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Shi Z, Das S, Morabito S, Miyoshi E, Stocksdale J, Emerson N, Srinivasan SS, Shahin A, Rahimzadeh N, Cao Z, Silva J, Castaneda AA, Head E, Thompson L, Swarup V. Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611761. [PMID: 39282421 PMCID: PMC11398495 DOI: 10.1101/2024.09.06.611761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The study of neurodegenerative diseases, particularly tauopathies like Pick's disease (PiD) and Alzheimer's disease (AD), offers insights into the underlying regulatory mechanisms. By investigating epigenomic variations in these conditions, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched non-coding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine-mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database (http://swaruplab.bio.uci.edu/scROAD) to visualize predicted single-cell TF occupancy and regulatory networks.
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Affiliation(s)
- Zechuan Shi
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Samuel Morabito
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
| | - Emily Miyoshi
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Nora Emerson
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Shushrruth Sai Srinivasan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Arshi Shahin
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Negin Rahimzadeh
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
| | - Zhenkun Cao
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Justine Silva
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Andres Alonso Castaneda
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Elizabeth Head
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Leslie Thompson
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
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Chai C, Gibson J, Li P, Pampari A, Patel A, Kundaje A, Wang B. Flexible use of conserved motif vocabularies constrains genome access in cell type evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.03.611027. [PMID: 39282369 PMCID: PMC11398382 DOI: 10.1101/2024.09.03.611027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Cell types evolve into a hierarchy with related types grouped into families. How cell type diversification is constrained by the stable separation between families over vast evolutionary times remains unknown. Here, integrating single-nucleus multiomic sequencing and deep learning, we show that hundreds of sequence features (motifs) divide into distinct sets associated with accessible genomes of specific cell type families. This division is conserved across highly divergent, early-branching animals including flatworms and cnidarians. While specific interactions between motifs delineate cell type relationships within families, surprisingly, these interactions are not conserved between species. Consistently, while deep learning models trained on one species can predict accessibility of other species' sequences, their predictions frequently rely on distinct, but synonymous, motif combinations. We propose that long-term stability of cell type families is maintained through genome access specified by conserved motif sets, or 'vocabularies', whereas cell types diversify through flexible use of motifs within each set.
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Affiliation(s)
- Chew Chai
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Jesse Gibson
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, USA
| | - Aman Patel
- Department of Computer Science, Stanford University, Stanford, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
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Liu J, Castillo-Hair SM, Du LY, Wang Y, Carte AN, Colomer-Rosell M, Yin C, Seelig G, Schier AF. Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609971. [PMID: 39253514 PMCID: PMC11383055 DOI: 10.1101/2024.08.27.609971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
The interplay between transcription factors and chromatin accessibility regulates cell type diversification during vertebrate embryogenesis. To systematically decipher the gene regulatory logic guiding this process, we generated a single-cell multi-omics atlas of RNA expression and chromatin accessibility during early zebrafish embryogenesis. We developed a deep learning model to predict chromatin accessibility based on DNA sequence and found that a small number of transcription factors underlie cell-type-specific chromatin landscapes. While Nanog is well-established in promoting pluripotency, we discovered a new function in priming the enhancer accessibility of mesendodermal genes. In addition to the classical stepwise mode of differentiation, we describe instant differentiation, where pluripotent cells skip intermediate fate transitions and terminally differentiate. Reconstruction of gene regulatory interactions reveals that this process is driven by a shallow network in which maternally deposited regulators activate a small set of transcription factors that co-regulate hundreds of differentiation genes. Notably, misexpression of these transcription factors in pluripotent cells is sufficient to ectopically activate their targets. This study provides a rich resource for analyzing embryonic gene regulation and reveals the regulatory logic of instant differentiation.
