1
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Liu C, Wang Y, Shi M, Tao X, Man D, Zhang J, Han B. hnRNPA0 promotes MYB expression by interacting with enhancer lncRNA MY34UE-AS in human leukemia cells. Biochem Biophys Res Commun 2024; 724:150221. [PMID: 38865811 DOI: 10.1016/j.bbrc.2024.150221] [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: 04/30/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
MYB is a key regulator of hematopoiesis and erythropoiesis, and dysregulation of MYB is closely involved in the development of leukemia, however the mechanism of MYB regulation remains still unclear so far. Our previous study identified a long noncoding RNA (lncRNA) derived from the -34 kb enhancer of the MYB locus, which can promote MYB expression, the proliferation and migration of human leukemia cells, and is therefore termed MY34UE-AS. Then the interacting partner proteins of MY34UE-AS were identified and studied in the present study. hnRNPA0 was identified as a binding partner of MY34UE-AS through RNA pulldown assay, which was further validated through RNA immunoprecipitation (RIP). hnRNPA0 interacted with MY34UE-AS mainly through its RRM2 domain. hnRNPA0 overexpression upregulated MYB and increased the proliferation and migration of K562 cells, whereas hnRNPA0 knockdown showed opposite effects. Rescue experiments showed MY34UE-AS was required for above mentioned functions of hnRNPA0. These results reveal that hnRNPA0 is involved in leukemia through upregulating MYB expression by interacting with MY34UE-AS, suggesting that the hnRNPA0/MY34UE-AS axis could serve as a potential target for leukemia treatment.
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Affiliation(s)
- Chao Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Yucheng Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Mengjie Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Xiaoxiao Tao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Da Man
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China.
| | - Junfang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, 201306, China.
| | - Bingshe Han
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306,China; National Demonstration Center for Experimental Fisheries Science Education,Shanghai Ocean University, Shanghai, 201306,China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, 201306, China.
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2
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Sang C, Li X, Liu J, Chen Z, Xia M, Yu M, Yu W. Reversible acetylation of HDAC8 regulates cell cycle. EMBO Rep 2024; 25:3925-3943. [PMID: 39043961 DOI: 10.1038/s44319-024-00210-w] [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: 11/14/2023] [Revised: 05/28/2024] [Accepted: 07/05/2024] [Indexed: 07/25/2024] Open
Abstract
HDAC8, a member of class I HDACs, plays a pivotal role in cell cycle regulation by deacetylating the cohesin subunit SMC3. While cyclins and CDKs are well-established cell cycle regulators, our knowledge of other regulators remains limited. Here we reveal the acetylation of K202 in HDAC8 as a key cell cycle regulator responsive to stress. K202 acetylation in HDAC8, primarily catalyzed by Tip60, restricts HDAC8 activity, leading to increased SMC3 acetylation and cell cycle arrest. Furthermore, cells expressing the mutant form of HDAC8 mimicking K202 acetylation display significant alterations in gene expression, potentially linked to changes in 3D genome structure, including enhanced chromatid loop interactions. K202 acetylation impairs cell cycle progression by disrupting the expression of cell cycle-related genes and sister chromatid cohesion, resulting in G2/M phase arrest. These findings indicate the reversible acetylation of HDAC8 as a cell cycle regulator, expanding our understanding of stress-responsive cell cycle dynamics.
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Affiliation(s)
- Chaowei Sang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Xuedong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Jingxuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Ziyin Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Minhui Xia
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Miao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China.
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3
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Lam JC, Aboreden NG, Midla SC, Wang S, Huang A, Keller CA, Giardine B, Henderson KA, Hardison RC, Zhang H, Blobel GA. YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle. Nat Genet 2024; 56:1938-1952. [PMID: 39210046 DOI: 10.1038/s41588-024-01871-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/16/2024] [Indexed: 09/04/2024]
Abstract
Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion. Integrating mitosis-to-G1-phase dynamics, we observed partial retention of YY1 on mitotic chromatin, predominantly at gene promoters, followed by rapid rebinding during mitotic exit, coinciding with enhancer-promoter loop establishment. YY1 degradation during the mitosis-to-G1-phase interval revealed a set of enhancer-promoter loops that require YY1 for establishment during G1-phase entry but not for maintenance in interphase, suggesting that cell cycle stage influences YY1's architectural function. Thus, as revealed here for YY1, chromatin architectural functions of transcription factors can vary in their interplay with CTCF and cohesin as well as by cell cycle stage.
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Affiliation(s)
- Jessica C Lam
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas G Aboreden
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C Midla
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Siqing Wang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Genomics Research Incubator, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Kate A Henderson
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Niharika, Ureka L, Roy A, Patra SK. Dissecting SOX2 expression and function reveals an association with multiple signaling pathways during embryonic development and in cancer progression. Biochim Biophys Acta Rev Cancer 2024; 1879:189136. [PMID: 38880162 DOI: 10.1016/j.bbcan.2024.189136] [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: 05/09/2023] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
SRY (Sex Determining Region) box 2 (SOX2) is an essential transcription factor that plays crucial roles in activating genes involved in pre- and post-embryonic development, adult tissue homeostasis, and lineage specifications. SOX2 maintains the self-renewal property of stem cells and is involved in the generation of induced pluripotency stem cells. SOX2 protein contains a particular high-mobility group domain that enables SOX2 to achieve the capacity to participate in a broad variety of functions. The information about the involvement of SOX2 with gene regulatory elements, signaling networks, and microRNA is gradually emerging, and the higher expression of SOX2 is functionally relevant to various cancer types. SOX2 facilitates the oncogenic phenotype via cellular proliferation and enhancement of invasive tumor properties. Evidence are accumulating in favor of three dimensional (higher order) folding of chromatin and epigenetic control of the SOX2 gene by chromatin modifications, which implies that the expression level of SOX2 can be modulated by epigenetic regulatory mechanisms, specifically, via DNA methylation and histone H3 modification. In view of this, and to focus further insights into the roles SOX2 plays in physiological functions, involvement of SOX2 during development, precisely, the advances of our knowledge in pre- and post-embryonic development, and interactions of SOX2 in this scenario with various signaling pathways in tumor development and cancer progression, its potential as a therapeutic target against many cancers are summarized and discussed in this article.
