351
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Rodriguez S, Ward A, Reckard AT, Shtanko Y, Hull-Crew C, Klocko AD. The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology. G3 (BETHESDA, MD.) 2022; 12:jkac053. [PMID: 35244156 PMCID: PMC9073679 DOI: 10.1093/g3journal/jkac053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/25/2022] [Indexed: 01/17/2023]
Abstract
The eukaryotic genome must be precisely organized for its proper function, as genome topology impacts transcriptional regulation, cell division, replication, and repair, among other essential processes. Disruptions to human genome topology can lead to diseases, including cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) to assess genome organization has revolutionized the study of nuclear genome topology; Hi-C has elucidated numerous genomic structures, including chromosomal territories, active/silent chromatin compartments, Topologically Associated Domains, and chromatin loops. While low-resolution heatmaps can provide important insights into chromosomal level contacts, high-resolution Hi-C datasets are required to reveal folding principles of individual genes. Of particular interest are high-resolution chromosome conformation datasets of organisms modeling the human genome. Here, we report the genome topology of the fungal model organism Neurospora crassa at a high resolution. Our composite Hi-C dataset, which merges 2 independent datasets generated with restriction enzymes that monitor euchromatin (DpnII) and heterochromatin (MseI), along with our DpnII/MseI double digest dataset, provide exquisite detail for both the conformation of entire chromosomes and the folding of chromatin at the resolution of individual genes. Within constitutive heterochromatin, we observe strong yet stochastic internal contacts, while euchromatin enriched with either activating or repressive histone post-translational modifications associates with constitutive heterochromatic regions, suggesting intercompartment contacts form to regulate transcription. Consistent with this, a strain with compromised heterochromatin experiences numerous changes in gene expression. Our high-resolution Neurospora Hi-C datasets are outstanding resources to the fungal community and provide valuable insights into higher organism genome topology.
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Affiliation(s)
- Sara Rodriguez
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Ashley Ward
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Andrew T Reckard
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Yulia Shtanko
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Andrew D Klocko
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
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352
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Brahmachari S, Contessoto V, Di Pierro M, Onuchic J. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Res 2022; 50:4258-4271. [PMID: 35420130 PMCID: PMC9071446 DOI: 10.1093/nar/gkac231] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023] Open
Abstract
The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
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Affiliation(s)
| | | | - Michele Di Pierro
- Department of Physics, and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston TX 77005, USA
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353
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Segueni J, Noordermeer D. CTCF: a misguided jack-of-all-trades in cancer cells. Comput Struct Biotechnol J 2022; 20:2685-2698. [PMID: 35685367 PMCID: PMC9166472 DOI: 10.1016/j.csbj.2022.05.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/13/2022] Open
Abstract
The emergence and progression of cancers is accompanied by a dysregulation of transcriptional programs. The three-dimensional (3D) organization of the human genome has emerged as an important multi-level mediator of gene transcription and regulation. In cancer cells, this organization can be restructured, providing a framework for the deregulation of gene activity. The CTCF protein, initially identified as the product from a tumor suppressor gene, is a jack-of-all-trades for the formation of 3D genome organization in normal cells. Here, we summarize how CTCF is involved in the multi-level organization of the human genome and we discuss emerging insights into how perturbed CTCF function and DNA binding causes the activation of oncogenes in cancer cells, mostly through a process of enhancer hijacking. Moreover, we highlight non-canonical functions of CTCF that can be relevant for the emergence of cancers as well. Finally, we provide guidelines for the computational identification of perturbed CTCF binding and reorganized 3D genome structure in cancer cells.
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354
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Razin SV, Kantidze OL. The twisted path of the 3D genome: where does it lead? Trends Biochem Sci 2022; 47:736-744. [DOI: 10.1016/j.tibs.2022.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/19/2022] [Accepted: 04/11/2022] [Indexed: 01/01/2023]
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355
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Zhou J. Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale. Nat Genet 2022; 54:725-734. [PMID: 35551308 PMCID: PMC9186125 DOI: 10.1038/s41588-022-01065-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 03/29/2022] [Indexed: 11/09/2022]
Abstract
To learn how genomic sequence influences multiscale three-dimensional (3D) genome architecture, this manuscript presents a sequence-based deep-learning approach, Orca, that predicts directly from sequence the 3D genome architecture from kilobase to whole-chromosome scale. Orca captures the sequence dependencies of structures including chromatin compartments and topologically associating domains, as well as diverse types of interactions from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions with cell-type specificity. Orca enables various applications including predicting structural variant effects on multiscale genome organization and it recapitulated effects of experimentally studied variants at varying sizes (300 bp to 90 Mb). Moreover, Orca enables in silico virtual screens to probe the sequence basis of 3D genome organization at different scales. At the submegabase scale, it predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, virtual screens of sequence activities suggest a model for the sequence basis of chromatin compartments with a prominent role of transcription start sites.
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Affiliation(s)
- Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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356
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Yesbolatova AK, Arai R, Sakaue T, Kimura A. Formulation of Chromatin Mobility as a Function of Nuclear Size during C. elegans Embryogenesis Using Polymer Physics Theories. PHYSICAL REVIEW LETTERS 2022; 128:178101. [PMID: 35570447 DOI: 10.1103/physrevlett.128.178101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases. Despite its biological implications, the underlying mechanism for this transition was unclear. By combining theory and experiment, we analyze the mean-square displacement (MSD) of the chromatin loci, and demonstrate that MSD-vs-time relationships in various nuclei collapse into a single master curve by normalizing them with the mesh size and the corresponding time scale. This enables us to identify the onset of the entangled dynamics with the size of tube diameter of chromatin polymer in the C. elegans embryo. Our dynamical scaling analysis predicts the transition between unentangled and entangled dynamics of chromatin polymers, the quantitative formula for MSD as a function of nuclear size and timescale, and provides testable hypotheses on chromatin mobility in other cell types and species.
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Affiliation(s)
- Aiya K Yesbolatova
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Ritsuko Arai
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Akatsuki Kimura
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
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357
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Aljahani A, Hua P, Karpinska MA, Quililan K, Davies JOJ, Oudelaar AM. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat Commun 2022; 13:2139. [PMID: 35440598 PMCID: PMC9019034 DOI: 10.1038/s41467-022-29696-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date (20 bp resolution) and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.