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Affiliation(s)
- Jialin Liu
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
| | | | - Lucia Y Du
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
| | - Yiqun Wang
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UCSD, La Jolla, CA, 92037, USA
| | - Adam N Carte
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, 02115, USA
| | - Mariona Colomer-Rosell
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
| | - Christopher Yin
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Alexander F Schier
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA
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Sun K, Liu X, Lan X. A single-cell atlas of chromatin accessibility in mouse organogenesis. Nat Cell Biol 2024; 26:1200-1211. [PMID: 38977846 DOI: 10.1038/s41556-024-01435-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/29/2024] [Indexed: 07/10/2024]
Abstract
Organogenesis is a highly complex and precisely regulated process. Here we profiled the chromatin accessibility in >350,000 cells derived from 13 mouse embryos at four developmental stages from embryonic day (E) 10.5 to E13.5 by SPATAC-seq in a single experiment. The resulting atlas revealed the status of 830,873 candidate cis-regulatory elements in 43 major cell types. By integrating the chromatin accessibility atlas with the previous transcriptomic dataset, we characterized cis-regulatory sequences and transcription factors associated with cell fate commitment, such as Nr5a2 in the development of gastrointestinal tract, which was preliminarily supported by the in vivo experiment in zebrafish. Finally, we integrated this atlas with the previous single-cell chromatin accessibility dataset from 13 adult mouse tissues to delineate the developmental stage-specific gene regulatory programmes within and across different cell types and identify potential molecular switches throughout lineage development. This comprehensive dataset provides a foundation for exploring transcriptional regulation in organogenesis.
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Affiliation(s)
- Keyong Sun
- School of Medicine, Tsinghua University, Beijing, China
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xin Liu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine, Tsinghua University, Beijing, China.
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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Li J, Zhang X, Wang X, Wang Z, Li X, Zheng J, Li J, Xu G, Sun C, Yi G, Yang N. Single-nucleus transcriptional and chromatin accessible profiles reveal critical cell types and molecular architecture underlying chicken sex determination. J Adv Res 2024:S2090-1232(24)00185-1. [PMID: 38734369 DOI: 10.1016/j.jare.2024.05.007] [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: 09/09/2023] [Revised: 01/23/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
INTRODUCTION Understanding the sex determination mechanisms in birds has great significance for the biological sciences and production in the poultry industry. Sex determination in chickens is a complex process that involves fate decisions of supporting cells such as granulosa or Sertoli cells. However, a systematic understanding of the genetic regulation and cell commitment process underlying sex determination in chickens is still lacking. OBJECTIVES We aimed to dissect the molecular characteristics associated with sex determination in the gonads of chicken embryos. METHODS Single-nucleus RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) analysis were conducted on the gonads of female and male chickens at embryonic day 3.5 (E3.5), E4.5, and E5.5. RESULTS Here, we provided a time-course transcriptional and chromatin accessible profiling of gonads during chicken sex determination at single-cell resolution. We uncovered differences in cell composition and developmental trajectories between female and male gonads and found that the divergence of transcription and accessibility in gonadal cells first emerged at E5.5. Furthermore, we revealed key cell-type-specific transcription factors (TFs) and regulatory networks that drive lineage commitment. Sex determination signaling pathways, dominated by BMP signaling, are preferentially activated in males during gonadal development. Further pseudotime analysis of the supporting cells indicated that granulosa cells were regulated mainly by the TEAD gene family and that Sertoli cells were driven by the DMRT1 regulons. Cross-species analysis suggested high conservation of both cell types and cell-lineage-specific TFs across the six vertebrates. CONCLUSIONS Overall, our study will contribute to accelerating the development of sex manipulation technology in the poultry industry and the application of chickens as a unique model for studying cell fate decisions.
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Affiliation(s)
- Jianbo Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Xiuan Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Xiqiong Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jiangxia Zheng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Junying Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Guiyun Xu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China.
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China.
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6
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Ma K, Yin K, Li J, Ma L, Zhou Q, Lu X, Li B, Li J, Wei G, Zhang G. The Hypothalamic Epigenetic Landscape in Dietary Obesity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306379. [PMID: 38115764 PMCID: PMC10916675 DOI: 10.1002/advs.202306379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Indexed: 12/21/2023]
Abstract
The hypothalamus in the brain plays a pivotal role in controlling energy balance in vertebrates. Nutritional excess through high-fat diet (HFD) feeding can dysregulate hypothalamic signaling at multiple levels. Yet, it remains largely unknown in what magnitude HFD feeding may impact epigenetics in this brain region. Here, it is shown that HFD feeding can significantly alter hypothalamic epigenetic events, including posttranslational histone modifications, DNA methylation, and chromatin accessibility. The authors comprehensively analyze the chromatin immunoprecipitation-sequencing (ChIP-seq), methylated DNA immunoprecipitation-sequencing (MeDIP-seq), single nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq), and RNA-seq data of the hypothalamus of C57 BL/6 mice fed with a chow or HFD for 1 to 6 months. The chromatins are categorized into 6 states using the obtained ChIP-seq data for H3K4me3, H3K27ac, H3K9me3, H3K27me3, and H3K36me3. A 1-month HFD feeding dysregulates histone modifications and DNA methylation more pronouncedly than that of 3- or 6-month. Besides, HFD feeding differentially impacts chromatin accessibility in hypothalamic cells. Thus, the epigenetic landscape is dysregulated in the hypothalamus of dietary obesity mice.
