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Lim J, Park C, Kim M, Kim H, Kim J, Lee DS. Advances in single-cell omics and multiomics for high-resolution molecular profiling. Exp Mol Med 2024; 56:515-526. [PMID: 38443594 PMCID: PMC10984936 DOI: 10.1038/s12276-024-01186-2] [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: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell omics technologies have revolutionized molecular profiling by providing high-resolution insights into cellular heterogeneity and complexity. Traditional bulk omics approaches average signals from heterogeneous cell populations, thereby obscuring important cellular nuances. Single-cell omics studies enable the analysis of individual cells and reveal diverse cell types, dynamic cellular states, and rare cell populations. These techniques offer unprecedented resolution and sensitivity, enabling researchers to unravel the molecular landscape of individual cells. Furthermore, the integration of multimodal omics data within a single cell provides a comprehensive and holistic view of cellular processes. By combining multiple omics dimensions, multimodal omics approaches can facilitate the elucidation of complex cellular interactions, regulatory networks, and molecular mechanisms. This integrative approach enhances our understanding of cellular systems, from development to disease. This review provides an overview of the recent advances in single-cell and multimodal omics for high-resolution molecular profiling. We discuss the principles and methodologies for representatives of each omics method, highlighting the strengths and limitations of the different techniques. In addition, we present case studies demonstrating the applications of single-cell and multimodal omics in various fields, including developmental biology, neurobiology, cancer research, immunology, and precision medicine.
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Affiliation(s)
- Jongsu Lim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Chanho Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Minjae Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Hyukhee Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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Chen PB, Chen R, LaPierre N, Chen Z, Mefford J, Marcus E, Heffel MG, Soto DC, Ernst J, Luo C, Flint J. Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574060. [PMID: 38260483 PMCID: PMC10802323 DOI: 10.1101/2024.01.03.574060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes, Lsamp, Ptprd, Nptx2 and Sh3gl, have known roles in synapse function; the fifth gene, Psip1, is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA 4933413L06Rik with no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.
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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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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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Acharya SN, Nichols RV, Rylaarsdam LE, O’Connell BL, Braun TP, Adey AC. sciMET-cap: High-throughput single-cell methylation analysis with a reduced sequencing burden. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548718. [PMID: 37502923 PMCID: PMC10369954 DOI: 10.1101/2023.07.12.548718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome-wide nature of DNA methylation results in a high sequencing burden per cell. Here, we leverage target enrichment with sciMET to capture sufficient information per cell for cell type assignment using substantially fewer sequence reads (sciMET-cap). Sufficient off-target coverage further enables the production of near-complete methylomes for individual cell types. We characterize sciMET-cap on human PBMCs and brain (middle frontal gyrus).
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Affiliation(s)
- Sonia N. Acharya
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Ruth V. Nichols
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Lauren E. Rylaarsdam
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Brendan L. O’Connell
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Theodore P. Braun
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Hematology/Medical Oncology, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Andrew C. Adey
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
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