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Affiliation(s)
- Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lina Ureka
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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5
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Mulero-Hernández J, Mironov V, Miñarro-Giménez JA, Kuiper M, Fernández-Breis J. Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation. Nucleic Acids Res 2024; 52:e69. [PMID: 38967009 PMCID: PMC11347148 DOI: 10.1093/nar/gkae566] [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: 01/12/2023] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative genome location aspect. Here, we exploit these location and functional aspects together to develop new strategies to enable advanced data querying. Many databases have been developed to provide information about enhancers, but a schema that allows the standardized representation of data, securing interoperability between resources, has been lacking. In this work, we use knowledge graphs for the standardized representation of enhancers and topologically associating domains, together with data about their target genes, transcription factors, location on the human genome, and functional data about diseases and gene ontology annotations. We used this schema to integrate twenty-five enhancer datasets and two domain datasets, creating the most powerful integrative resource in this field to date. The knowledge graphs have been implemented using the Resource Description Framework and integrated within the open-access BioGateway knowledge network, generating a resource that contains an interoperable set of knowledge graphs (enhancers, TADs, genes, proteins, diseases, GO terms, and interactions between domains). We show how advanced queries, which combine functional and location restrictions, can be used to develop new hypotheses about functional aspects of gene expression regulation.
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Affiliation(s)
- Juan Mulero-Hernández
- Departamento de Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, Instituto Murciano de Investigación Biosanitaria (IMIB),30100 Murcia, Spain
| | - Vladimir Mironov
- Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - José Antonio Miñarro-Giménez
- Departamento de Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, Instituto Murciano de Investigación Biosanitaria (IMIB),30100 Murcia, Spain
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Jesualdo Tomás Fernández-Breis
- Departamento de Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, Instituto Murciano de Investigación Biosanitaria (IMIB),30100 Murcia, Spain
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6
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Ealo T, Sanchez-Gaya V, Respuela P, Muñoz-San Martín M, Martin-Batista E, Haro E, Rada-Iglesias A. Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition. Nat Commun 2024; 15:7258. [PMID: 39179577 PMCID: PMC11344162 DOI: 10.1038/s41467-024-51602-4] [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: 01/23/2024] [Accepted: 08/10/2024] [Indexed: 08/26/2024] Open
Abstract
The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow some physical crosstalk across regulatory domains, which is at odds with the specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites cooperatively foster the robust insulation of regulatory domains. By genetically dissecting a couple of representative loci in mouse embryonic stem cells, we show that CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), while developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the insulation of regulatory domains, which in turn might help interpreting the pathological consequences of certain structural variants.
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Affiliation(s)
- Thais Ealo
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - Victor Sanchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
| | - Patricia Respuela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - María Muñoz-San Martín
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
- Service of Neurology, University Hospital Marqués de Valdecilla, Universidad de Cantabria and IDIVAL, Santander, Spain
| | | | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
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7
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Newman SA. Form, function, mind: What doesn't compute (and what might). Biochem Biophys Res Commun 2024; 721:150141. [PMID: 38781663 DOI: 10.1016/j.bbrc.2024.150141] [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: 10/24/2023] [Revised: 03/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.
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8
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Denaud S, Bardou M, Papadopoulos GL, Grob S, Di Stefano M, Sabarís G, Nollmann M, Schuettengruber B, Cavalli G. A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication. Nat Struct Mol Biol 2024:10.1038/s41594-024-01375-7. [PMID: 39152239 DOI: 10.1038/s41594-024-01375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Three-dimensional (3D) genome folding has a fundamental role in the regulation of developmental genes by facilitating or constraining chromatin interactions between cis-regulatory elements (CREs). Polycomb response elements (PREs) are a specific kind of CRE involved in the memory of transcriptional states in Drosophila melanogaster. PREs act as nucleation sites for Polycomb group (PcG) proteins, which deposit the repressive histone mark H3K27me3, leading to the formation of a class of topologically associating domain (TAD) called a Polycomb domain. PREs can establish looping contacts that stabilize the gene repression of key developmental genes during development. However, the mechanism by which PRE loops fine-tune gene expression is unknown. Using clustered regularly interspaced short palindromic repeats and Cas9 genome engineering, we specifically perturbed PRE contacts or enhancer function and used complementary approaches including 4C-seq, Hi-C and Hi-M to analyze how chromatin architecture perturbation affects gene expression. Our results suggest that the PRE loop at the dac gene locus acts as a constitutive 3D chromatin scaffold during Drosophila development that forms independently of gene expression states and has a versatile function; it restricts enhancer-promoter communication and contributes to enhancer specificity.
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Affiliation(s)
- Sandrine Denaud
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France
| | - Marion Bardou
- Centre de Biologie Structurale, IUMR5048 CNRS, INSERM U1054, University of Montpellier, Montpellier, France
| | | | - Stefan Grob
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Marco Di Stefano
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France
| | - Gonzalo Sabarís
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, IUMR5048 CNRS, INSERM U1054, University of Montpellier, Montpellier, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France.
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9
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Lao Z, Kamat KD, Jiang Z, Zhang B. OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 2024; 13:RP93223. [PMID: 39146200 PMCID: PMC11326778 DOI: 10.7554/elife.93223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024] Open
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of 'fixed points' within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Kartik D Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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10
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Liu Y, Hoskins I, Geng M, Zhao Q, Chacko J, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Rao S, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of Translation Efficiency Covariation (TEC), identifying coordinated translation patterns across cell types. We nominate potential mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and helps uncover gene functions. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish translational covariation as a conserved organizing principle of mammalian transcriptomes.
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Affiliation(s)
- Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Geng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kangsheng Qi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Yochen Zhong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Sail Biomedicines, Cambridge, MA, 02141, USA
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11
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Liu B, Zhang W, Zeng X, Loza M, Park SJ, Nakai K. TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer. Front Genet 2024; 15:1444459. [PMID: 39184348 PMCID: PMC11341371 DOI: 10.3389/fgene.2024.1444459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024] Open
Abstract
The detection of enhancer-promoter interactions (EPIs) is crucial for understanding gene expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI, a deep learning model based on Transformer designed to detect these interactions solely from DNA sequences. The performance of TF-EPI surpassed that of other state-of-the-art methods on multiple benchmark datasets. Importantly, by utilizing the attention mechanism of the Transformer, we identified distinct cell type-specific motifs and sequences in enhancers and promoters, which were validated against databases such as JASPAR and UniBind, highlighting the potential of our method in discovering new biological insights. Moreover, our analysis of the transcription factors (TFs) corresponding to these motifs and short sequence pairs revealed the heterogeneity and commonality of gene regulatory mechanisms and demonstrated the ability to identify TFs relevant to the source information of the cell line. Finally, the introduction of transfer learning can mitigate the challenges posed by cell type-specific gene regulation, yielding enhanced accuracy in cross-cell line EPI detection. Overall, our work unveils important sequence information for the investigation of enhancer-promoter pairs based on the attention mechanism of the Transformer, providing an important milestone in the investigation of cis-regulatory grammar.