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Affiliation(s)
- Kai Ma
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic DiseaseThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310003China
| | - Kaili Yin
- Key Laboratory of Environmental HealthMinistry of EducationDepartment of ToxicologySchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Institute for Brain ResearchCollaborative Innovation Center for Brain ScienceHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Jiong Li
- Key Laboratory of Environmental HealthMinistry of EducationDepartment of ToxicologySchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Institute for Brain ResearchCollaborative Innovation Center for Brain ScienceHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Li Ma
- CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences (CAS)CASShanghai200031China
| | - Qun Zhou
- Key Laboratory of Environmental HealthMinistry of EducationDepartment of ToxicologySchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Institute for Brain ResearchCollaborative Innovation Center for Brain ScienceHuazhong University of Science and TechnologyWuhanHubei430030China
| | - Xiyuan Lu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Bo Li
- Department of EndocrinologyXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Juxue Li
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Gang Wei
- CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences (CAS)CASShanghai200031China
| | - Guo Zhang
- Key Laboratory of Environmental HealthMinistry of EducationDepartment of ToxicologySchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei430030China
- Institute for Brain ResearchCollaborative Innovation Center for Brain ScienceHuazhong University of Science and TechnologyWuhanHubei430030China
- Department of Pathophysiology, School of Basic Medical SciencesHenan UniversityKaifengHenan475004China
- Institute of Metabolism and HealthHenan UniversityKaifengHenanChina
- Zhongzhou LaboratoryZhengzhouHenan450046China
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7
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Yang F, Zhao Z, Zhang D, Xiong Y, Dong X, Wang Y, Yang M, Pan T, Liu C, Liu K, Lin Y, Liu Y, Tu Q, Dang Y, Xia M, Mi D, Zhou W, Xu Z. Single-cell multi-omics analysis of lineage development and spatial organization in the human fetal cerebellum. Cell Discov 2024; 10:22. [PMID: 38409116 PMCID: PMC10897198 DOI: 10.1038/s41421-024-00656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Human cerebellum encompasses numerous neurons, exhibiting a distinct developmental paradigm from cerebrum. Here we conducted scRNA-seq, scATAC-seq and spatial transcriptomic analyses of fetal samples from gestational week (GW) 13 to 18 to explore the emergence of cellular diversity and developmental programs in the developing human cerebellum. We identified transitory granule cell progenitors that are conserved across species. Special patterns in both granule cells and Purkinje cells were dissected multidimensionally. Species-specific gene expression patterns of cerebellar lobes were characterized and we found that PARM1 exhibited inconsistent distribution in human and mouse granule cells. A novel cluster of potential neuroepithelium at the rhombic lip was identified. We also resolved various subtypes of Purkinje cells and unipolar brush cells and revealed gene regulatory networks controlling their diversification. Therefore, our study offers a valuable multi-omics landscape of human fetal cerebellum and advances our understanding of development and spatial organization of human cerebellum.
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Affiliation(s)
- Fuqiang Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziqi Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yu Xiong
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yuchen Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Min Yang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | | | - Chuanyu Liu
- BGI-Beijing, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Kaiyi Liu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yifeng Lin
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yongjie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qiang Tu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yashan Dang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China
| | - Mingyang Xia
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.
| | - Da Mi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Wenhao Zhou
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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8
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Observing mammalian cerebellum development through an evolutionary lens. Nature 2024:10.1038/d41586-023-03836-3. [PMID: 38200332 DOI: 10.1038/d41586-023-03836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
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9
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Qian FC, Zhou LW, Zhu YB, Li YY, Yu ZM, Feng CC, Fang QL, Zhao Y, Cai FH, Wang QY, Tang HF, Li CQ. scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species. Nucleic Acids Res 2024; 52:D285-D292. [PMID: 37897340 PMCID: PMC10767920 DOI: 10.1093/nar/gkad924] [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: 08/15/2023] [Revised: 09/14/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.
