1
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Bower G, Hollingsworth EW, Jacinto S, Clock B, Cao K, Liu M, Dziulko A, Alcaina-Caro A, Xu Q, Skowronska-Krawczyk D, Lopez-Rios J, Dickel DE, Bardet AF, Pennacchio LA, Visel A, Kvon EZ. Conserved Cis -Acting Range Extender Element Mediates Extreme Long-Range Enhancer Activity in Mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595809. [PMID: 38826394 PMCID: PMC11142232 DOI: 10.1101/2024.05.26.595809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
While most mammalian enhancers regulate their cognate promoters over moderate distances of tens of kilobases (kb), some enhancers act over distances in the megabase range. The sequence features enabling such extreme-distance enhancer-promoter interactions remain elusive. Here, we used in vivo enhancer replacement experiments in mice to show that short- and medium-range enhancers cannot initiate gene expression at extreme-distance range. We uncover a novel conserved cis -acting element, R ange EX tender (REX), that confers extreme-distance regulatory activity and is located next to a long-range enhancer of Sall1 . The REX element itself has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of the REX increased the range of an enhancer by an order of magnitude, from its native 71kb to 840kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs. These motifs are enriched around long-range limb enhancers genome-wide, including the ZRS, a benchmark long-range limb enhancer of Shh . Mutating the [C/T]AATTA motifs within the ZRS does not affect its limb-specific enhancer activity at short range, but selectively abolishes its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature globally associated with long-range enhancer-promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer extreme-distance gene activation by remote enhancers.
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2
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Pacalin NM, Steinhart Z, Shi Q, Belk JA, Dorovskyi D, Kraft K, Parker KR, Shy BR, Marson A, Chang HY. Bidirectional epigenetic editing reveals hierarchies in gene regulation. Nat Biotechnol 2024:10.1038/s41587-024-02213-3. [PMID: 38760566 DOI: 10.1038/s41587-024-02213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/19/2024] [Indexed: 05/19/2024]
Abstract
CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, in which we apply activating (CRISPRa) and repressive (CRISPRi) perturbations to two loci simultaneously in the same cell. We developed CRISPRai Perturb-seq by coupling dual perturbation gRNA detection with single-cell RNA sequencing, enabling study of pooled perturbations in a mixed single-cell population. We applied this platform to study the genetic interaction between two hematopoietic lineage transcription factors, SPI1 and GATA1, and discovered novel characteristics of their co-regulation on downstream target genes, including differences in SPI1 and GATA1 occupancy at genes that are regulated through different modes. We also studied the regulatory landscape of IL2 (interleukin-2) in Jurkat T cells, primary T cells and chimeric antigen receptor (CAR) T cells and elucidated mechanisms of enhancer-mediated IL2 gene regulation. CRISPRai facilitates investigation of context-specific genetic interactions, provides new insights into gene regulation and will enable exploration of non-coding disease-associated variants.
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Affiliation(s)
- Naomi M Pacalin
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Dmytro Dorovskyi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
- Cartography Biosciences, Inc., South San Francisco, CA, USA
| | - Brian R Shy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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3
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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. Mol Cell 2024; 84:1842-1854.e7. [PMID: 38759624 PMCID: PMC11104518 DOI: 10.1016/j.molcel.2024.04.013] [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: 10/10/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
Genomic context critically modulates regulatory function but is difficult to manipulate systematically. The murine insulin-like growth factor 2 (Igf2)/H19 locus is a paradigmatic model of enhancer selectivity, whereby CTCF occupancy at an imprinting control region directs downstream enhancers to activate either H19 or Igf2. We used synthetic regulatory genomics to repeatedly replace the native locus with 157-kb payloads, and we systematically dissected its architecture. Enhancer deletion and ectopic delivery revealed previously uncharacterized long-range regulatory dependencies at the native locus. Exchanging the H19 enhancer cluster with the Sox2 locus control region (LCR) showed that the H19 enhancers relied on their native surroundings while the Sox2 LCR functioned autonomously. Analysis of regulatory DNA actuation across cell types revealed that these enhancer clusters typify broader classes of context sensitivity genome wide. These results show that unexpected dependencies influence even well-studied loci, and our approach permits large-scale manipulation of complete loci to investigate the relationship between regulatory architecture and function.