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Affiliation(s)
- Bowen Liu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Weihang Zhang
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Xin Zeng
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Martin Loza
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Sung-Joon Park
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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12
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Patarca R, Haseltine WA. Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2. Int J Mol Sci 2024; 25:8012. [PMID: 39125583 PMCID: PMC11311688 DOI: 10.3390/ijms25158012] [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: 06/26/2024] [Revised: 07/13/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Coronaviruses constitute a global threat to human and animal health. It is essential to investigate the long-distance RNA-RNA interactions that approximate remote regulatory elements in strategies, including genome circularization, discontinuous transcription, and transcriptional enhancers, aimed at the rapid replication of their large genomes, pathogenicity, and immune evasion. Based on the primary sequences and modeled RNA-RNA interactions of two experimentally defined coronaviral enhancers, we detected via an in silico primary and secondary structural analysis potential enhancers in various coronaviruses, from the phylogenetically ancient avian infectious bronchitis virus (IBV) to the recently emerged SARS-CoV-2. These potential enhancers possess a core duplex-forming region that could transition between closed and open states, as molecular switches directed by viral or host factors. The duplex open state would pair with remote sequences in the viral genome and modulate the expression of downstream crucial genes involved in viral replication and host immune evasion. Consistently, variations in the predicted IBV enhancer region or its distant targets coincide with cases of viral attenuation, possibly driven by decreased open reading frame (ORF)3a immune evasion protein expression. If validated experimentally, the annotated enhancer sequences could inform structural prediction tools and antiviral interventions.
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Affiliation(s)
- Roberto Patarca
- ACCESS Health International, 384 West Lane, Ridgefield, CT 06877, USA;
- Feinstein Institutes for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
| | - William A. Haseltine
- ACCESS Health International, 384 West Lane, Ridgefield, CT 06877, USA;
- Feinstein Institutes for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
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13
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Kim J, Diaz LF, Miller MJ, Leadem B, Krivega I, Dean A. An enhancer RNA recruits KMT2A to regulate transcription of Myb. Cell Rep 2024; 43:114378. [PMID: 38889007 PMCID: PMC11369905 DOI: 10.1016/j.celrep.2024.114378] [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: 10/23/2023] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter. We identified a long non-coding RNA (Myrlin) originating from the -81-kb murine Myb enhancer. Myrlin and Myb are coordinately regulated during erythroid differentiation. Myrlin TSS deletion using CRISPR-Cas9 reduced Myrlin and Myb expression and LDB1 complex occupancy at the Myb enhancers, compromising enhancer contacts and reducing RNA Pol II occupancy in the locus. In contrast, CRISPRi silencing of Myrlin left LDB1 and the Myb enhancer hub unperturbed, although Myrlin and Myb expressions were downregulated, decoupling transcription and chromatin looping. Myrlin interacts with the KMT2A/MLL1 complex. Myrlin CRISPRi compromised KMT2A occupancy in the Myb locus, decreasing CDK9 and RNA Pol II binding and resulting in Pol II pausing in the Myb first exon/intron. Thus, Myrlin directly participates in activating Myb transcription by recruiting KMT2A.
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Affiliation(s)
- Juhyun Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Luis F Diaz
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Matthew J Miller
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; University of Iowa Medical School, Iowa City, IA 52242, USA
| | - Benjamin Leadem
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; GeneDx, Gaithersburg, MD 20877, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Sonothera, South San Francisco, CA 94080, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Yao L, Xie P, Guan J, Chung CR, Huang Y, Pang Y, Wu H, Chiang YC, Lee TY. CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. J Chem Inf Model 2024; 64:5725-5736. [PMID: 38946113 PMCID: PMC11267569 DOI: 10.1021/acs.jcim.4c00546] [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: 03/29/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/02/2024]
Abstract
Enhancers are a class of noncoding DNA, serving as crucial regulatory elements in governing gene expression by binding to transcription factors. The identification of enhancers holds paramount importance in the field of biology. However, traditional experimental methods for enhancer identification demand substantial human and material resources. Consequently, there is a growing interest in employing computational methods for enhancer prediction. In this study, we propose a two-stage framework based on deep learning, termed CapsEnhancer, for the identification of enhancers and their strengths. CapsEnhancer utilizes chaos game representation to encode DNA sequences into unique images and employs a capsule network to extract local and global features from sequence "images". Experimental results demonstrate that CapsEnhancer achieves state-of-the-art performance in both stages. In the first and second stages, the accuracy surpasses the previous best methods by 8 and 3.5%, reaching accuracies of 94.5 and 95%, respectively. Notably, this study represents the pioneering application of computer vision methods to enhancer identification tasks. Our work not only contributes novel insights to enhancer identification but also provides a fresh perspective for other biological sequence analysis tasks.
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Affiliation(s)
- Lantian Yao
- Kobilka
Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School
of Science and Engineering, The Chinese
University of Hong Kong, Shenzhen 518172, China
| | - Peilin Xie
- Kobilka
Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jiahui Guan
- School
of Medicine, The Chinese University of Hong
Kong, Shenzhen 518172, China
| | - Chia-Ru Chung
- Department
of Computer Science and Information Engineering, National Central University, Taoyuan 320317, Taiwan
| | - Yixian Huang
- School
of Medicine, The Chinese University of Hong
Kong, Shenzhen 518172, China
| | - Yuxuan Pang
- Division
of Health Medical Intelligence, Human Genome Center, The Institute
of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Huacong Wu
- School
of Medicine, The Chinese University of Hong
Kong, Shenzhen 518172, China
| | - Ying-Chih Chiang
- Kobilka
Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School
of Medicine, The Chinese University of Hong
Kong, Shenzhen 518172, China
| | - Tzong-Yi Lee
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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15
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Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
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Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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16
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Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE, Boettiger AN, Wysocka J. Long range regulation of transcription scales with genomic distance in a gene specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604327. [PMID: 39071420 PMCID: PMC11275926 DOI: 10.1101/2024.07.19.604327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
While critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here we bypass the need for sequence-specific transcription factors and recruit activators directly using CARGO-VPR, an approach for targeting dCas9-VPR using a multiplexed array of RNA guides. We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible by single dCas9. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mESCs, where neither gene is expressed. We demonstrate that while activator recruitment to any tested region results in transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence or presence of the repressive chromatin marks at the locus.