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Affiliation(s)
- Feng-Cui Qian
- The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Li-Wei Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan-Bing Zhu
- Beijing Clinical Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yan-Yu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Zheng-Min Yu
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
| | - Chen-Chen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Qiao-Li Fang
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
| | - Yu Zhao
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
| | - Fu-Hong Cai
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
| | - Qiu-Yu Wang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hui-Fang Tang
- The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Chun-Quan Li
- The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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10
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Sepp M, Leiss K, Murat F, Okonechnikov K, Joshi P, Leushkin E, Spänig L, Mbengue N, Schneider C, Schmidt J, Trost N, Schauer M, Khaitovich P, Lisgo S, Palkovits M, Giere P, Kutscher LM, Anders S, Cardoso-Moreira M, Sarropoulos I, Pfister SM, Kaessmann H. Cellular development and evolution of the mammalian cerebellum. Nature 2024; 625:788-796. [PMID: 38029793 PMCID: PMC10808058 DOI: 10.1038/s41586-023-06884-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
The expansion of the neocortex, a hallmark of mammalian evolution1,2, was accompanied by an increase in cerebellar neuron numbers3. However, little is known about the evolution of the cellular programmes underlying the development of the cerebellum in mammals. In this study we generated single-nucleus RNA-sequencing data for around 400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse and the marsupial opossum. We established a consensus classification of the cellular diversity in the developing mammalian cerebellum and validated it by spatial mapping in the fetal human cerebellum. Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Global transcriptome profiles, conserved cell-state markers and gene-expression trajectories across neuronal differentiation show that cerebellar cell-type-defining programmes have been overall preserved for at least 160 million years. However, we also identified many orthologous genes that gained or lost expression in cerebellar neural cell types in one of the species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level. In sum, our study unveils shared and lineage-specific gene-expression programmes governing the development of cerebellar cells and expands our understanding of mammalian brain evolution.
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Affiliation(s)
- Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Lisa Spänig
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Noe Mbengue
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Céline Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Nils Trost
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Maria Schauer
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Philipp Khaitovich
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Miklós Palkovits
- Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary
| | - Peter Giere
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- BioQuant, Heidelberg University, Heidelberg, Germany
| | | | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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11
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Jin L, Chen Y, Muzaffar S, Li C, Mier-Aguilar CA, Khan J, Kashyap MP, Liu S, Srivastava R, Deshane JS, Townes TM, Elewski BE, Elmets CA, Crossman DK, Raman C, Athar M. Epigenetic switch reshapes epithelial progenitor cell signatures and drives inflammatory pathogenesis in hidradenitis suppurativa. Proc Natl Acad Sci U S A 2023; 120:e2315096120. [PMID: 38011564 PMCID: PMC10710069 DOI: 10.1073/pnas.2315096120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Hidradenitis suppurativa (HS) is a complex inflammatory skin disease with undefined mechanistic underpinnings. Here, we investigated HS epithelial cells and demonstrated that HS basal progenitors modulate their lineage restriction and give rise to pathogenic keratinocyte clones, resulting in epidermal hyperproliferation and dysregulated inflammation in HS. When comparing to healthy epithelial stem/progenitor cells, in HS, we identified changes in gene signatures that revolve around the mitotic cell cycle, DNA damage response and repair, as well as cell-cell adhesion and chromatin remodeling. By reconstructing cell differentiation trajectory and CellChat modeling, we identified a keratinocyte population specific to HS. This population is marked by S100A7/8/9 and KRT6 family members, triggering IL1, IL10, and complement inflammatory cascades. These signals, along with HS-specific proinflammatory cytokines and chemokines, contribute to the recruitment of certain immune cells during the disease progression. Furthermore, we revealed a previously uncharacterized role of S100A8 in regulating the local chromatin environment of target loci in HS keratinocytes. Through the integration of genomic and epigenomic datasets, we identified genome-wide chromatin rewiring alongside the switch of transcription factors (TFs), which mediated HS transcriptional profiles. Importantly, we identified numerous clinically relevant inflammatory enhancers and their coordinated TFs in HS basal CD49fhigh cells. The disruption of the S100A enhancer using the CRISPR/Cas9-mediated approach or the pharmacological inhibition of the interferon regulatory transcription factor 3 (IRF3) efficiently reduced the production of HS-associated inflammatory regulators. Our study not only uncovers the plasticity of epidermal progenitor cells in HS but also elucidates the epigenetic mechanisms underlying HS pathogenesis.
