent-gene coregulation is a widespread, yet underappreciated, transcriptional mechanism. IMPORTANCE The spatial positioning of genes throughout the genome arrangement can alter their expression in many eukaryotic organisms. Often this results in a genomic context-specific effect on transcription. One example of this is through the clustering of functionally related genes, which results in adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiae. In the present study, we set out to systematically characterize the prevalence of this phenomenon, finding the genomic organization of functionally related genes into clusters is a characteristic of myriad gene families. These arrangements are found in many evolutionarily divergent fungi and thus represent a widespread, yet underappreciated, layer of transcriptional regulation.
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Jeronimo C, Robert F. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol 2017; 27:765-783. [DOI: 10.1016/j.tcb.2017.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/15/2022]
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Bossi F, Fan J, Xiao J, Chandra L, Shen M, Dorone Y, Wagner D, Rhee SY. Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC Genomics 2017; 18:480. [PMID: 28651538 PMCID: PMC5485742 DOI: 10.1186/s12864-017-3853-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized. RESULTS To identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function. This method predicted 43 transcriptional regulator families in Arabidopsis thaliana, 7 families in Drosophila melanogaster, and 9 families in Homo sapiens. Literature curation validated 12 of the predicted families to be involved in transcriptional regulation. We tested 33 out of the 195 Arabidopsis putative transcriptional regulators for their ability to activate transcription of a reporter gene in planta and found twelve coactivators, five of which had no prior literature support. To investigate mechanisms of action in which the predicted regulators might work, we looked for interactors of an Arabidopsis candidate that did not show transactivation activity in planta and found that it might work with other members of its own family and a subunit of the Polycomb Repressive Complex 2 to regulate transcription. CONCLUSIONS Our results demonstrate the feasibility of assigning molecular function to proteins of unknown function without depending on sequence similarity. In particular, we identified novel transcriptional regulators using biological features enriched in transcription factors. The predictions reported here should accelerate the characterization of novel regulators.
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Affiliation(s)
- Flavia Bossi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305 USA
| | - Jue Fan
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305 USA
| | - Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6084 USA
| | - Lilyana Chandra
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305 USA
| | - Max Shen
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6084 USA
| | - Yanniv Dorone
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305 USA
- Department of Biology, Stanford University, Stanford, California, 94305 USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6084 USA
| | - Seung Y. Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305 USA
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Dodson AE, Rine J. Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae. Genetics 2016; 204:1065-1074. [PMID: 27655944 PMCID: PMC5105842 DOI: 10.1534/genetics.116.194696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/16/2016] [Indexed: 11/18/2022] Open
Abstract
In Saccharomyces cerevisiae, a small, intergenic region known as the recombination enhancer regulates donor selection during mating-type switching and also helps shape the conformation of chromosome III. Using an assay that detects transient losses of heterochromatic repression, we found that the recombination enhancer also acts at a distance in cis to modify the stability of gene silencing. In a mating-type-specific manner, the recombination enhancer destabilized the heterochromatic repression of a gene located ∼17 kbp away. This effect depended on a subregion of the recombination enhancer that is largely sufficient to determine donor preference. Therefore, this subregion affects both recombination and transcription from a distance. These observations identify a rare example of long-range transcriptional regulation in yeast and raise the question of whether other cis elements also mediate dual effects on recombination and gene expression.
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Affiliation(s)
- Anne E Dodson
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
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Grünberg S, Henikoff S, Hahn S, Zentner GE. Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters. EMBO J 2016; 35:2435-2446. [PMID: 27797823 DOI: 10.15252/embj.201695020] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 11/09/2022] Open
Abstract
Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes. Using the same approach to map TFIID, we find that TFIID is associated with both TFIID- and SAGA-dependent genes and that TFIID and Mediator occupancy is cooperative. Our results clarify Mediator recruitment and binding to the genome, showing that Mediator binding to UASs is widespread, partially uncoupled from transcription, and mediated in part by TFIID.
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Affiliation(s)
- Sebastian Grünberg
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Beagrie RA, Pombo A. Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. Bioessays 2016; 38:881-93. [PMID: 27452946 DOI: 10.1002/bies.201600032] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Enhancers can stimulate transcription by a number of different mechanisms which control different stages of the transcription cycle of their target genes, from recruitment of the transcription machinery to elongation by RNA polymerase. These mechanisms may not be mutually exclusive, as a single enhancer may act through different pathways by binding multiple transcription factors. Multiple enhancers may also work together to regulate transcription of a shared target gene. Most of the evidence supporting different enhancer mechanisms comes from the study of single genes, but new high-throughput experimental frameworks offer the opportunity to integrate and generalize disparate mechanisms identified at single genes. This effort is especially important if we are to fully understand how sequence variation within enhancers contributes to human disease.
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Affiliation(s)
- Robert A Beagrie
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
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