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17
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Du J, Liu Y, Sun J, Yao E, Xu J, Wu X, Xu L, Zhou M, Yang G, Jiang X. ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis. Nat Commun 2024; 15:5994. [PMID: 39013863 PMCID: PMC11252270 DOI: 10.1038/s41467-024-50225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/02/2024] [Indexed: 07/18/2024] Open
Abstract
Chromatin remodeler ARID1A regulates gene transcription by modulating nucleosome positioning and chromatin accessibility. While ARID1A-mediated stage and lineage-restricted gene regulation during cell fate canalization remains unresolved. Using osteoclastogenesis as a model, we show that ARID1A transcriptionally safeguards the osteoclast (OC) fate canalization during proliferation-differentiation switching at single-cell resolution. Notably, ARID1A is indispensable for the transcriptional apparatus condensates formation with coactivator BRD4/lineage-specifying transcription factor (TF) PU.1 at Nfatc1 super-enhancer during safeguarding the OC fate canalization. Besides, the antagonist function between ARID1A-cBAF and BRD9-ncBAF complex during osteoclastogenesis has been validated with in vitro assay and compound mutant mouse model. Furthermore, the antagonistic function of ARID1A-"accelerator" and BRD9-"brake" both depend on coactivator BRD4-"clutch" during osteoclastogenesis. Overall, these results uncover sophisticated cooperation between chromatin remodeler ARID1A, coactivator, and lineage-specifying TF at super-enhancer of lineage master TF in a condensate manner, and antagonist between distinct BAF complexes in the proper and balanced cell fate canalization.
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Affiliation(s)
- Jiahui Du
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Yili Liu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Jinrui Sun
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Enhui Yao
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Jingyi Xu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Xiaolin Wu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Ling Xu
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Mingliang Zhou
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
| | - Guangzheng Yang
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China.
| | - Xinquan Jiang
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China.
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18
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [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: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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19
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Yu H, Wu D, Mishra S, Shen G, Sun H, Hu M, Li Y. SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. Commun Biol 2024; 7:834. [PMID: 38982263 PMCID: PMC11233503 DOI: 10.1038/s42003-024-06428-7] [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: 01/26/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024] Open
Abstract
Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in the nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE .
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Affiliation(s)
- Hongyu Yu
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daiqing Wu
- Department of Statistics, University of Toronto, Ontario, Canada
| | - Shreya Mishra
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Guning Shen
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Huaigu Sun
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Yun Li
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.
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20
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Sokolov V, Kyrchanova O, Klimenko N, Fedotova A, Ibragimov A, Maksimenko O, Georgiev P. New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity. Nucleic Acids Res 2024; 52:6886-6905. [PMID: 38769058 PMCID: PMC11229372 DOI: 10.1093/nar/gkae393] [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: 09/08/2023] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.
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Affiliation(s)
- Vladimir Sokolov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna Fedotova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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21
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Faggion S, Bonfatti V, Carnier P. Genome-Wide Association Study for Weight Loss at the End of Dry-Curing of Hams Produced from Purebred Heavy Pigs. Animals (Basel) 2024; 14:1983. [PMID: 38998095 PMCID: PMC11240668 DOI: 10.3390/ani14131983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
Dissecting the genetics of production traits in livestock is of outmost importance, both to understand biological mechanisms underlying those traits and to facilitate the design of selection programs incorporating that information. For the pig industry, traits related to curing are key for protected designation of origin productions. In particular, appropriate ham weight loss after dry-curing ensures high quality of the final product and avoids economic losses. In this study, we analyzed data (N = 410) of ham weight loss after approximately 20 months of dry-curing. The animals used for ham production were purebred pigs belonging to a commercial line. A genome-wide association study (GWAS) of 29,844 SNP markers revealed the polygenic nature of the trait: 221 loci explaining a small percentage of the variance (0.3-1.65%) were identified on almost all Sus scrofa chromosomes. Post-GWAS analyses revealed 32 windows located within regulatory regions and 94 windows located in intronic regions of specific genes. In total, 30 candidate genes encoding receptors and enzymes associated with ham weight loss (MTHFD1L, DUSP8), proteolysis (SPARCL1, MYH8), drip loss (TNNI2), growth (CDCA3, LSP1, CSMD1, AP2A2, TSPAN4), and fat metabolism (AGPAT4, IGF2R, PTDSS2, HRAS, TALDO1, BRSK2, TNNI2, SYT8, GTF2I, GTF2IRD1, LPCAT3, ATN1, GNB3, CMIP, SORCS2, CCSER1, SPP1) were detected.
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Affiliation(s)
- Sara Faggion
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Padova, Italy
| | - Valentina Bonfatti
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Padova, Italy
| | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Padova, Italy
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22
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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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23
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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24
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Lu Z, Zheng X, Shi M, Yin Y, Liang Y, Zou Z, Ding C, He Y, Zhou Y, Li X. Lactylation: The emerging frontier in post-translational modification. Front Genet 2024; 15:1423213. [PMID: 38993478 PMCID: PMC11236606 DOI: 10.3389/fgene.2024.1423213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Lactate, a metabolic byproduct, has gained recognition as a highly influential signaling molecule. Lactylation, an emerging form of post-translational modification derived from lactate, plays a crucial role in numerous cellular processes such as inflammation, embryonic development, tumor proliferation, and metabolism. However, the precise molecular mechanisms through which lactylation governs these biological functions in both physiological and pathological contexts remain elusive. Hence, it is imperative to provide a comprehensive overview of lactylation in order to elucidate its significance in biological processes and establish a foundation for forthcoming investigations. This review aims to succinctly outline the process of lactylation modification and the characterization of protein lactylation across diverse organisms. Additionally, A summary of the regulatory mechanisms of lactylation in cellular processes and specific diseases is presented. Finally, this review concludes by delineating existing research gaps in lactylation and proposing primary directions for future investigations.
