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Carilli M, Gorin G, Choi Y, Chari T, Pachter L. Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data. Nat Methods 2024; 21:1466-1469. [PMID: 39054391 DOI: 10.1038/s41592-024-02365-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
Here we present biVI, which combines the variational autoencoder framework of scVI with biophysical models describing the transcription and splicing kinetics of RNA molecules. We demonstrate on simulated and experimental single-cell RNA sequencing data that biVI retains the variational autoencoder's ability to capture cell type structure in a low-dimensional space while further enabling genome-wide exploration of the biophysical mechanisms, such as system burst sizes and degradation rates, that underlie observations.
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Affiliation(s)
- Maria Carilli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Fauna Bio, Emeryville, CA, USA
| | - Yongin Choi
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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2
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Pang QY, Chiu YC, Huang RYJ. Regulating epithelial-mesenchymal plasticity from 3D genome organization. Commun Biol 2024; 7:750. [PMID: 38902393 PMCID: PMC11190238 DOI: 10.1038/s42003-024-06441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.
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Affiliation(s)
- Qing You Pang
- Neuro-Oncology Research Laboratory, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, 10051, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
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3
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Han MH, Park J, Park M. Advances in the multimodal analysis of the 3D chromatin structure and gene regulation. Exp Mol Med 2024; 56:763-771. [PMID: 38658704 PMCID: PMC11059362 DOI: 10.1038/s12276-024-01246-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Recent studies have demonstrated that the three-dimensional conformation of the chromatin plays a crucial role in gene regulation, with aberrations potentially leading to various diseases. Advanced methodologies have revealed a link between the chromatin conformation and biological function. This review divides these methodologies into sequencing-based and imaging-based methodologies, tracing their development over time. We particularly highlight innovative techniques that facilitate the simultaneous mapping of RNAs, histone modifications, and proteins within the context of the 3D architecture of chromatin. This multimodal integration substantially improves our ability to establish a robust connection between the spatial arrangement of molecular components in the nucleus and their functional roles. Achieving a comprehensive understanding of gene regulation requires capturing diverse data modalities within individual cells, enabling the direct inference of functional relationships between these components. In this context, imaging-based technologies have emerged as an especially promising approach for gathering spatial information across multiple components in the same cell.
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Affiliation(s)
- Man-Hyuk Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Minhee Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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4
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Woodworth MA, Lakadamyali M. Toward a comprehensive view of gene architecture during transcription. Curr Opin Genet Dev 2024; 85:102154. [PMID: 38309073 PMCID: PMC10989512 DOI: 10.1016/j.gde.2024.102154] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
The activation of genes within the nucleus of eukaryotic cells is a tightly regulated process, orchestrated by a complex interplay of various physical properties and interacting factors. Studying the multitude of components and features that collectively contribute to gene activation has proven challenging due to the complexities of simultaneously visualizing the dynamic and transiently interacting elements that coalesce within the small space occupied by each individual gene. However, various labeling and imaging advances are now starting to overcome this challenge, enabling visualization of gene activation at different lengths and timescales. In this review, we aim to highlight these microscopy-based advances and suggest how they can be combined to provide a comprehensive view of the mechanisms regulating gene activation.
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Affiliation(s)
- Marcus A Woodworth
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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5
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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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Binan L, Danquah S, Valakh V, Simonton B, Bezney J, Nehme R, Cleary B, Farhi SL. Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569494. [PMID: 38076932 PMCID: PMC10705493 DOI: 10.1101/2023.11.30.569494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a generally applicable method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
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Affiliation(s)
- Loϊc Binan
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vera Valakh
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Present address: The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Jon Bezney
- Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Samouil L Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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7
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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Tan L, Shi J, Moghadami S, Parasar B, Wright CP, Seo Y, Vallejo K, Cobos I, Duncan L, Chen R, Deisseroth K. Lifelong restructuring of 3D genome architecture in cerebellar granule cells. Science 2023; 381:1112-1119. [PMID: 37676945 PMCID: PMC11059189 DOI: 10.1126/science.adh3253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
The cerebellum contains most of the neurons in the human brain and exhibits distinctive modes of development and aging. In this work, by developing our single-cell three-dimensional (3D) genome assay-diploid chromosome conformation capture, or Dip-C-into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we resolved the first 3D genome structures of single cerebellar cells, created life-spanning 3D genome atlases for both humans and mice, and jointly measured transcriptome and chromatin accessibility during development. We found that although the transcriptome and chromatin accessibility of cerebellar granule neurons mature in early postnatal life, 3D genome architecture gradually remodels throughout life, establishing ultra-long-range intrachromosomal contacts and specific interchromosomal contacts that are rarely seen in neurons. These results reveal unexpected evolutionarily conserved molecular processes that underlie distinctive features of neural development and aging across the mammalian life span.
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Affiliation(s)
- Longzhi Tan
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | - Jenny Shi
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Siavash Moghadami
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305
| | - Bibudha Parasar
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
| | - Cydney P. Wright
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
- Department of Biology, Stanford University, Stanford, CA, 94305
| | - Yunji Seo
- Department of Neurobiology, Stanford University, Stanford, CA, 94305
| | - Kristen Vallejo
- Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Inma Cobos
- Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305
- Howard Hughes Medical Institute, Stanford, CA, 94305
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9
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Agredo A, Kasinski AL. Histone 4 lysine 20 tri-methylation: a key epigenetic regulator in chromatin structure and disease. Front Genet 2023; 14:1243395. [PMID: 37671044 PMCID: PMC10475950 DOI: 10.3389/fgene.2023.1243395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
Chromatin is a vital and dynamic structure that is carefully regulated to maintain proper cell homeostasis. A great deal of this regulation is dependent on histone proteins which have the ability to be dynamically modified on their tails via various post-translational modifications (PTMs). While multiple histone PTMs are studied and often work in concert to facilitate gene expression, here we focus on the tri-methylation of histone H4 on lysine 20 (H4K20me3) and its function in chromatin structure, cell cycle, DNA repair, and development. The recent studies evaluated in this review have shed light on how H4K20me3 is established and regulated by various interacting partners and how H4K20me3 and the proteins that interact with this PTM are involved in various diseases. Through analyzing the current literature on H4K20me3 function and regulation, we aim to summarize this knowledge and highlights gaps that remain in the field.
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Affiliation(s)
- Alejandra Agredo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Life Sciences Interdisciplinary Program (PULSe), Purdue University, West Lafayette, IN, United States
| | - Andrea L. Kasinski
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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