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Affiliation(s)
- Abrar Aljahani
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | | | - Kimberly Quililan
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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358
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Sefer E. A comparison of topologically associating domain callers over mammals at high resolution. BMC Bioinformatics 2022; 23:127. [PMID: 35413815 PMCID: PMC9006547 DOI: 10.1186/s12859-022-04674-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over High-throughput Chromosome Conformation Capture (Hi-C) interaction dataset. Substantial degree of efforts have been devoted to develop techniques for inferring TADs from Hi-C interaction dataset. Many TAD-calling methods have been developed which differ in their criteria and assumptions in TAD inference. Correspondingly, TADs inferred via these callers vary in terms of both similarities and biological features they are enriched in. RESULT We have carried out a systematic comparison of 27 TAD-calling methods over mammals. We use Micro-C, a recent high-resolution variant of Hi-C, to compare TADs at a very high resolution, and classify the methods into 3 categories: feature-based methods, Clustering methods, Graph-partitioning methods. We have evaluated TAD boundaries, gaps between adjacent TADs, and quality of TADs across various criteria. We also found particularly CTCF and Cohesin proteins to be effective in formation of TADs with corner dots. We have also assessed the callers performance on simulated datasets since a gold standard for TADs is missing. TAD sizes and numbers change remarkably between TAD callers and dataset resolutions, indicating that TADs are hierarchically-organized domains, instead of disjoint regions. A core subset of feature-based TAD callers regularly perform the best while inferring reproducible domains, which are also enriched for TAD related biological properties. CONCLUSION We have analyzed the fundamental principles of TAD-calling methods, and identified the existing situation in TAD inference across high resolution Micro-C interaction datasets over mammals. We come up with a systematic, comprehensive, and concise framework to evaluate the TAD-calling methods performance across Micro-C datasets. Our research will be useful in selecting appropriate methods for TAD inference and evaluation based on available data, experimental design, and biological question of interest. We also introduce our analysis as a benchmarking tool with publicly available source code.
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Affiliation(s)
- Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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359
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Xie L, Dong P, Qi Y, Hsieh THS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z. BRD2 compartmentalizes the accessible genome. Nat Genet 2022; 54:481-491. [PMID: 35410381 PMCID: PMC9099420 DOI: 10.1038/s41588-022-01044-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/01/2022] [Indexed: 12/15/2022]
Abstract
Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associated domains (TADs). While the formation of TADs is dependent on Cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after Cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on one hand by Cohesin and on the other by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-Cohesin interplay model of nuclear topology, where genome compartmentalization results from a competition between loop extrusion and chromatin state-specific affinity interactions.
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360
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Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome. Life (Basel) 2022; 12:life12040541. [PMID: 35455033 PMCID: PMC9026121 DOI: 10.3390/life12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.
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361
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Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L, Wen X, Li H, Chen H, Nie Y, Li D, Liu S, Figueroa DS, Ay F, Xu W, Zhang S, Li W, Cui J, Hoffman AR, Guo H, Hu JF. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. J Cell Biol 2022; 221:213009. [PMID: 35171230 PMCID: PMC8855478 DOI: 10.1083/jcb.202009134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/01/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
The molecular circuitry that causes stem cells to exit from pluripotency remains largely uncharacterized. Using chromatin RNA in situ reverse transcription sequencing, we identified Peln1 as a novel chromatin RNA component in the promoter complex of Oct4, a stem cell master transcription factor gene. Peln1 was negatively associated with pluripotent status during somatic reprogramming. Peln1 overexpression caused E14 cells to exit from pluripotency, while Peln1 downregulation induced robust reprogramming. Mechanistically, we discovered that Peln1 interacted with the Oct4 promoter and recruited the DNA methyltransferase DNMT3A. By de novo altering the epigenotype in the Oct4 promoter, Peln1 dismantled the intrachromosomal loop that is required for the maintenance of pluripotency. Using RNA reverse transcription-associated trap sequencing, we showed that Peln1 targets multiple pathway genes that are associated with stem cell self-renewal. These findings demonstrate that Peln1 can act as a new epigenetic player and use a trans mechanism to induce an exit from the pluripotent state in stem cells.
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Affiliation(s)
- Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Zhonghua Du
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Xue Wen
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Li
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | | | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Andrew R Hoffman
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Guo
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
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362
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Chang L, Li M, Shao S, Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A, Li C, Sun Y. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Protein Cell 2022; 13:258-280. [PMID: 33155082 PMCID: PMC8934373 DOI: 10.1007/s13238-020-00794-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.
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Affiliation(s)
- Lei Chang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Chen Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Shanshan Ai
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiwen Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoying Fan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Aibin He
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Statistical Science, Peking University, Beijing, 100871 China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
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363
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Krietenstein N, Rando OJ. Mammalian Micro-C-XL. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2458:321-332. [PMID: 35103975 DOI: 10.1007/978-1-0716-2140-0_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromosome Conformation Capture (3C) methods are a family of sequencing-based assays to measure the three-dimensional structure of genomes, with Hi-C as the most prominent method in widespread use. The Micro-C-XL protocol is technical variant that improves the resolution and signal-to-noise ratio of the Hi-C protocol and therefore offers enhanced detection of chromatin features such as chromosome loops and fine-grained resolution of topologically associated domains. Here we describe a detailed step-by-step protocol for Micro-C-XL in mammalian cells.
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Affiliation(s)
- Nils Krietenstein
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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364
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Herrmann JC, Beagrie RA, Hughes JR. Making connections: enhancers in cellular differentiation. Trends Genet 2022; 38:395-408. [PMID: 34753603 DOI: 10.1016/j.tig.2021.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 01/23/2023]
Abstract
Deciphering the process by which hundreds of distinct cell types emerge from a single zygote to form a complex multicellular organism remains one of the greatest challenges in biological research. Enhancers are known to be central to cell type-specific gene expression, yet many questions regarding how these genomic elements interact both temporally and spatially with other cis- and trans-acting factors to control transcriptional activity during differentiation and development remain unanswered. Here, we review our current understanding of the role of enhancers and their interactions in this context and highlight recent progress achieved with experimental methods of unprecedented resolution.