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Affiliation(s)
- Zhou Lu
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Xueting Zheng
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Mingsong Shi
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yuan Yin
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yuanyuan Liang
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Zhiyan Zou
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Chenghe Ding
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yuanjing He
- Department of Gastroenterology, National Clinical Key Specialty, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yan Zhou
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Xiaoan Li
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
- Department of Gastroenterology, National Clinical Key Specialty, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
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25
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Abewe H, Richey A, Vahrenkamp JM, Ginley-Hidinger M, Rush CM, Kitchen N, Zhang X, Gertz J. Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598690. [PMID: 38915540 PMCID: PMC11195280 DOI: 10.1101/2024.06.12.598690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Transcriptional enhancers can regulate individual or multiple genes through long-range three-dimensional (3D) genome interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChiP to capture changes in 3D genome interactions between active regulatory regions of endometrial cancer cells in response to estrogen treatment and uncovered significant differential long-range interactions that are strongly enriched for estrogen receptor α (ER) bound sites (ERBS). The ERBS anchoring differential loops with either a gene's promoter or distal regions were correlated with larger transcriptional responses to estrogen compared to ERBS not involved in differential interactions. To functionally test this observation, CRISPR-based Enhancer-i was used to deactivate specific ERBS, which revealed a wide range of effects on the transcriptional response to estrogen. However, these effects are only subtly and not significantly stronger for ERBS in differential loops. In addition, we observed an enrichment of 3D interactions between the promoters of estrogen up-regulated genes and found that looped promoters can work together cooperatively. Overall, our work suggests that changes in 3D genome structure upon estrogen treatment identify some functionally important regulatory regions; however, these changes aren't required for a transcriptional response to E2 in endometrial cancer cells.
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Affiliation(s)
- Hosiana Abewe
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandra Richey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Jeffery M Vahrenkamp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Craig M Rush
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Noel Kitchen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Xiaoyang Zhang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
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26
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Ridnik M, Abberbock E, Alipov V, Lhermann SZ, Kaufman S, Lubman M, Poulat F, Gonen N. Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination. Nucleic Acids Res 2024; 52:5514-5528. [PMID: 38499491 PMCID: PMC11162780 DOI: 10.1093/nar/gkae178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Male development in mammals depends on the activity of the two SOX gene: Sry and Sox9, in the embryonic testis. As deletion of Enhancer 13 (Enh13) of the Sox9 gene results in XY male-to-female sex reversal, we explored the critical elements necessary for its function and hence, for testis and male development. Here, we demonstrate that while microdeletions of individual transcription factor binding sites (TFBS) in Enh13 lead to normal testicular development, combined microdeletions of just two SRY/SOX binding motifs can alone fully abolish Enh13 activity leading to XY male-to-female sex reversal. This suggests that for proper male development to occur, these few nucleotides of non-coding DNA must be intact. Interestingly, we show that depending on the nature of these TFBS mutations, dramatically different phenotypic outcomes can occur, providing a molecular explanation for the distinct clinical outcomes observed in patients harboring different variants in the same enhancer.
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Affiliation(s)
- Meshi Ridnik
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Elisheva Abberbock
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Veronica Alipov
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shelly Ziv Lhermann
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shoham Kaufman
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maor Lubman
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Francis Poulat
- Group “Development and Pathology of the Gonad”. Department of Genetics, Cell Biology and Development, Institute of Human Genetics, CNRS-University of Montpellier UMR9002, Montpellier, France
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
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27
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Melkus G, Sizovs A, Rucevskis P, Silina S. Transcriptional Hubs Within Cliques in Ensemble Hi-C Chromatin Interaction Networks. J Comput Biol 2024; 31:589-596. [PMID: 38768423 DOI: 10.1089/cmb.2024.0515] [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] [Indexed: 05/22/2024] Open
Abstract
Chromatin conformation capture technologies permit the study of chromatin spatial organization on a genome-wide scale at a variety of resolutions. Despite the increasing precision and resolution of high-throughput chromatin conformation capture (Hi-C) methods, it remains challenging to conclusively link transcriptional activity to spatial organizational phenomena. We have developed a clique-based approach for analyzing Hi-C data that helps identify chromosomal hotspots that feature considerable enrichment of chromatin annotations for transcriptional start sites and, building on previously published work, show that these chromosomal hotspots are not only significantly enriched in RNA polymerase II binding sites as identified by the ENCODE project, but also identify a noticeable increase in FANTOM5 and GTEx transcription within our identified cliques across a variety of tissue types. From the obtained data, we surmise that our cliques are a suitable method for identifying transcription factories in Hi-C data, and outline further extensions to the method that may make it useful for locating regions of increased transcriptional activity in datasets where in-depth expression or polymerase data may not be available.
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Affiliation(s)
- Gatis Melkus
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Andrejs Sizovs
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Peteris Rucevskis
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Sandra Silina
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
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28
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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] [Grants] [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, Range EXtender (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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Affiliation(s)
- Grace Bower
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
- Medical Scientist Training Program, University of California, Irvine, CA 92967, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Kaitlyn Cao
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Mandy Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Adam Dziulko
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Qianlan Xu
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anaïs F. Bardet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U1258, 67400 Illkirch, France
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
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29
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He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell 2024; 187:2746-2766.e25. [PMID: 38631355 DOI: 10.1016/j.cell.2024.03.023] [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: 06/09/2023] [Revised: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
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Affiliation(s)
- Jinnan He
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangru Huo
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Zeran Jia
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiming Yan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Yu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haozhi Qu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunxin Xie
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Junsong Yuan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Zheng
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yanyan Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Minglei Shi
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Michael Q Zhang
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Yinqing Li
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
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30
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Wu C, Huang J. Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns. BMC Genomics 2024; 25:483. [PMID: 38750461 PMCID: PMC11097474 DOI: 10.1186/s12864-024-10408-w] [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: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Multiple enhancers co-regulating the same gene is prevalent and plays a crucial role during development and disease. However, how multiple enhancers coordinate the same gene expression across various cell types remains largely unexplored at genome scale. RESULTS We develop a computational approach that enables the quantitative assessment of enhancer specificity and selectivity across diverse cell types, leveraging enhancer-promoter (E-P) interactions data. We observe two well-known gene regulation patterns controlled by enhancer clusters, which regulate the same gene either in a limited number of cell types (Specific pattern, Spe) or in the majority of cell types (Conserved pattern, Con), both of which are enriched for super-enhancers (SEs). We identify a previously overlooked pattern (Variable pattern, Var) that multiple enhancers link to the same gene, but rarely coexist in the same cell type. These three patterns control the genes associating with distinct biological function and exhibit unique epigenetic features. Specifically, we discover a subset of Var patterns contains Shared enhancers with stable enhancer-promoter interactions in the majority of cell types, which might contribute to maintaining gene expression by recruiting abundant CTCF. CONCLUSIONS Together, our findings reveal three distinct E-P regulation patterns across different cell types, providing insights into deciphering the complexity of gene transcriptional regulation.
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Affiliation(s)
- Chengyi Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, Fujian, China.
