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Gutnik S, You JE, Sawh AN, Andriollo A, Mango SE. Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes. Genome Biol 2024; 25:71. [PMID: 38486337 PMCID: PMC10941459 DOI: 10.1186/s13059-024-03199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
Recent advances in microscopy have enabled studying chromosome organization at the single-molecule level, yet little is known about inherited chromosome organization. Here we adapt single-molecule chromosome tracing to distinguish two C. elegans strains (N2 and HI) and find that while their organization is similar, the N2 chromosome influences the folding parameters of the HI chromosome, in particular the step size, across generations. Furthermore, homologous chromosomes overlap frequently, but alignment between homologous regions is rare, suggesting that transvection is unlikely. We present a powerful tool to investigate chromosome architecture and to track the parent of origin.
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Affiliation(s)
- Silvia Gutnik
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Current address: University Children's Hospital Zürich, Pediatric Oncology and Children's Research Center, Balgrist Campus AG, Lengghalde 5, 8008, Zürich, Switzerland
| | - Jia Emil You
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Ahilya N Sawh
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Current address: Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Aude Andriollo
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Susan E Mango
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
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2
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Murphy SE, Boettiger AN. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Nat Genet 2024; 56:493-504. [PMID: 38361032 DOI: 10.1038/s41588-024-01661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Polycomb group proteins have a critical role in silencing transcription during development. It is commonly proposed that Polycomb-dependent changes in genome folding, which compact chromatin, contribute directly to repression by blocking the binding of activating complexes. Recently, it has also been argued that liquid-liquid demixing of Polycomb proteins facilitates this compaction and repression by phase-separating target genes into a membraneless compartment. To test these models, we used Optical Reconstruction of Chromatin Architecture to trace the Hoxa gene cluster, a canonical Polycomb target, in thousands of single cells. Across multiple cell types, we find that Polycomb-bound chromatin frequently explores decompact states and partial mixing with neighboring chromatin, while remaining uniformly repressed, challenging the repression-by-compaction or phase-separation models. Using polymer simulations, we show that these observed flexible ensembles can be explained by 'spatial feedback'-transient contacts that contribute to the propagation of the epigenetic state (epigenetic memory), without inducing a globular organization.
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Affiliation(s)
- Sedona Eve Murphy
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
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3
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Devos X, Fiche JB, Bardou M, Messina O, Houbron C, Gurgo J, Schaeffer M, Götz M, Walter T, Mueller F, Nollmann M. pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging. Genome Biol 2024; 25:47. [PMID: 38351149 PMCID: PMC10863255 DOI: 10.1186/s13059-024-03178-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based methods have emerged, giving rise to the field of spatial genomics. Here, we present pyHiM, a user-friendly python toolbox specifically designed for the analysis of multiplexed DNA-FISH data and the reconstruction of chromatin traces in individual cells. pyHiM employs a modular architecture, allowing independent execution of analysis steps and customization according to sample specificity and computing resources. pyHiM aims to facilitate the democratization and standardization of spatial genomics analysis.
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Affiliation(s)
- Xavier Devos
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Marion Bardou
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Olivier Messina
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Christophe Houbron
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Julian Gurgo
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Marie Schaeffer
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Markus Götz
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, 75006, Paris, France
- Institut Curie, 75248, Paris, Cedex, France
- INSERM, U900, 75248, Paris, Cedex, France
| | - Florian Mueller
- Imaging and Modeling Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France.
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Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 2024; 25:123-141. [PMID: 37673975 PMCID: PMC11127719 DOI: 10.1038/s41576-023-00638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
Abstract
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.
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Affiliation(s)
- Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Lorenzo Boninsegna
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Muyu Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tom Misteli
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Frank Alber
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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Yu H, Wu D, Shen G, Hu M, Li Y. SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575427. [PMID: 38293083 PMCID: PMC10827092 DOI: 10.1101/2024.01.12.575427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE.
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Affiliation(s)
- Hongyu Yu
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daiqing Wu
- Department of Mathematics, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guning Shen
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Yun Li
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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Mukamel EA, Liu H, Behrens MM, Ecker JR. Cell type-specific enrichment of somatic aneuploidy in the mammalian brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572285. [PMID: 38187559 PMCID: PMC10769240 DOI: 10.1101/2023.12.18.572285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Somatic mutations alter the genomes of a subset of an individual's brain cells1-3, impacting gene regulation and contributing to disease processes4,5. Mosaic single nucleotide variants have been characterized with single-cell resolution in the brain2,3, but we have limited information about large-scale structural variation, including whole-chromosome duplication or loss1,6,7. We used a dataset of over 415,000 single-cell DNA methylation and chromatin conformation profiles across the adult mouse brain to identify aneuploid cells comprehensively. Whole-chromosome loss or duplication occurred in <1% of cells, with rates up to 1.8% in non-neuronal cell types, including oligodendrocyte precursors and pericytes. Among all aneuploidies, we observed a strong enrichment of trisomy on chromosome 16, which is syntenic with human chromosome 21 and constitutively trisomic in Down syndrome. Chromosome 16 trisomy occurred in multiple cell types and across brain regions, suggesting that nondisjunction is a recurrent feature of somatic variation in the brain.
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Affiliation(s)
- Eran A. Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, University of California, San Diego, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, University of California, San Diego, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, University of California, San Diego, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
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Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X. Cell-type-specific 3D-genome organization and transcription regulation in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.570024. [PMID: 38105994 PMCID: PMC10723369 DOI: 10.1101/2023.12.04.570024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
3D organization of the genome plays a critical role in regulating gene expression. However, it remains unclear how chromatin organization differs among different cell types in the brain. Here we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the primary motor cortex of the mouse brain. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the physical size of the cell nucleus to the active-inactive chromatin compartmentalization and radial positioning of chromatin loci within the nucleus. These cell-type-dependent variations in nuclear architecture and chromatin organization exhibited strong correlation with both total transcriptional activity of the cell and transcriptional regulation of cell-type-specific marker genes. Moreover, we found that the methylated-DNA-binding protein MeCP2 regulates transcription in a divergent manner, depending on the nuclear radial positions of chromatin loci, through modulating active-inactive chromatin compartmentalization.
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Affiliation(s)
- Shiwei Liu
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Pu Zheng
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Cosmos Yuqi Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Nathan R. Zemke
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
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