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Affiliation(s)
- Jennifer C Herrmann
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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365
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enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions. Genes (Basel) 2022; 13:genes13030472. [PMID: 35328026 PMCID: PMC8949577 DOI: 10.3390/genes13030472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
Accumulating evidence suggests that the physical interactions between genomic regions play critical roles in the regulation of genome functions, such as transcription and epigenetic regulation. Various methods to detect the physical interactions between genomic regions have been developed. We recently developed a method to search for genomic regions interacting with a locus of interest in a non-biased manner that combines pull-down of the locus using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and next-generation sequencing (NGS) analysis (enChIP-Seq). The clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a nuclease-dead form of Cas9 (dCas9) and a guide RNA (gRNA), or transcription activator-like (TAL) proteins, can be used for enChIP. In enChIP-Seq, it is necessary to compare multiple datasets of enChIP-Seq data to unambiguously detect specific interactions. However, it is not always easy to analyze enChIP-Seq datasets to subtract non-specific interactions or identify common interactions. To facilitate such analysis, we developed the enChIP-Seq analyzer software. It enables easy extraction of common signals as well as subtraction of non-specific signals observed in negative control samples, thereby streamlining extraction of specific enChIP-Seq signals. enChIP-Seq analyzer will help users analyze enChIP-Seq data and identify physical interactions between genomic regions.
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366
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Yan J, Huangfu D. Epigenome rewiring in human pluripotent stem cells. Trends Cell Biol 2022; 32:259-271. [PMID: 34955367 PMCID: PMC8840982 DOI: 10.1016/j.tcb.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/10/2023]
Abstract
The epigenome plays a crucial role in modulating the activity of regulatory elements, thereby orchestrating diverse transcriptional programs during embryonic development. Human (h)PSC stepwise differentiation provides an excellent platform for capturing dynamic epigenomic events during lineage transition in human development. Here we discuss how recent technological advances, from epigenomic mapping to targeted perturbation, are providing a more comprehensive appreciation of remodeling of the chromatin landscape during human development with implications for aberrant rewiring in disease. We predict that the continuous innovation of hPSC differentiation methods, epigenome mapping, and CRISPR (clustered regularly interspaced short palindromic repeats) perturbation technologies will allow researchers to build toward not only a comprehensive understanding of the epigenomic mechanisms governing development, but also a highly flexible way to model diseases with opportunities for translation.
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Affiliation(s)
- Jielin Yan
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Danwei Huangfu
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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367
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Novel histone deacetylase inhibitor CT-101 induces γ-globin gene expression in sickle erythroid progenitors with targeted epigenetic effects. Blood Cells Mol Dis 2022; 93:102626. [PMID: 34856533 PMCID: PMC9733664 DOI: 10.1016/j.bcmd.2021.102626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Induction of fetal hemoglobin (HbF) expression ameliorates the clinical severity and prolong survival in persons with sickle cell disease (SCD). Hydroxyurea (HU) is the only FDA-approved HbF inducer however, additional therapeutics that produce an additive effect in SCD are needed. To this end, development of potent Class I histone deacetylase inhibitors (HDACi) for HbF induction represents a rational molecularly targeted approach. In studies here, we evaluated CT-101, a novel Class I-restricted HDACi, a Largazole derivative, for pharmacodynamics, cytotoxicity, and targeted epigenetic effects. In SCD-derived erythroid progenitors, CT-101 induced HbF expression with additive activity in combination with HU. CT-101 preferentially activated γ-globin gene transcription, increased acetylated histone H3 levels, and conferred an open chromatin conformation in the γ-globin promoter. These data indicate CT-101 represents a strong potential candidate as a molecularly targeted inducer of HbF.
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368
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Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin. Biochem Soc Trans 2022; 50:199-212. [PMID: 35166326 PMCID: PMC9847230 DOI: 10.1042/bst20210959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/30/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023]
Abstract
Defining the genome-wide chromatin landscape has been a goal of experimentalists for decades. Here we review highlights of these efforts, from seminal experiments showing discontinuities in chromatin structure related to gene activation to extensions of these methods elucidating general features of chromatin related to gene states by exploiting deep sequencing methods. We also review chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
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369
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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370
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Li A, Liu A, Wu S, Qu K, Hu H, Yang J, Shrestha N, Liu J, Ren G. Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108. BMC PLANT BIOLOGY 2022; 22:77. [PMID: 35193491 PMCID: PMC8862580 DOI: 10.1186/s12870-022-03469-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However, they are still a largely unexplored feature in most plant genomes. Here, we present the whole-genome landscape of SVs between two model legume Medicago truncatula ecotypes-Jemalong A17 and R108- that have been extensively used in various legume biology studies. RESULTS To catalogue SVs, we first resolved the previously published R108 genome assembly (R108 v1.0) to chromosome-scale using 124 × Hi-C data, resulting in a high-quality genome assembly. The inter-chromosomal reciprocal translocations between chromosomes 4 and 8 were confirmed by performing syntenic analysis between the two genomes. Combined with the Hi-C data, it appears that these translocation events had a significant effect on chromatin organization. Using both whole-genome and short-read alignments, we identified the genomic landscape of SVs between the two genomes, some of which may account for several phenotypic differences, including their differential responses to aluminum toxicity and iron deficiency, and the development of different anthocyanin leaf markings. We also found extensive SVs within the nodule-specific cysteine-rich gene family which encodes antimicrobial peptides essential for terminal bacteroid differentiation during nitrogen-fixing symbiosis. CONCLUSIONS Our results provide a near-complete R108 genome assembly and the first genomic landscape of SVs obtained by comparing two M. truncatula ecotypes. This may provide valuable genomic resources for the functional and molecular research of legume biology in the future.
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Affiliation(s)
- Ao Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Kunjing Qu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jinli Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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371
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Dias JD, Sarica N, Cournac A, Koszul R, Neuveut C. Crosstalk between Hepatitis B Virus and the 3D Genome Structure. Viruses 2022; 14:445. [PMID: 35216038 PMCID: PMC8877387 DOI: 10.3390/v14020445] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses that transcribe their DNA within the nucleus have to adapt to the existing cellular mechanisms that govern transcriptional regulation. Recent technological breakthroughs have highlighted the highly hierarchical organization of the cellular genome and its role in the regulation of gene expression. This review provides an updated overview on the current knowledge on how the hepatitis B virus interacts with the cellular 3D genome and its consequences on viral and cellular gene expression. We also briefly discuss the strategies developed by other DNA viruses to co-opt and sometimes subvert cellular genome spatial organization.