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31
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Le DJ, Hafner A, Gaddam S, Wang KC, Boettiger AN. Super-enhancer interactomes from single cells link clustering and transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593251. [PMID: 38766104 PMCID: PMC11100725 DOI: 10.1101/2024.05.08.593251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Regulation of gene expression hinges on the interplay between enhancers and promoters, traditionally explored through pairwise analyses. Recent advancements in mapping genome folding, like GAM, SPRITE, and multi-contact Hi-C, have uncovered multi-way interactions among super-enhancers (SEs), spanning megabases, yet have not measured their frequency in single cells or the relationship between clustering and transcription. To close this gap, here we used multiplexed imaging to map the 3D positions of 376 SEs across thousands of mammalian nuclei. Notably, our single-cell images reveal that while SE-SE contacts are rare, SEs often form looser associations we termed "communities". These communities, averaging 4-5 SEs, assemble cooperatively under the combined effects of genomic tethers, Pol2 clustering, and nuclear compartmentalization. Larger communities are associated with more frequent and larger transcriptional bursts. Our work provides insights about the SE interactome in single cells that challenge existing hypotheses on SE clustering in the context of transcriptional regulation.
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Affiliation(s)
- Derek J. Le
- Department of Developmental Biology, Stanford University, Stanford, CA, United States
- Cancer Biology Program, Stanford University, Stanford, CA, United States
- Department of Dermatology, Stanford University, Stanford, CA, United States
- These authors contributed equally
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, United States
- These authors contributed equally
| | - Sadhana Gaddam
- Department of Dermatology, Stanford University, Stanford, CA, United States
| | - Kevin C. Wang
- Department of Dermatology, Stanford University, Stanford, CA, United States
| | - Alistair N. Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA, United States
- Lead contact
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32
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Baudic M, Murata H, Bosada FM, Melo US, Aizawa T, Lindenbaum P, van der Maarel LE, Guedon A, Baron E, Fremy E, Foucal A, Ishikawa T, Ushinohama H, Jurgens SJ, Choi SH, Kyndt F, Le Scouarnec S, Wakker V, Thollet A, Rajalu A, Takaki T, Ohno S, Shimizu W, Horie M, Kimura T, Ellinor PT, Petit F, Dulac Y, Bru P, Boland A, Deleuze JF, Redon R, Le Marec H, Le Tourneau T, Gourraud JB, Yoshida Y, Makita N, Vieyres C, Makiyama T, Mundlos S, Christoffels VM, Probst V, Schott JJ, Barc J. TAD boundary deletion causes PITX2-related cardiac electrical and structural defects. Nat Commun 2024; 15:3380. [PMID: 38643172 PMCID: PMC11032321 DOI: 10.1038/s41467-024-47739-x] [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: 02/17/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.
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Affiliation(s)
- Manon Baudic
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Hiroshige Murata
- The Department of Cardiovascular Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Fernanda M Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353, Berlin, Germany
| | - Takanori Aizawa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Pierre Lindenbaum
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Lieve E van der Maarel
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Amaury Guedon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Estelle Baron
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Enora Fremy
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Adrien Foucal
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Taisuke Ishikawa
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Hiroya Ushinohama
- Department of Cardiology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Florence Kyndt
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Solena Le Scouarnec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Aurélie Thollet
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Annabelle Rajalu
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Tadashi Takaki
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Takeda-CiRA Joint Program for iPS Cell Applications, Fujisawa, Japan
- Department of Pancreatic Islet Cell Transplantation, National Center for Global Health and Medicine, Tokyo, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Wataru Shimizu
- The Department of Cardiovascular Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Ohtsu, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, Hôpital Jeanne de Flandre, F-59000, Lille, France
- University of Lille, EA 7364-RADEME, F-59000, Lille, France
| | - Yves Dulac
- Unité de Cardiologie Pédiatrique, Hôpital des Enfants, F-31000, Toulouse, France
| | - Paul Bru
- Service de Cardiologie, GH La Rochelle, F-17019, La Rochelle, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Hervé Le Marec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Thierry Le Tourneau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Jean-Baptiste Gourraud
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands
| | - Yoshinori Yoshida
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Naomasa Makita
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
- Department of Cardiology, Sapporo Teishinkai Hospital, Sapporo, Japan
| | - Claude Vieyres
- Cabinet Cardiologique, Clinique St. Joseph, F-16000, Angoulême, France
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Community Medicine Supporting System, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Stephan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353, Berlin, Germany
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Vincent Probst
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands
| | - Jean-Jacques Schott
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands.
| | - Julien Barc
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands.
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Abnizova I, Stapel C, Boekhorst RT, Lee JTH, Hemberg M. Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation. BMC Biol 2024; 22:78. [PMID: 38600550 PMCID: PMC11005181 DOI: 10.1186/s12915-024-01869-2] [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: 08/23/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Regulation of transcription is central to the emergence of new cell types during development, and it often involves activation of genes via proximal and distal regulatory regions. The activity of regulatory elements is determined by transcription factors (TFs) and epigenetic marks, but despite extensive mapping of such patterns, the extraction of regulatory principles remains challenging. RESULTS Here we study differentially and similarly expressed genes along with their associated epigenomic profiles, chromatin accessibility and DNA methylation, during lineage specification at gastrulation in mice. Comparison of the three lineages allows us to identify genomic and epigenomic features that distinguish the two classes of genes. We show that differentially expressed genes are primarily regulated by distal elements, while similarly expressed genes are controlled by proximal housekeeping regulatory programs. Differentially expressed genes are relatively isolated within topologically associated domains, while similarly expressed genes tend to be located in gene clusters. Transcription of differentially expressed genes is associated with differentially open chromatin at distal elements including enhancers, while that of similarly expressed genes is associated with ubiquitously accessible chromatin at promoters. CONCLUSION Based on these associations of (linearly) distal genes' transcription start sites (TSSs) and putative enhancers for developmental genes, our findings allow us to link putative enhancers to their target promoters and to infer lineage-specific repertoires of putative driver transcription factors, within which we define subgroups of pioneers and co-operators.
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Affiliation(s)
- Irina Abnizova
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Carine Stapel
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Martin Hemberg
- Wellcome Sanger Institute, Hinxton, UK.
- The Gene Lay Institute of Immunology and Inflammation Brigham & Women's Hospital and Harvard Medical School, Boston, USA.
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34
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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35
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Kim KL, Rahme GJ, Goel VY, El Farran CA, Hansen AS, Bernstein BE. Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. Mol Cell 2024; 84:1365-1376.e7. [PMID: 38452764 PMCID: PMC10997458 DOI: 10.1016/j.molcel.2024.02.007] [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: 10/03/2023] [Revised: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 03/09/2024]
Abstract
Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.
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Affiliation(s)
- Kyung Lock Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Gilbert J Rahme
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Viraat Y Goel
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Chadi A El Farran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Anders S Hansen
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA.