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Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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4
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Camellato BR, Brosh R, Ashe HJ, Maurano MT, Boeke JD. Synthetic reversed sequences reveal default genomic states. Nature 2024; 628:373-380. [PMID: 38448583 PMCID: PMC11006607 DOI: 10.1038/s41586-024-07128-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in 'default genomic states' between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.
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Affiliation(s)
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York, NY, USA.
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5
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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.02.547201. [PMID: 37781588 PMCID: PMC10541140 DOI: 10.1101/2023.07.02.547201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting activity of payloads delivered at the endogenous Igf2/H19 locus or ectopically at Hprt revealed that the Igf2/H19 locus includes additional, previously unknown long-range regulatory elements. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate the relationship between locus architecture and function.
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Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- These authors contributed equally
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- These authors contributed equally
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J. Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Highmark Health, Pittsburgh, PA 15222, USA
| | - Megan S. Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Present address: Neochromosome Inc., Long Island City, NY 11101, USA
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Lead contact
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Zhou H, Ning Y, Jian Y, Zhang M, Klakong M, Guo F, Shao Q, Li Y, Yang P, Li Z, Yang L, Li S, Ding W. Functional analysis of a down-regulated transcription factor-SoxNeuroA gene involved in the acaricidal mechanism of scopoletin against spider mites. PEST MANAGEMENT SCIENCE 2024; 80:1593-1606. [PMID: 37986233 DOI: 10.1002/ps.7892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Insight into the mode of action of plant-derived acaricides will help in the development of sustainable control strategies for mite pests. Scopoletin, a promising plant-derived bioactive compound, displays prominent acaricidal activity against Tetranychus cinnabarinus. The transcription factor SoxNeuroA plays a vital role in maintaining calcium ion (Ca2+ ) homeostasis. Down-regulation of SoxNeuroA gene expression occurs in scopoletin-exposed mites, but the functional role of this gene remains unknown. RESULTS A SoxNeuroA gene from T. cinnabarinus (TcSoxNeuroA) was first cloned and identified. Reverse transcription polymerase chain reaction (RT-PCR), quantitative real-time polymerase chain reaction (qPCR), and Western blotting assays all confirmed that the gene expression and protein levels of TcSoxNeuroA were significantly reduced under scopoletin exposure. Furthermore, RNA interference silencing of the weakly expressed SoxNeuroA gene significantly enhanced the susceptibility of mites to scopoletin, suggesting that the acaricidal mechanism of scopoletin was mediated by the weakly expressed SoxNeuroA gene. Additionally, yeast one-hybrid (Y1H) and dual-luciferase reporter assays revealed that TcSoxNeuroA was a repressor of Orai1 Ca2+ channel gene transcription, and the key binding sequence was ATCAAAG (positions -361 to -368 of the Orai1 promoter). Importantly, site-directed mutagenesis and microscale thermophoresis assays further indicated that ASP185, ARG189, and LYS217, which were key predicted hydrogen-bonding sites in the molecular docking model, may be the vital binding sites for scopoletin in TcSoxNeuroA. CONCLUSION These results demonstrate that the acaricidal mechanism of scopoletin involves inhibition of the transcription factor SoxNeuroA, thus inducing the activation of the Orai1 Ca2+ channel, eventually leading to Ca2+ overload and lethality. Elucidation of the transcription factor-targeted mechanism for this potent plant-derived acaricide has vital implications for the design of next-generation green acaricides with novel targets. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Hong Zhou
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Yeshuang Ning
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Yufan Jian
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Miao Zhang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Matthana Klakong
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Fuyou Guo
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Qingyi Shao
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Yanhong Li
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Pinglong Yang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Zongquan Li
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Liang Yang
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Shili Li
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Wei Ding
- Institute of Pesticide Science, College of Plant Protection, Southwest University, Chongqing, P. R. China
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7
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Du M, Stitzinger SH, Spille JH, Cho WK, Lee C, Hijaz M, Quintana A, Cissé II. Direct observation of a condensate effect on super-enhancer controlled gene bursting. Cell 2024; 187:331-344.e17. [PMID: 38194964 DOI: 10.1016/j.cell.2023.12.005] [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: 05/09/2023] [Revised: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
Enhancers are distal DNA elements believed to loop and contact promoters to control gene expression. Recently, we found diffraction-sized transcriptional condensates at genes controlled by clusters of enhancers (super-enhancers). However, a direct function of endogenous condensates in controlling gene expression remains elusive. Here, we develop live-cell super-resolution and multi-color 3D-imaging approaches to investigate putative roles of endogenous condensates in the regulation of super-enhancer controlled gene Sox2. In contrast to enhancer distance, we find instead that the condensate's positional dynamics are a better predictor of gene expression. A basal gene bursting occurs when the condensate is far (>1 μm), but burst size and frequency are enhanced when the condensate moves in proximity (<1 μm). Perturbations of cohesin and local DNA elements do not prevent basal bursting but affect the condensate and its burst enhancement. We propose a three-way kissing model whereby the condensate interacts transiently with gene locus and regulatory DNA elements to control gene bursting.