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Affiliation(s)
- João Diogo Dias
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
| | - Nazim Sarica
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
| | - Axel Cournac
- Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.C.); (R.K.)
| | - Romain Koszul
- Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.C.); (R.K.)
| | - Christine Neuveut
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
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372
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Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol 2022; 24:327-339. [PMID: 35177821 DOI: 10.1038/s41556-022-00847-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription.
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Affiliation(s)
- Susanne Leidescher
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Johannes Ribisel
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Ullrich
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Yana Feodorova
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Department of Medical Biology, Medical University of Plovdiv; Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Erica Hildebrand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Sebastian Bultmann
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Stephanie Link
- BioMedizinisches Center, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Thanisch
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christopher Mulholland
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Heinrich Leonhardt
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Irina Solovei
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.
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373
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Liu M, Xu K, Saaoud F, Shao Y, Zhang R, Lu Y, Sun Y, Drummer C, Li L, Wu S, Kunapuli SP, Criner GJ, Sun J, Shan H, Jiang X, Wang H, Yang X. 29 m 6A-RNA Methylation (Epitranscriptomic) Regulators Are Regulated in 41 Diseases including Atherosclerosis and Tumors Potentially via ROS Regulation - 102 Transcriptomic Dataset Analyses. J Immunol Res 2022; 2022:1433323. [PMID: 35211628 PMCID: PMC8863469 DOI: 10.1155/2022/1433323] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
We performed a database mining on 102 transcriptomic datasets for the expressions of 29 m6A-RNA methylation (epitranscriptomic) regulators (m6A-RMRs) in 41 diseases and cancers and made significant findings: (1) a few m6A-RMRs were upregulated; and most m6A-RMRs were downregulated in sepsis, acute respiratory distress syndrome, shock, and trauma; (2) half of 29 m6A-RMRs were downregulated in atherosclerosis; (3) inflammatory bowel disease and rheumatoid arthritis modulated m6A-RMRs more than lupus and psoriasis; (4) some organ failures shared eight upregulated m6A-RMRs; end-stage renal failure (ESRF) downregulated 85% of m6A-RMRs; (5) Middle-East respiratory syndrome coronavirus infections modulated m6A-RMRs the most among viral infections; (6) proinflammatory oxPAPC modulated m6A-RMRs more than DAMP stimulation including LPS and oxLDL; (7) upregulated m6A-RMRs were more than downregulated m6A-RMRs in cancer types; five types of cancers upregulated ≥10 m6A-RMRs; (8) proinflammatory M1 macrophages upregulated seven m6A-RMRs; (9) 86% of m6A-RMRs were differentially expressed in the six clusters of CD4+Foxp3+ immunosuppressive Treg, and 8 out of 12 Treg signatures regulated m6A-RMRs; (10) immune checkpoint receptors TIM3, TIGIT, PD-L2, and CTLA4 modulated m6A-RMRs, and inhibition of CD40 upregulated m6A-RMRs; (11) cytokines and interferons modulated m6A-RMRs; (12) NF-κB and JAK/STAT pathways upregulated more than downregulated m6A-RMRs whereas TP53, PTEN, and APC did the opposite; (13) methionine-homocysteine-methyl cycle enzyme Mthfd1 downregulated more than upregulated m6A-RMRs; (14) m6A writer RBM15 and one m6A eraser FTO, H3K4 methyltransferase MLL1, and DNA methyltransferase, DNMT1, regulated m6A-RMRs; and (15) 40 out of 165 ROS regulators were modulated by m6A eraser FTO and two m6A writers METTL3 and WTAP. Our findings shed new light on the functions of upregulated m6A-RMRs in 41 diseases and cancers, nine cellular and molecular mechanisms, novel therapeutic targets for inflammatory disorders, metabolic cardiovascular diseases, autoimmune diseases, organ failures, and cancers.
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Affiliation(s)
- Ming Liu
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Keman Xu
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Fatma Saaoud
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Ying Shao
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Ruijing Zhang
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Department of Nephrology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Yifan Lu
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Yu Sun
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Charles Drummer
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Li Li
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Sheng Wu
- Metabolic Disease Research; Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Satya P. Kunapuli
- Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Gerard J. Criner
- Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jianxin Sun
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Huimin Shan
- Metabolic Disease Research; Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Xiaohua Jiang
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Metabolic Disease Research; Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Hong Wang
- Metabolic Disease Research; Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Metabolic Disease Research; Inflammation, Translational & Clinical Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
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374
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Chang JM, Weng YF, Chang WT, Lin FA, Cavalli G. HiCmapTools: a tool to access HiC contact maps. BMC Bioinformatics 2022; 23:64. [PMID: 35144531 PMCID: PMC8832839 DOI: 10.1186/s12859-022-04589-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to extract biological information from HiC datasets. Results We present HiCmapTools, a tool for biologists to efficiently calculate and analyze HiC maps. The complete program provides multi-query modes and analysis tools. We have validated its utility on two real biological questions: TAD loop and TAD intra-density. Conclusions HiCmapTools supports seven access options so that biologists can quantify contact frequency of the interest sites. The tool has been implemented in C++ and R and is freely available at https://github.com/changlabtw/hicmaptools and documented at https://hicmaptools.readthedocs.io/. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04589-y.
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Affiliation(s)
- Jia-Ming Chang
- Department of Computer Science, National Chengchi University, 11605, Taipei City, Taiwan.
| | - Yi-Fu Weng
- Department of Computer Science, National Chengchi University, 11605, Taipei City, Taiwan
| | - Wei-Ting Chang
- Department of Computer Science, National Chengchi University, 11605, Taipei City, Taiwan
| | - Fu-An Lin
- Department of Computer Science, National Chengchi University, 11605, Taipei City, Taiwan
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France
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375
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Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles. Nat Commun 2022; 13:757. [PMID: 35140210 PMCID: PMC8828778 DOI: 10.1038/s41467-022-28416-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
Numerous intra- and inter-chromosomal contacts have been mapped in eukaryotic genomes, but it remains challenging to link these 3D structures to their regulatory functions. To establish the causal relationships between chromosome conformation and genome functions, we develop a method, Chemically Induced Chromosomal Interaction (CICI), to selectively perturb the chromosome conformation at targeted loci. Using this method, long-distance chromosomal interactions can be induced dynamically between intra- or inter-chromosomal loci pairs, including the ones with very low Hi-C contact frequencies. Measurement of CICI formation time allows us to probe chromosome encounter dynamics between different loci pairs across the cell cycle. We also conduct two functional tests of CICI. We perturb the chromosome conformation near a DNA double-strand break and observe altered donor preference in homologous recombination; we force interactions between early and late-firing DNA replication origins and find no significant changes in replication timing. These results suggest that chromosome conformation plays a deterministic role in homology-directed DNA repair, but not in the establishment of replication timing. Overall, our study demonstrates that CICI is a powerful tool to study chromosome dynamics and 3D genome function. Methods to selectively manipulate specific long-distance chromosomal interactions are limited. Here the authors develop a method called Chemically Induced Chromosomal Interaction (CICI) to engineer interactions and demonstrate that 3D conformation plays a causal role in establishing donor DNA preference during DNA repair.