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Affiliation(s)
- Lin Jin
- Center for Epigenomics and Translational Research in Inflammatory Skin Diseases, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Suhail Muzaffar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Chao Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Carlos A. Mier-Aguilar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Jasim Khan
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Mahendra P. Kashyap
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Shanrun Liu
- Institutional Research Core Program, Flow Cytometry and Singe Cell Core, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Ritesh Srivastava
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Tim M. Townes
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Boni E. Elewski
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Craig A. Elmets
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Chander Raman
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Mohammad Athar
- Center for Epigenomics and Translational Research in Inflammatory Skin Diseases, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
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12
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Zu S, Li YE, Wang K, Armand EJ, Mamde S, Amaral ML, Wang Y, Chu A, Xie Y, Miller M, Xu J, Wang Z, Zhang K, Jia B, Hou X, Lin L, Yang Q, Lee S, Li B, Kuan S, Liu H, Zhou J, Pinto-Duarte A, Lucero J, Osteen J, Nunn M, Smith KA, Tasic B, Yao Z, Zeng H, Wang Z, Shang J, Behrens MM, Ecker JR, Wang A, Preissl S, Ren B. Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature 2023; 624:378-389. [PMID: 38092917 PMCID: PMC10719105 DOI: 10.1038/s41586-023-06824-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are moderately conserved in the human brain. The mouse-specific cCREs-specifically, those identified from a subset of cortical excitatory neurons-are strongly enriched for transposable elements, suggesting a potential role for transposable elements in the emergence of new regulatory programs and neuronal diversity. Finally, we infer the gene regulatory networks in over 260 subclasses of mouse brain cells and develop deep-learning models to predict the activities of gene regulatory elements in different brain cell types from the DNA sequence alone. Our results provide a resource for the analysis of cell-type-specific gene regulation programs in both mouse and human brains.
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Affiliation(s)
- Songpeng Zu
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
- Department of Neurosurgery and Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Kangli Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sainath Mamde
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Maria Luisa Amaral
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Yuelai Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Andre Chu
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Jie Xu
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Kai Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Bojing Jia
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Qian Yang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Samantha Kuan
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Jacinta Lucero
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia Osteen
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Michael Nunn
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zihan Wang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jingbo Shang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | | | - Joseph R Ecker
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA.
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13
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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14
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Nishino T, Ranade SS, Pelonero A, van Soldt BJ, Ye L, Alexanian M, Koback F, Huang Y, Sadagopan N, Lam A, Zholudeva LV, Li F, Padmanabhan A, Thomas R, van Bemmel JG, Gifford CA, Costa MW, Srivastava D. Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1190-1203. [PMID: 39183978 PMCID: PMC11343316 DOI: 10.1038/s44161-023-00367-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/19/2023] [Indexed: 08/27/2024]
Abstract
Maternal diabetes mellitus is among the most frequent environmental contributors to congenital birth defects, including heart defects and craniofacial anomalies, yet the cell types affected and mechanisms of disruption are largely unknown. Using multi-modal single cell analyses, here we show that maternal diabetes affects the epigenomic landscape of specific subsets of cardiac and craniofacial progenitors during embryogenesis. A previously unrecognized cardiac progenitor subpopulation expressing the homeodomain-containing protein ALX3 showed prominent chromatin accessibility changes and acquired a more posterior identity. Similarly, a subpopulation of neural crest-derived cells in the second pharyngeal arch, which contributes to craniofacial structures, displayed abnormalities in the epigenetic landscape and axial patterning defects. Chromatin accessibility changes in both populations were associated with increased retinoic acid signaling, known to establish anterior-posterior identity. This work highlights how an environmental insult can have highly selective epigenomic consequences on discrete cell types leading to developmental patterning defects.