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Affiliation(s)
- Manyu Du
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Simon Hendrik Stitzinger
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Jan-Hendrik Spille
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Won-Ki Cho
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Choongman Lee
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Mohammed Hijaz
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Andrea Quintana
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Ibrahim I Cissé
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany.
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8
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Chen LF, Long HK. Topology regulatory elements: From shaping genome architecture to gene regulation. Curr Opin Struct Biol 2023; 83:102723. [PMID: 37931379 PMCID: PMC7615376 DOI: 10.1016/j.sbi.2023.102723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
The importance of 3D genome topology in the control of gene expression is becoming increasingly apparent, while regulatory mechanisms remain incompletely understood. Several recent studies have identified architectural elements that influence developmental gene expression by shaping locus topology. We refer to these elements as topological regulatory elements (TopoREs) to reflect their dual roles in genome organisation and gene expression. Importantly, these elements do not harbour autonomous transcriptional activation capacity, and instead appear to facilitate enhancer-promoter interactions, contributing to robust and precise timing of transcription. We discuss examples of TopoREs from two classes that are either dependent or independent of CTCF binding. Importantly, identification and interpretation of TopoRE function may shed light on multiple aspects of gene regulation, including the relationship between enhancer-promoter proximity and transcription, and enhancer-promoter specificity. Ultimately, understanding TopoRE diversity and function will aid in the interpretation of how human sequence variation can impact transcription and contribute to disease phenotypes.
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Affiliation(s)
- Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannah Katherine Long
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, UK.
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9
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Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM. An encyclopedia of enhancer-gene regulatory interactions in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.563812. [PMID: 38014075 PMCID: PMC10680627 DOI: 10.1101/2023.11.09.563812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and largescale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 elementgene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancerpromoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.
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Affiliation(s)
- Andreas R. Gschwind
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Kristy S. Mualim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institute of Science, Stanford, CA, USA
| | - Alireza Karbalayghareh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maya U. Sheth
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kushal K. Dey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Evelyn Jagoda
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramil N. Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Wang Xi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anthony S. Tan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Hank Jones
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - X. Rosa Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - David Yao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Benjamin T. James
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Muhammad S. Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA
| | - Neva C. Durand
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Suhas S. P. Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Ragini Mahajan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Benjamin R. Doughty
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kalina Andreeva
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob C. Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Artificial Intelligence Laboratory, Illumina, Inc., San Diego, CA, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Present Address: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Tri C. Nguyen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | | | - Hilary K. Finucane
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill E. Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Michael A. Beer
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - John A. Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Erez Lieberman Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Lars M. Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jesse M. Engreitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
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10
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Smith A, Auer D, Johnson M, Sanchez E, Ross H, Ward C, Chakravarti A, Kapoor A. Cardiac muscle-restricted partial loss of Nos1ap expression has limited but significant impact on electrocardiographic features. G3 (BETHESDA, MD.) 2023; 13:jkad208. [PMID: 37708408 PMCID: PMC10627271 DOI: 10.1093/g3journal/jkad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/16/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Genome-wide association studies have identified sequence polymorphisms in a functional enhancer of the NOS1AP gene as the most common genetic regulator of QT interval and human cardiac NOS1AP gene expression in the general population. Functional studies based on in vitro overexpression in murine cardiomyocytes and ex vivo knockdown in zebrafish embryonic hearts, by us and others, have also demonstrated that NOS1AP expression levels can alter cellular electrophysiology. Here, to explore the role of NOS1AP in cardiac electrophysiology at an organismal level, we generated and characterized constitutive and heart muscle-restricted Nos1ap knockout mice to assess whether NOS1AP disruption alters the QT interval in vivo. Constitutive loss of Nos1ap led to genetic background-dependent variable lethality at or right before birth. Heart muscle-restricted Nos1ap knockout, generated using cardiac-specific alpha-myosin heavy chain promoter-driven tamoxifen-inducible Cre, resulted in tissue-level Nos1ap expression reduced by half. This partial loss of expression had no detectable effect on the QT interval or other electrocardiographic and echocardiographic parameters, except for a small but significant reduction in the QRS interval. Given that challenges associated with defining the end of the T wave on murine electrocardiogram can limit identification of subtle effects on the QT interval and that common noncoding NOS1AP variants are also associated with the QRS interval, our findings support the role of NOS1AP in regulation of the cardiac electrical cycle.