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376
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Long H, Reeves R, Simon MM. Mouse genomic and cellular annotations. Mamm Genome 2022; 33:19-30. [PMID: 35124726 PMCID: PMC8913471 DOI: 10.1007/s00335-021-09936-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022]
Abstract
AbstractMice have emerged as one of the most popular and valuable model organisms in the research of human biology. This is due to their genetic and physiological similarity to humans, short generation times, availability of genetically homologous inbred strains, and relatively easy laboratory maintenance. Therefore, following the release of the initial human reference genome, the generation of the mouse reference genome was prioritised and represented an important scientific resource for the mouse genetics community. In 2002, the Mouse Genome Sequencing Consortium published an initial draft of the mouse reference genome which contained ~ 96% of the euchromatic genome of female C57BL/6 J mice. Almost two decades on from the publication of the initial draft, sequencing efforts have continued to increase the completeness and accuracy of the C57BL/6 J reference genome alongside advances in genome annotation. Additionally new sequencing technologies have provided a wealth of data that has added to the repertoire of annotations associated with traditional genomic annotations. Including but not limited to advances in regulatory elements, the 3D genome and individual cellular states. In this review we focus on the reference genome C57BL/6 J and summarise the different aspects of genomic and cellular annotations, as well as their relevance to mouse genetic research. We denote a genomic annotation as a functional unit of the genome. Cellular annotations are annotations of cell type or state, defined by the transcriptomic expression profile of a cell. Due to the wide-ranging number and diversity of annotations describing the mouse genome, we focus on gene, repeat and regulatory element annotation as well as two relatively new technologies; 3D genome architecture and single-cell sequencing outlining their utility in genetic research and their current challenges.
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Affiliation(s)
- Helen Long
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, OX11 0RD, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Richard Reeves
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Michelle M Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, OX11 0RD, UK.
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377
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Abstract
Lamins interact with a host of nuclear membrane proteins, transcription factors, chromatin regulators, signaling molecules, splicing factors, and even chromatin itself to form a nuclear subcompartment, the nuclear lamina, that is involved in a variety of cellular processes such as the governance of nuclear integrity, nuclear positioning, mitosis, DNA repair, DNA replication, splicing, signaling, mechanotransduction and -sensation, transcriptional regulation, and genome organization. Lamins are the primary scaffold for this nuclear subcompartment, but interactions with lamin-associated peptides in the inner nuclear membrane are self-reinforcing and mutually required. Lamins also interact, directly and indirectly, with peripheral heterochromatin domains called lamina-associated domains (LADs) and help to regulate dynamic 3D genome organization and expression of developmentally regulated genes.
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Affiliation(s)
- Xianrong Wong
- Laboratory of Developmental and Regenerative Biology, Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138648
| | - Ashley J Melendez-Perez
- Department of Biological Chemistry and Center for Epigenetics, Johns Hopkins University of Medicine, Baltimore, Maryland 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry and Center for Epigenetics, Johns Hopkins University of Medicine, Baltimore, Maryland 21205, USA
- Sidney Kimmel Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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378
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Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JOJ, Oudelaar AM, Hughes JR. Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nat Protoc 2022; 17:445-475. [PMID: 35121852 PMCID: PMC7613269 DOI: 10.1038/s41596-021-00651-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/27/2021] [Indexed: 12/16/2022]
Abstract
Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols. Capture-C methods use oligonucleotides to enrich for interactions of interest from sequencing-ready 3C libraries. This approach is modular and has been adapted and optimized to work for sampling of disperse DNA elements (NuTi Capture-C), including from low cell inputs (LI Capture-C), as well as to generate Hi-C like maps for specific regions of interest (Tiled-C) and to interrogate multiway interactions (Tri-C). We present the design, experimental protocol and analysis pipeline for NuTi Capture-C in addition to the variations for generation of LI Capture-C, Tiled-C and Tri-C data. The entire procedure can be performed in 3 weeks and requires standard molecular biology skills and equipment, access to a next-generation sequencing platform, and basic bioinformatic skills. Implemented with other sequencing technologies, these methods can be used to identify regulatory interactions and to compare the structural organization of the genome in different cell types and genetic models.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kevin Rue-Albrecht
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Sims
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Haematology Theme, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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379
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Huang N, Seow WQ, Appert A, Dong Y, Stempor P, Ahringer J. Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation. Genome Res 2022; 32:357-366. [PMID: 34933938 PMCID: PMC8805715 DOI: 10.1101/gr.275669.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/19/2021] [Indexed: 11/25/2022]
Abstract
Nuclear organization and chromatin interactions are important for genome function, yet determining chromatin connections at high resolution remains a major challenge. To address this, we developed Accessible Region Conformation Capture (ARC-C), which profiles interactions between regulatory elements genome-wide without a capture step. Applied to Caenorhabditis elegans, ARC-C identifies approximately 15,000 significant interactions between regulatory elements at 500-bp resolution. Of 105 TFs or chromatin regulators tested, we find that the binding sites of 60 are enriched for interacting with each other, making them candidates for mediating interactions. These include cohesin and condensin II. Applying ARC-C to a mutant of transcription factor BLMP-1 detected changes in interactions between its targets. ARC-C simultaneously profiles domain-level architecture, and we observe that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) that interact with A/B (active/inactive) compartment-like structure. Furthermore, we discover that inactive compartment interactions are dependent on H3K9 methylation. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.