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Affiliation(s)
- Tomohiro Nishino
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Sanjeev S. Ranade
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Angelo Pelonero
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Benjamin J. van Soldt
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Lin Ye
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Michael Alexanian
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Frances Koback
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Nandhini Sadagopan
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Francisco; San Francisco, CA, USA
| | - Adrienne Lam
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Lyandysha V. Zholudeva
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Feiya Li
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Francisco; San Francisco, CA, USA
| | | | - Joke G. van Bemmel
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Casey A. Gifford
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Mauro W. Costa
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Deepak Srivastava
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
- Division of Cardiology, Department of Pediatrics, University of California, San Francisco; San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco; San Francisco, CA, USA
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15
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Zhong S, Wang M, Huang L, Chen Y, Ge Y, Zhang J, Shi Y, Dong H, Zhou X, Wang B, Lu T, Jing X, Lu Y, Zhang J, Wang X, Wu Q. Single-cell epigenomics and spatiotemporal transcriptomics reveal human cerebellar development. Nat Commun 2023; 14:7613. [PMID: 37993461 PMCID: PMC10665552 DOI: 10.1038/s41467-023-43568-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Human cerebellar development is orchestrated by molecular regulatory networks to achieve cytoarchitecture and coordinate motor and cognitive functions. Here, we combined single-cell transcriptomics, spatial transcriptomics and single cell chromatin accessibility states to systematically depict an integrative spatiotemporal landscape of human fetal cerebellar development. We revealed that combinations of transcription factors and cis-regulatory elements (CREs) play roles in governing progenitor differentiation and cell fate determination along trajectories in a hierarchical manner, providing a gene expression regulatory map of cell fate and spatial information for these cells. We also illustrated that granule cells located in different regions of the cerebellar cortex showed distinct molecular signatures regulated by different signals during development. Finally, we mapped single-nucleotide polymorphisms (SNPs) of disorders related to cerebellar dysfunction and discovered that several disorder-associated genes showed spatiotemporal and cell type-specific expression patterns only in humans, indicating the cellular basis and possible mechanisms of the pathogenesis of neuropsychiatric disorders.
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Affiliation(s)
- Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- Changping Laboratory, Beijing, 102206, China.
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Youqiao Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yuxin Ge
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Jiyao Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, 519031, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- Changping Laboratory, Beijing, 102206, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Jing
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junjing Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- Changping Laboratory, Beijing, 102206, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- Changping Laboratory, Beijing, 102206, China.
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16
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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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17
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Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, Zeng H, Ren B, Ecker JR, Mukamel EA. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. CELL GENOMICS 2023; 3:100342. [PMID: 37492103 PMCID: PMC10363915 DOI: 10.1016/j.xgen.2023.100342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 07/27/2023]
Abstract
Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our predictions by comparing them with chromatin conformation data and causal enhancer perturbation experiments. Our study shows how controlling for gene co-expression enables robust enhancer-gene linkage using single-cell sequencing data.
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Affiliation(s)
- Fangming Xie
- Department of Physics, University of California San Diego, La Jolla, CA 92037, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ethan J. Armand
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Jacinta D. Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Olivier B. Poirion
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
- The Jackson Laboratory, Farmington, CT, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Angeline C. Rivkin
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eran A. Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037, USA
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18
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Ramirez M, Robert R, Yeung J, Wu J, Abdalla-Wyse A, Goldowitz D. Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis. BMC Genomics 2023; 24:351. [PMID: 37365500 DOI: 10.1186/s12864-023-09368-4] [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: 10/04/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The development of the brain requires precise coordination of molecular processes across many cell-types. Underpinning these events are gene expression programs which require intricate regulation by non-coding regulatory sequences known as enhancers. In the context of the developing brain, transcribed enhancers (TEs) regulate temporally-specific expression of genes critical for cell identity and differentiation. Transcription of non-coding RNAs at active enhancer sequences, known as enhancer RNAs (eRNAs), is tightly associated with enhancer activity and has been correlated with target gene expression. TEs have been characterized in a multitude of developing tissues, however their regulatory role has yet to be described in the context of embryonic and early postnatal brain development. In this study, eRNA transcription was analyzed to identify TEs active during cerebellar development, as a proxy for the developing brain. Cap Analysis of Gene Expression followed by sequencing (CAGE-seq) was conducted at 12 stages throughout embryonic and early postnatal cerebellar development. RESULTS Temporal analysis of eRNA transcription identified clusters of TEs that peak in activity during either embryonic or postnatal times, highlighting their importance for temporally specific developmental events. Functional analysis of putative target genes identified molecular mechanisms under TE regulation revealing that TEs regulate genes involved in biological processes specific to neurons. We validate enhancer activity using in situ hybridization of eRNA expression from TEs predicted to regulate Nfib, a gene critical for cerebellar granule cell differentiation. CONCLUSIONS The results of this analysis provide a valuable dataset for the identification of cerebellar enhancers and provide insight into the molecular mechanisms critical for brain development under TE regulation. This dataset is shared with the community through an online resource ( https://goldowitzlab.shinyapps.io/trans-enh-app/ ).