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36
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Chen Z, Snetkova V, Bower G, Jacinto S, Clock B, Dizehchi A, Barozzi I, Mannion BJ, Alcaina-Caro A, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA, Kvon EZ. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. Nat Genet 2024; 56:675-685. [PMID: 38509385 PMCID: PMC11203181 DOI: 10.1038/s41588-024-01681-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
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Affiliation(s)
- Zhuoxin Chen
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grace Bower
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Atrin Dizehchi
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Octant, Inc, Emeryville, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA.
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Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024; 25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events.
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Affiliation(s)
- Dong-Woo Hwang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anna Maekiniemi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Hanae Sato
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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38
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Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [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: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
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Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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Melnikova LS, Molodina VV, Georgiev PG, Golovnin AK. Role of Mod(mdg4)-67.2 Protein in Interactions between Su(Hw)-Dependent Complexes and Their Recruitment to Chromatin. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:626-636. [PMID: 38831500 DOI: 10.1134/s0006297924040035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 06/05/2024]
Abstract
Su(Hw) belongs to the class of proteins that organize chromosome architecture, determine promoter activity, and participate in formation of the boundaries/insulators between the regulatory domains. This protein contains a cluster of 12 zinc fingers of the C2H2 type, some of which are responsible for binding to the consensus site. The Su(Hw) protein forms complex with the Mod(mdg4)-67.2 and the CP190 proteins, where the last one binds to all known Drosophila insulators. To further study functioning of the Su(Hw)-dependent complexes, we used the previously described su(Hw)E8 mutation with inactive seventh zinc finger, which produces mutant protein that cannot bind to the consensus site. The present work shows that the Su(Hw)E8 protein continues to directly interact with the CP190 and Mod(mdg4)-67.2 proteins. Through interaction with Mod(mdg4)-67.2, the Su(Hw)E8 protein can be recruited into the Su(Hw)-dependent complexes formed on chromatin and enhance their insulator activity. Our results demonstrate that the Su(Hw) dependent complexes without bound DNA can be recruited to the Su(Hw) binding sites through the specific protein-protein interactions that are stabilized by Mod(mdg4)-67.2.
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Affiliation(s)
- Larisa S Melnikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Varvara V Molodina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Pavel G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Anton K Golovnin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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40
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Kamalyan S, Kyrchanova O, Klimenko N, Babosha V, Vasileva Y, Belova E, Fursenko D, Maksimenko O, Georgiev P. The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality. Epigenetics Chromatin 2024; 17:9. [PMID: 38561749 PMCID: PMC10983669 DOI: 10.1186/s13072-024-00534-w] [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: 08/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND CTCF is highly likely to be the ancestor of proteins that contain large clusters of C2H2 zinc finger domains, and its conservation is observed across most bilaterian organisms. In mammals, CTCF is the primary architectural protein involved in organizing chromosome topology and mediating enhancer-promoter interactions over long distances. In Drosophila, CTCF (dCTCF) cooperates with other architectural proteins to establish long-range interactions and chromatin boundaries. CTCFs of various organisms contain an unstructured N-terminal dimerization domain (DD) and clusters comprising eleven zinc-finger domains of the C2H2 type. The Drosophila (dCTCF) and human (hCTCF) CTCFs share sequence homology in only five C2H2 domains that specifically bind to a conserved 15 bp motif. RESULTS Previously, we demonstrated that CTCFs from different organisms carry unstructured N-terminal dimerization domains (DDs) that lack sequence homology. Here we used the CTCFattP(mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD. Additionally, we observed a strong impact on the binding of the dCTCF mutant to chromatin upon deletion of the DD. However, chromatin binding was restored in transgenic flies expressing a chimeric CTCF protein with the DD of hCTCF. Although the chimeric protein exhibited lower expression levels than those of the dCTCF variants, it efficiently bound to chromatin similarly to the wild type (wt) protein. CONCLUSIONS Our findings suggest that one of the evolutionarily conserved functions of the unstructured N-terminal dimerization domain is to recruit dCTCF to its genomic sites in vivo.
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Affiliation(s)
- Sofia Kamalyan
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Yulia Vasileva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Dariya Fursenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
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41
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Lao Z, Kamat K, Jiang Z, Zhang B. OpenNucleome for high resolution nuclear structural and dynamical modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562451. [PMID: 37905090 PMCID: PMC10614770 DOI: 10.1101/2023.10.16.562451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of "fixed points" within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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Mohammed J, Arora N, Matthews HS, Hansen K, Bader M, Walsh S, Shaffer JR, Weinberg SM, Swigut T, Claes P, Selleri L, Wysocka J. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis. eLife 2024; 13:e82564. [PMID: 38483448 PMCID: PMC10939500 DOI: 10.7554/elife.82564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/18/2024] [Indexed: 03/17/2024] Open
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic variants linked to phenotypic traits and disease risk. However, mechanistic understanding of how GWAS variants influence complex morphological traits and can, in certain cases, simultaneously confer normal-range phenotypic variation and disease predisposition, is still largely lacking. Here, we focus on rs6740960, a single nucleotide polymorphism (SNP) at the 2p21 locus, which in GWAS studies has been associated both with normal-range variation in jaw shape and with an increased risk of non-syndromic orofacial clefting. Using in vitro derived embryonic cell types relevant for human facial morphogenesis, we show that this SNP resides in an enhancer that regulates chondrocytic expression of PKDCC - a gene encoding a tyrosine kinase involved in chondrogenesis and skeletal development. In agreement, we demonstrate that the rs6740960 SNP is sufficient to confer chondrocyte-specific differences in PKDCC expression. By deploying dense landmark morphometric analysis of skull elements in mice, we show that changes in Pkdcc dosage are associated with quantitative changes in the maxilla, mandible, and palatine bone shape that are concordant with the facial phenotypes and disease predisposition seen in humans. We further demonstrate that the frequency of the rs6740960 variant strongly deviated among different human populations, and that the activity of its cognate enhancer diverged in hominids. Our study provides a mechanistic explanation of how a common SNP can mediate normal-range and disease-associated morphological variation, with implications for the evolution of human facial features.
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Affiliation(s)
- Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Harold S Matthews
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Susan Walsh
- Department of Biology, Indiana University IndianapolisIndianapolisUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
- Department of Anthropology, University of PittsburghPittsburghUnited States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Peter Claes
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
- Department of Electrical Engineering, ESAT/PSI, KU LeuvenLeuvenBelgium
- Murdoch Children’s Research InstituteMelbourneAustralia
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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Balasubramanian D, Borges Pinto P, Grasso A, Vincent S, Tarayre H, Lajoignie D, Ghavi-Helm Y. Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries. Nucleic Acids Res 2024; 52:1702-1719. [PMID: 38084924 PMCID: PMC10899756 DOI: 10.1093/nar/gkad1183] [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: 04/25/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/29/2024] Open
Abstract
Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.