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Affiliation(s)
- Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Wei Qiang Seow
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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380
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Xue Y, Yang Y, Tian H, Quan H, Liu S, Zhang L, Yang L, Zhu H, Wu H, Gao YQ. Computational characterization of domain-segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis. Mol Oncol 2022; 16:699-716. [PMID: 34708506 PMCID: PMC8807360 DOI: 10.1002/1878-0261.13127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/17/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
The high-order chromatin structure, together with DNA methylation and other epigenetic marks, plays a vital role in gene regulation and displays abnormal status in cancer cells. Theoretical analyses are expected to provide a more unified understanding of the multi-omics data on the large variety of samples, and hopefully a common picture of carcinogenesis. In particular, we are interested in the question of whether an underlying origin DNA sequence exists for these epigenetic alterations. The human genome consists of two types of megabase-sized domain based on the distribution of CpG islands (CGIs) that show distinct structural, epigenetic, and transcriptional properties: CGI-rich and CGI-poor domains. Through an integrated analysis of chromatin structure, DNA methylation, and RNA sequencing data, we found that, in carcinogenesis, the two different types of domain display different structural changes and have an increased number of DNA methylation differences and transcriptional-level differences, compared with in noncancer cells. We also compared the structural features among carcinogenesis, senescence, and mitosis, showing the possible connection between chromatin structure and cell state, which could affect vital cancer-related properties. In summary, chromatin structure, DNA methylation, and gene expression, as well as their changes observed in several types of cancers, show a dependence on multiscale DNA sequence heterogeneity.
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Affiliation(s)
- Yue Xue
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Ying Yang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Hao Tian
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Hui Quan
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Sirui Liu
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Ling Zhang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and DifferentiationSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and DifferentiationSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and DifferentiationSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
- Peking University Institute of HematologyNational Clinical Research Center for Hematologic DiseasePeking University People’s HospitalBeijingChina
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
- Beijing Advanced Innovation Center for Genomics (ICG)Peking UniversityBeijingChina
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381
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Long HS, Greenaway S, Powell G, Mallon AM, Lindgren CM, Simon MM. Making sense of the linear genome, gene function and TADs. Epigenetics Chromatin 2022; 15:4. [PMID: 35090532 PMCID: PMC8800309 DOI: 10.1186/s13072-022-00436-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Topologically associating domains (TADs) are thought to act as functional units in the genome. TADs co-localise genes and their regulatory elements as well as forming the unit of genome switching between active and inactive compartments. This has led to the speculation that genes which are required for similar processes may fall within the same TADs, allowing them to share regulatory programs and efficiently switch between chromatin compartments. However, evidence to link genes within TADs to the same regulatory program is limited. RESULTS We investigated the functional similarity of genes which fall within the same TAD. To do this we developed a TAD randomisation algorithm to generate sets of "random TADs" to act as null distributions. We found that while pairs of paralogous genes are enriched in TADs overall, they are largely depleted in TADs with CCCTC-binding factor (CTCF) ChIP-seq peaks at both boundaries. By assessing gene constraint as a proxy for functional importance we found that genes which singly occupy a TAD have greater functional importance than genes which share a TAD, and these genes are enriched for developmental processes. We found little evidence that pairs of genes in CTCF bound TADs are more likely to be co-expressed or share functional annotations than can be explained by their linear proximity alone. CONCLUSIONS These results suggest that algorithmically defined TADs consist of two functionally different groups, those which are bound by CTCF and those which are not. We detected no association between genes sharing the same CTCF TADs and increased co-expression or functional similarity, other than that explained by linear genome proximity. We do, however, find that functionally important genes are more likely to fall within a TAD on their own suggesting that TADs play an important role in the insulation of these genes.
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Affiliation(s)
- Helen S Long
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mammalian Genetics Unit, Harwell Institute, Didcot, UK.
| | | | - George Powell
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mammalian Genetics Unit, Harwell Institute, Didcot, UK
| | | | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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382
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Aljogol D, Thompson IR, Osborne CS, Mifsud B. Comparison of Capture Hi-C Analytical Pipelines. Front Genet 2022; 13:786501. [PMID: 35198004 PMCID: PMC8859814 DOI: 10.3389/fgene.2022.786501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
It is now evident that DNA forms an organized nuclear architecture, which is essential to maintain the structural and functional integrity of the genome. Chromatin organization can be systematically studied due to the recent boom in chromosome conformation capture technologies (e.g., 3C and its successors 4C, 5C and Hi-C), which is accompanied by the development of computational pipelines to identify biologically meaningful chromatin contacts in such data. However, not all tools are applicable to all experimental designs and all structural features. Capture Hi-C (CHi-C) is a method that uses an intermediate hybridization step to target and select predefined regions of interest in a Hi-C library, thereby increasing effective sequencing depth for those regions. It allows researchers to investigate fine chromatin structures at high resolution, for instance promoter-enhancer loops, but it introduces additional biases with the capture step, and therefore requires specialized pipelines. Here, we compare multiple analytical pipelines for CHi-C data analysis. We consider the effect of retaining multi-mapping reads and compare the efficiency of different statistical approaches in both identifying reproducible interactions and determining biologically significant interactions. At restriction fragment level resolution, the number of multi-mapping reads that could be rescued was negligible. The number of identified interactions varied widely, depending on the analytical method, indicating large differences in type I and type II error rates. The optimal pipeline depends on the project-specific tolerance level of false positive and false negative chromatin contacts.
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Affiliation(s)
- Dina Aljogol
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - I. Richard Thompson
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Cameron S. Osborne
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- *Correspondence: Borbala Mifsud,
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383
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Feng L, Lin H, Kang M, Ren Y, Yu X, Xu Z, Wang S, Li T, Yang W, Hu Q. A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation. DNA Res 2022; 29:dsac004. [PMID: 35094078 PMCID: PMC8801980 DOI: 10.1093/dnares/dsac004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/23/2022] Open
Abstract
It remains largely unknown how plants adapt to high-altitude habitats. Crucihimalaya (Brassicaceae) is an alpine genus occurring in the Qinghai-Tibet Plateau characterized by cold temperatures and strong ultraviolet radiation. Here, we generated a chromosome-level genome for C. lasiocarpa with a total size of 255.8 Mb and a scaffold N50 size of 31.9 Mb. We first examined the karyotype origin of this species and found that the karyotype of five chromosomes resembled the ancestral karyotype of the Brassicaceae family, while the other three showed strong chromosomal structural variations. In combination with the rough genome sequence of another congener (C. himalaica), we found that the significantly expanded gene families and positively selected genes involved in alpine adaptation have occurred since the origin of this genus. Our new findings provide valuable information for the chromosomal karyotype evolution of Brassicaceae and investigations of high-altitude environment adaptation of the genus.