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Affiliation(s)
- Alexa Smith
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dallas Auer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Morgan Johnson
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ernesto Sanchez
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Holly Ross
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher Ward
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY 10016, USA
| | - Ashish Kapoor
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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11
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Thomas HF, Buecker C. What is an enhancer? Bioessays 2023; 45:e2300044. [PMID: 37256273 DOI: 10.1002/bies.202300044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Tight control of the transcription process is essential for the correct spatial and temporal gene expression pattern during development and in homeostasis. Enhancers are at the core of correct transcriptional activation. The original definition of an enhancer is straightforward: a DNA sequence that activates transcription independent of orientation and direction. Dissection of numerous enhancer loci has shown that many enhancer-like elements might not conform to the original definition, suggesting that enhancers and enhancer-like elements might use multiple different mechanisms to contribute to transcriptional activation. Here, we review methodologies to identify enhancers and enhancer-like elements and discuss pitfalls and consequences for our understanding of transcriptional regulation.
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12
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van Staalduinen J, van Staveren T, Grosveld F, Wendt KS. Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics. Epigenetics Chromatin 2023; 16:27. [PMID: 37349773 PMCID: PMC10288748 DOI: 10.1186/s13072-023-00503-9] [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] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Our understanding of the organization of the chromatin fiber within the cell nucleus has made great progress in the last few years. High-resolution techniques based on next-generation sequencing as well as optical imaging that can investigate chromatin conformations down to the single cell level have revealed that chromatin structure is highly heterogeneous at the level of the individual allele. While TAD boundaries and enhancer-promoter pairs emerge as hotspots of 3D proximity, the spatiotemporal dynamics of these different types of chromatin contacts remain largely unexplored. Investigation of chromatin contacts in live single cells is necessary to close this knowledge gap and further enhance the current models of 3D genome organization and enhancer-promoter communication. In this review, we first discuss the potential of single locus labeling to study architectural and enhancer-promoter contacts and provide an overview of the available single locus labeling techniques such as FROS, TALE, CRISPR-dCas9 and ANCHOR, and discuss the latest developments and applications of these systems.
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Affiliation(s)
- Jente van Staalduinen
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.
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13
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Zhao Y, Coelho C, Lauer S, Majewski M, Laurent JM, Brosh R, Boeke JD. CREEPY: CRISPR-mediated editing of synthetic episomes in yeast. Nucleic Acids Res 2023:gkad491. [PMID: 37326023 PMCID: PMC10359617 DOI: 10.1093/nar/gkad491] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
Use of synthetic genomics to design and build 'big' DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, introducing designer variations to episomal assemblies with high efficiency and fidelity remains challenging. Here we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, a method for rapid engineering of large synthetic episomal DNA constructs. We demonstrate that CRISPR editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes. We optimize CREEPY for efficient and precise multiplex editing of >100 kb yeast episomes, providing an expanded toolkit for synthetic genomics.
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Affiliation(s)
- Yu Zhao
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Camila Coelho
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Miłosz Majewski
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
- Maastricht Science Programme, Maastricht University, Maastricht6200MD, The Netherlands
| | - Jon M Laurent
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY11201, USA
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14
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Mach P, Giorgetti L. Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev 2023; 80:102052. [PMID: 37257410 PMCID: PMC10293802 DOI: 10.1016/j.gde.2023.102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/02/2023]
Abstract
The spatiotemporal control of gene expression in complex multicellular organisms relies on noncoding regulatory sequences such as enhancers, which activate transcription of target genes often over large genomic distances. Despite the advances in the identification and characterization of enhancers, the principles and mechanisms by which enhancers select and control their target genes remain largely unknown. Here, we review recent interdisciplinary and quantitative approaches based on emerging techniques that aim to address open questions in the field, notably how regulatory information is encoded in the DNA sequence, how this information is transferred from enhancers to promoters, and how these processes are regulated in time.
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Affiliation(s)
- Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland. https://twitter.com/@MachPia
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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