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, 950 W 28th Ave, V6H 3V5, Vancouver, BC, Canada.
- University of British Columbia, V6T 1Z4, Vancouver, BC, Canada.
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19
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Lowenstein ED, Cui K, Hernandez-Miranda LR. Regulation of early cerebellar development. FEBS J 2023; 290:2786-2804. [PMID: 35262281 DOI: 10.1111/febs.16426] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022]
Abstract
The study of cerebellar development has been at the forefront of neuroscience since the pioneering work of Wilhelm His Sr., Santiago Ramón y Cajal and many others since the 19th century. They laid the foundation to identify the circuitry of the cerebellum, already revealing its stereotypic three-layered cortex and discerning several of its neuronal components. Their work was fundamental in the acceptance of the neuron doctrine, which acknowledges the key role of individual neurons in forming the basic units of the nervous system. Increasing evidence shows that the cerebellum performs a variety of homeostatic and higher order neuronal functions beyond the mere control of motor behaviour. Over the last three decades, many studies have revealed the molecular machinery that regulates distinct aspects of cerebellar development, from the establishment of a cerebellar anlage in the posterior brain to the identification of cerebellar neuron diversity at the single cell level. In this review, we focus on summarizing our current knowledge on early cerebellar development with a particular emphasis on the molecular determinants that secure neuron specification and contribute to the diversity of cerebellar neurons.
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Affiliation(s)
| | - Ke Cui
- Institut für Zell- and Neurobiologie, Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Luis Rodrigo Hernandez-Miranda
- Institut für Zell- and Neurobiologie, Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
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20
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Krup AL, Winchester SAB, Ranade SS, Agrawal A, Devine WP, Sinha T, Choudhary K, Dominguez MH, Thomas R, Black BL, Srivastava D, Bruneau BG. A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors. Development 2023; 150:dev201229. [PMID: 36994838 PMCID: PMC10259516 DOI: 10.1242/dev.201229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/21/2023] [Indexed: 03/31/2023]
Abstract
Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood owing, in part, to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single-cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently expressed mesodermal transcription factor, is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mislocalized, prompting us to investigate the scope of the role of Mesp1 in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and crucial cardiac transcription factors, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single-cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.
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Affiliation(s)
- Alexis Leigh Krup
- Biomedical Sciences Program, University of California, San Francisco, CA 94158, USA
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sarah A. B. Winchester
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sanjeev S. Ranade
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ayushi Agrawal
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - W. Patrick Devine
- Department of Pathology, University of California, San Francisco, CA 94158, USA
| | - Tanvi Sinha
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Krishna Choudhary
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Martin H. Dominguez
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
- Department of Medicine, Division of Cardiology, University of California, San Francisco, CA 94158, USA
- Cardiovascular Institute and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Reuben Thomas
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Deepak Srivastava
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA
- Roddenberry Center for Stem Cell Biology and Medicine, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Benoit G. Bruneau
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA
- Roddenberry Center for Stem Cell Biology and Medicine, Gladstone Institutes, San Francisco, CA 94158, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94158, USA
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21
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Behrens MM, Lein ES, Ecker JR, Ren B. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536119. [PMID: 37066152 PMCID: PMC10104177 DOI: 10.1101/2023.04.08.536119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Sequence divergence of cis- regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis -regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis -regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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22
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Tan L, Shi J, Moghadami S, Wright CP, Parasar B, Seo Y, Vallejo K, Cobos I, Duncan L, Chen R, Deisseroth K. Cerebellar Granule Cells Develop Non-neuronal 3D Genome Architecture over the Lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530020. [PMID: 36865235 PMCID: PMC9980173 DOI: 10.1101/2023.02.25.530020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The cerebellum contains most of the neurons in the human brain, and exhibits unique modes of development, malformation, and aging. For example, granule cells-the most abundant neuron type-develop unusually late and exhibit unique nuclear morphology. Here, by developing our high-resolution single-cell 3D genome assay Dip-C into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we were able to resolve the first 3D genome structures of single cerebellar cells, create life-spanning 3D genome atlases for both human and mouse, and jointly measure transcriptome and chromatin accessibility during development. We found that while the transcriptome and chromatin accessibility of human granule cells exhibit a characteristic maturation pattern within the first year of postnatal life, 3D genome architecture gradually remodels throughout life into a non-neuronal state with ultra-long-range intra-chromosomal contacts and specific inter-chromosomal contacts. This 3D genome remodeling is conserved in mice, and robust to heterozygous deletion of chromatin remodeling disease-associated genes (Chd8 or Arid1b). Together these results reveal unexpected and evolutionarily-conserved molecular processes underlying the unique development and aging of the mammalian cerebellum.