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Affiliation(s)
- Landi Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Hao Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yumeng Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xi Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhanpeng Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shuo Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ting Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenjie Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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384
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Yadav VK, Singh S, Yadav A, Agarwal N, Singh B, Jalmi SK, Yadav VK, Tiwari VK, Kumar V, Singh R, Sawant SV. Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis. Front Genet 2022; 12:799805. [PMID: 35069698 PMCID: PMC8766718 DOI: 10.3389/fgene.2021.799805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/15/2021] [Indexed: 11/26/2022] Open
Abstract
Stresses have been known to cause various responses like cellular physiology, gene regulation, and genome remodeling in the organism to cope and survive. Here, we assessed the impact of stress conditions on the chromatin-interactome network of Arabidopsis thaliana. We identified thousands of chromatin interactions in native as well as in salicylic acid treatment and high temperature conditions in a genome-wide fashion. Our analysis revealed the definite pattern of chromatin interactions and stress conditions could modulate the dynamics of chromatin interactions. We found the heterochromatic region of the genome actively involved in the chromatin interactions. We further observed that the establishment or loss of interactions in response to stress does not result in the global change in the expression profile of interacting genes; however, interacting regions (genes) containing motifs for known TFs showed either lower expression or no difference than non-interacting genes. The present study also revealed that interactions preferred among the same epigenetic state (ES) suggest interactions clustered the same ES together in the 3D space of the nucleus. Our analysis showed that stress conditions affect the dynamics of chromatin interactions among the chromatin loci and these interaction networks govern the folding principle of chromatin by bringing together similar epigenetic marks.
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Affiliation(s)
- Vikash Kumar Yadav
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Swadha Singh
- CSIR-National Botanical Research Institute, Lucknow, India.,School of Natural Sciences, University of California, Merced, Merced, CA, United States
| | - Amrita Yadav
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Neha Agarwal
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Babita Singh
- CSIR-National Botanical Research Institute, Lucknow, India
| | | | | | - Vipin Kumar Tiwari
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Verandra Kumar
- Department of Botany, Manyawar Kanshiram Government Degree College, Aligarh, India
| | | | - Samir Vishwanath Sawant
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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385
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Tartour K, Padmanabhan K. The Clock Takes Shape-24 h Dynamics in Genome Topology. Front Cell Dev Biol 2022; 9:799971. [PMID: 35047508 PMCID: PMC8762244 DOI: 10.3389/fcell.2021.799971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Circadian rhythms orchestrate organismal physiology and behavior in order to anticipate daily changes in the environment. Virtually all cells have an internal rhythm that is synchronized every day by Zeitgebers (environmental cues). The synchrony between clocks within the animal enables the fitness and the health of organisms. Conversely, disruption of rhythms is linked to a variety of disorders: aging, cancer, metabolic diseases, and psychological disorders among others. At the cellular level, mammalian circadian rhythms are built on several layers of complexity. The transcriptional-translational feedback loop (TTFL) was the first to be described in the 90s. Thereafter oscillations in epigenetic marks highlighted the role of chromatin state in organizing the TTFL. More recently, studies on the 3D organization of the genome suggest that genome topology could be yet another layer of control on cellular circadian rhythms. The dynamic nature of genome topology over a solar day implies that the 3D mammalian genome has to be considered in the fourth dimension-in time. Whether oscillations in genome topology are a consequence of 24 h gene-expression or a driver of transcriptional cycles remains an open question. All said and done, circadian clock-gated phenomena such as gene expression, DNA damage response, cell metabolism and animal behavior-go hand in hand with 24 h rhythms in genome topology.
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Affiliation(s)
- Kévin Tartour
- Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard, Lyon, France
| | - Kiran Padmanabhan
- Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard, Lyon, France
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386
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2223-2235. [DOI: 10.1093/hmg/ddac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/11/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
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387
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Dobson T, Swaminathan J. Chromatin Immunoprecipitation Assays on Medulloblastoma Cell Line DAOY. Methods Mol Biol 2022; 2423:39-50. [PMID: 34978686 DOI: 10.1007/978-1-0716-1952-0_4] [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: 06/14/2023]
Abstract
Studies of DNA-protein interactions have revealed regulatory mechanisms of DNA replication, repair, remodeling, and transcription. Perturbation of any or all of these processes result in differential gene expression that can lead to tumor development. Chromatin immunoprecipitation assay (ChIP), currently the only method available to explore DNA-binding in vivo, has become a vastly utilized tool for cancer research. In this article we discuss an assay specified for a pediatric medulloblastoma (MB) cell line DAOY used to determine binding of transcription factors, to detect histone modifications, and to identify novel therapeutic targets.
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Affiliation(s)
- Tara Dobson
- Department of Pediatrics, UT MD Anderson Cancer Center, Houston, TX, USA
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388
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Zhan Y, Giorgetti L, Tiana G. Polymer Folding Simulations from Hi-C Data. Methods Mol Biol 2022; 2301:259-265. [PMID: 34415540 DOI: 10.1007/978-1-0716-1390-0_13] [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: 06/13/2023]
Abstract
In the absence of a clear molecular understanding of the mechanism that stabilizes specific contacts in interphasic chromatin, we resort to the principle of maximum entropy to build a polymeric model based on the Hi-C data of the specific system one wants to study. The interactions are set by an iterative Monte Carlo algorithm to reproduce the average contacts summarized by the Hi-C map. The study of the ensemble of conformations generated by the algorithm can report a much richer set of information than the experimental map alone, including colocalization of multiple sites, fluctuations of the contacts, and kinetical properties.
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Affiliation(s)
- Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Guido Tiana
- Department of Physics, University of Milano and INFN, Milan, Italy.
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389
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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390
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Zufferey M, Tavernari D, Ciriello G. Methods for the Analysis of Topologically Associating Domains (TADs). Methods Mol Biol 2022; 2301:39-59. [PMID: 34415530 DOI: 10.1007/978-1-0716-1390-0_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus, allow building genome-scale maps of intra- and inter-chromosomal contacts (contact maps). Statistical and algorithmic analyses of Hi-C data consist in extracting information from these contact maps. One of the most striking patterns observed in intra-chromosomal Hi-C contact maps emerged from genomic regions that exhibit dense intra-region but sparse inter-region contacts. These have been termed topologically associating domains (TADs). The identification of TADs from Hi-C contact maps is of great interest as they have been shown to act as unit of chromosome organization and, potentially, functional activity. Several approaches have been developed to identify TADs (TAD callers). However, results from these methods are often dependent on data resolution and poorly concordant. In this chapter, we present four TAD callers and we provide detailed protocols for their use. In addition, we show how to compare TADs identified by different callers and how to assess the enrichment for TAD-associated biological features. TAD calling has become a key step in the study of chromatin 3D organization in different cellular contexts. Here we provide guidelines to improve the robustness and quality of these analyses.