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Affiliation(s)
- Deevitha Balasubramanian
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
- Indian Institute of Science Education and Research (IISER) Tirupati; Tirupati 517507 Andhra Pradesh, India
| | - Pedro Borges Pinto
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Alexia Grasso
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Séverine Vincent
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Hélène Tarayre
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Damien Lajoignie
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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45
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Lin YH, Lehle JD, McCarrey JR. Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells. Front Cell Dev Biol 2024; 12:1306530. [PMID: 38410371 PMCID: PMC10895008 DOI: 10.3389/fcell.2024.1306530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction: Retention of source cell-type epigenetic memory may mitigate the potential for induced pluripotent stem cells (iPSCs) to fully achieve transitions in cell fate in vitro. While this may not preclude the use of iPSC-derived somatic cell types for therapeutic applications, it becomes a major concern impacting the potential use of iPSC-derived germline cell types for reproductive applications. The transition from a source somatic cell type to iPSCs and then on to germ-cell like cells (GCLCs) recapitulates two major epigenetic reprogramming events that normally occur during development in vivo-embryonic reprogramming in the epiblast and germline reprogramming in primordial germ cells (PGCs). We examined the extent of epigenetic and transcriptomic memory persisting first during the transition from differentiated source cell types to iPSCs, and then during the transition from iPSCs to PGC-like cells (PGCLCs). Methods: We derived iPSCs from four differentiated mouse cell types including two somatic and two germ cell types and tested the extent to which each resulting iPSC line resembled a) a validated ES cell reference line, and b) their respective source cell types, on the basis of genome-wide gene expression and DNA methylation patterns. We then induced each iPSC line to form PGCLCs, and assessed epigenomic and transcriptomic memory in each compared to endogenous PGCs/M-prospermatogonia. Results: In each iPSC line, we found residual gene expression and epigenetic programming patterns characteristic of the corresponding source differentiated cell type from which each was derived. However, upon deriving PGCLCs, we found very little evidence of lingering epigenetic or transcriptomic memory of the original source cell type. Discussion: This result indicates that derivation of iPSCs and then GCLCs from differentiated source cell types in vitro recapitulates the two-phase epigenetic reprogramming that normally occurs in vivo, and that, to a significant extent, germline cell types derived in vitro from pluripotent cells accurately recapitulate epigenetic programming and gene expression patterns corresponding to equivalent endogenous germ cell types, suggesting that they have the potential to form the basis of in vitro gametogenesis as a useful therapeutic strategy for treatment of infertility.
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Affiliation(s)
- Yu-Huey Lin
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Jake D Lehle
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [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: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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47
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Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [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] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
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Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
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48
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Achiro JM, Tao Y, Gao F, Lin CH, Watanabe M, Neumann S, Coppola G, Black DL, Martin KC. Aging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampus. Front Mol Neurosci 2024; 17:1334862. [PMID: 38318533 PMCID: PMC10839115 DOI: 10.3389/fnmol.2024.1334862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Aging-related memory impairment and pathological memory disorders such as Alzheimer's disease differ between males and females, and yet little is known about how aging-related changes in the transcriptome and chromatin environment differ between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus in both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response and synaptic function and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic function. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE-1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Sex differences in gene expression and chromatin accessibility were amplified with aging, findings that may shed light on sex differences in aging-related and pathological memory loss.
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Affiliation(s)
- Jennifer M. Achiro
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Yang Tao
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Fuying Gao
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Marika Watanabe
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Sylvia Neumann
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas L. Black
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Kelsey C. Martin
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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49
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Lavezzo GM, Lauretto MDS, Andrioli LPM, Machado-Lima A. Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites. Genet Mol Biol 2024; 46:e20230048. [PMID: 38285430 PMCID: PMC10945726 DOI: 10.1590/1678-4685-gmb-2023-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/18/2023] [Indexed: 01/30/2024] Open
Abstract
Prediction of transcription factor binding sites (TFBS) is an example of application of Bioinformatics where DNA molecules are represented as sequences of A, C, G and T symbols. The most used model in this problem is Position Weight Matrix (PWM). Notwithstanding the advantage of being simple, PWMs cannot capture dependency between nucleotide positions, which may affect prediction performance. Acyclic Probabilistic Finite Automata (APFA) is an alternative model able to accommodate position dependencies. However, APFA is a more complex model, which means more parameters have to be learned. In this paper, we propose an innovative method to identify when position dependencies influence preference for PWMs or APFAs. This implied using position dependency features extracted from 1106 sets of TFBS to infer a decision tree able to predict which is the best model - PWM or APFA - for a given set of TFBSs. According to our results, as few as three pinpointed features are able to choose the best model, providing a balance of performance (average precision) and model simplicity.
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Affiliation(s)
- Guilherme Miura Lavezzo
- Universidade de São Paulo, Instituto de Matemática e Estatística,
Programa Interunidades de Pós-Graduação em Bioinformática, São Paulo, SP,
Brazil
| | | | | | - Ariane Machado-Lima
- Universidade de São Paulo, Escola de Artes, Ciências e Humanidades,
São Paulo, SP, Brazil
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50
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Ahmad K, Brahma S, Henikoff S. Epigenetic pioneering by SWI/SNF family remodelers. Mol Cell 2024; 84:194-201. [PMID: 38016477 PMCID: PMC10842064 DOI: 10.1016/j.molcel.2023.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/20/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
In eukaryotic genomes, transcriptional machinery and nucleosomes compete for binding to DNA sequences; thus, a crucial aspect of gene regulatory element function is to modulate chromatin accessibility for transcription factor (TF) and RNA polymerase binding. Recent structural studies have revealed multiple modes of TF engagement with nucleosomes, but how initial "pioneering" results in steady-state DNA accessibility for further TF binding and RNA polymerase II (RNAPII) engagement has been unclear. Even less well understood is how distant sites of open chromatin interact with one another, such as when developmental enhancers activate promoters to release RNAPII for productive elongation. Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer-promoter contacts. Consideration of the nucleosome unwrapping and ATP hydrolysis activities of SWI/SNF complexes, together with their architectural features, may reconcile steady-state TF occupancy with rapid TF dynamics observed by live imaging.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sandipan Brahma
- University of Nebraska Medical Center, Department of Genetics, Cell Biology & Anatomy, Omaha, NE, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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