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Affiliation(s)
- Marie Zufferey
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland. .,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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391
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Singh RS, Angra V, Singh A, Masih GD, Medhi B. Integrative omics - An arsenal for drug discovery. Indian J Pharmacol 2022; 54:1-6. [PMID: 35343200 PMCID: PMC9012413 DOI: 10.4103/ijp.ijp_53_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Rahul Soloman Singh
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vani Angra
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashutosh Singh
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Gladson David Masih
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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392
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Abstract
The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.
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393
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Bilotti K, Potapov V, Pryor JM, Duckworth AT, Keck J, Lohman GJS. OUP accepted manuscript. Nucleic Acids Res 2022; 50:4647-4658. [PMID: 35438779 PMCID: PMC9071435 DOI: 10.1093/nar/gkac241] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 03/07/2022] [Accepted: 03/31/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - John M Pryor
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Gregory J S Lohman
- To whom correspondence should be addressed. Tel: +1 978 998 7916; Fax: +1 978 921 1350;
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394
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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395
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Abstract
Many population-based methods investigating chromatin dynamics and organization in eukaryotes are based on the chromosome conformation capture (3C) method. Here, we provide an updated version of the quantitative 3C (3C-qPCR) protocol for improved and simplified quantitative analyses of intra-chromosomal contacts.
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Affiliation(s)
- Cosette Rebouissou
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Séphora Sallis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
- Laboratoire de génétique moléculaire du développement, Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.
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396
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Lochs SJA, Kind J. Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq. Methods Mol Biol 2022; 2532:215-241. [PMID: 35867252 DOI: 10.1007/978-1-0716-2497-5_11] [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: 06/15/2023]
Abstract
Spatial genome organization is considered to play an important role in mammalian cells, by guiding gene expression programs and supporting lineage specification. Yet it is still an outstanding question in the field what the direct impact of spatial genome organization on gene expression is. To elucidate this relationship further, we have recently developed scDam&T-seq, a method that simultaneously quantifies protein-DNA interactions and transcriptomes in single cells. This method efficiently combines two preexisting methods: DamID for measuring protein-DNA contacts and CEL-Seq2 for quantification of the transcriptome in single cells. scDam&T-seq has been successfully applied to measure DNA contacts with the nuclear lamina, while at the same time revealing the effect of these contacts on gene expression. This method is applicable to many different proteins of interest and can thereby aid in studying the relationship between protein-DNA interactions and gene expression in single cells.
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Affiliation(s)
- Silke J A Lochs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Radboud University & Oncode Institute, Utrecht, The Netherlands
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Radboud University & Oncode Institute, Utrecht, The Netherlands.
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397
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Carron L, Morlot JB, Lesne A, Mozziconacci J. The 3D Organization of Chromatin Colors in Mammalian Nuclei. Methods Mol Biol 2022; 2301:317-336. [PMID: 34415544 DOI: 10.1007/978-1-0716-1390-0_17] [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: 06/13/2023]
Abstract
While many computational methods have been proposed for 3D chromosome reconstruction from chromosomal contact maps, these methods are rarely used for the interpretation of such experimental data, in particular Hi-C data. We posit that this is due to the lack of an easy-to-use implementation of the proposed algorithms, as well as to the important computational cost of most methods. We here give a detailed implementation of the fast ShRec3D algorithm. We provide a tutorial that will enable the reader to reconstruct 3D consensus structures for human chromosomes and to decorate these structures with chromatin epigenetic states. We use this methodology to show that the bivalent chromatin, including Polycomb-rich domains, is spatially segregated and located in between the active and the quiescent chromatin compartments.
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Affiliation(s)
- Leopold Carron
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France
- Sorbonne Université, CNRS, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Jean-Baptiste Morlot
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France
| | - Annick Lesne
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France.
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
| | - Julien Mozziconacci
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France.
- Muséum National d'Histoire Naturelle, Structure et Instabilité des Genomes, Paris, France.
- Institut Universitaire de France (IUF), Paris, France.
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398
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Mahmood SR, El Said NH, Percipalle P. The Role of Nuclear Actin in Genome Organization and Gene Expression Regulation During Differentiation. Results Probl Cell Differ 2022; 70:607-624. [PMID: 36348124 DOI: 10.1007/978-3-031-06573-6_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the cell nucleus, actin participates in numerous essential processes. Actin is involved in chromatin as part of specific ATP-dependent chromatin remodeling complexes and associates with the RNA polymerase machinery to regulate transcription at multiple levels. Emerging evidence has also shown that the nuclear actin pool controls the architecture of the mammalian genome playing an important role in its hierarchical organization into transcriptionally active and repressed compartments, contributing to the clustering of RNA polymerase II into transcriptional hubs. Here, we review the most recent literature and discuss how actin involvement in genome organization impacts the regulation of gene programs that are activated or repressed during differentiation and development. As in the cytoplasm, we propose that nuclear actin is involved in key nuclear tasks in complex with different types of actin-binding proteins that regulate actin function and bridge interactions between actin and various nuclear components.
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Affiliation(s)
- Syed Raza Mahmood
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Department of Biology, New York University, New York, NY, USA
| | - Nadine Hosny El Said
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.
- Department of Biology, New York University, New York, NY, USA.
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.
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399
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Miranda M, Noordermeer D, Moindrot B. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq. Methods Mol Biol 2022; 2532:15-33. [PMID: 35867243 DOI: 10.1007/978-1-0716-2497-5_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.
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Affiliation(s)
- Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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400
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Irgen-Gioro S, Yoshida S, Walling V, Chong S. Fixation can change the appearance of phase separation in living cells. eLife 2022; 11:79903. [PMID: 36444977 PMCID: PMC9817179 DOI: 10.7554/elife.79903] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.
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Affiliation(s)
- Shawn Irgen-Gioro
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States,Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Victoria Walling
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
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