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Affiliation(s)
- Longzhi Tan
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Jenny Shi
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Bioengineering, Stanford University, Stanford, CA
- Department of Chemistry, Stanford University, Stanford, CA
| | - Siavash Moghadami
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Cydney P. Wright
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
| | - Bibudha Parasar
- Department of Neurobiology, Stanford University, Stanford, CA
| | - Yunji Seo
- Department of Neurobiology, Stanford University, Stanford, CA
| | | | - Inma Cobos
- Department of Pathology, Stanford University, Stanford, CA
| | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford, CA
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23
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Hong D, Lin H, Liu L, Shu M, Dai J, Lu F, Tong M, Huang J. Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis. Brief Bioinform 2023; 24:6868525. [PMID: 36464486 DOI: 10.1093/bib/bbac508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 12/09/2022] Open
Abstract
Many enhancers exist as clusters in the genome and control cell identity and disease genes; however, the underlying mechanism remains largely unknown. Here, we introduce an algorithm, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression profiles. The complexity of enhancer networks is assessed by two metrics: the number of enhancers and the frequency of predicted enhancer interactions (PEIs) based on chromatin co-accessibility. We apply eNet algorithm to a human blood dataset and find cell identity and disease genes tend to be regulated by complex enhancer networks. The network hub enhancers (enhancers with frequent PEIs) are the most functionally important. Compared with super-enhancers, enhancer networks show better performance in predicting cell identity and disease genes. eNet is robust and widely applicable in various human or mouse tissues datasets. Thus, we propose a model of enhancer networks containing three modes: Simple, Multiple and Complex, which are distinguished by their complexity in regulating gene expression. Taken together, our work provides an unsupervised approach to simultaneously identify key cell identity and disease genes and explore the underlying regulatory relationships among enhancers in single cells.
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Affiliation(s)
- Danni Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongli Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lifang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Muya Shu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
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24
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Xu F, Cong P, Lu Z, Shi L, Xiong L, Zhao G. Integration of ATAC-Seq and RNA-Seq identifies key genes and pathways involved in the neuroprotection of S-adenosylmethionine against perioperative neurocognitive disorder. Comput Struct Biotechnol J 2023; 21:1942-1954. [PMID: 36942104 PMCID: PMC10024148 DOI: 10.1016/j.csbj.2023.03.001] [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: 08/20/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023] Open
Abstract
The gene-regulatory landscape is highly dynamic in healthy and diseased brains. DNA methylation is a well-known epigenetic modification that regulates gene expression, and our previous study demonstrated that S-adenosylmethionine (SAM), a methylome modulator, was a neuroprotectant against perioperative neurocognitive disorder (PND). However, the underlying mechanism remains to be elucidated. Here, we integrated an assay for transposase-accessible chromatin by sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to identify the key genes and pathways involved in the neuroprotection of SAM against PND. Our RNA-seq data demonstrated that genes involved in biological processes such as Wnt signaling, inflammatory response, transcription and long-term potentiation likely mediate the neuroprotection of SAM. Our ATAC-seq data provided comprehensive maps of chromatin accessibility changes induced by laparotomy and laparotomy + SAM treatment, and functional annotation of the regions with high variations in chromatin accessibility highlighted the role of the Wnt signaling pathway in PND pathogenesis and SAM treatment. Further motif analysis identified key transcription factors (e.g., CTCF, TFDP1, TCFL5, KLF15, ZBTB14, TFAP2E) that may participate in the neuroprotection of SAM. In conclusion, the current study provides an epigenomic perspective to understand the pathogenesis of PND and its treatment by SAM.
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Affiliation(s)
- Feifei Xu
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Peilin Cong
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Translational Research Institute of Brain and Brain-Like Intelligence Affiliated to Tongji University School of Medicine, Shanghai Key Laboratory of Brain and Functional Modulation, Shanghai 200434, China
| | - Zhihong Lu
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Liwen Shi
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Lize Xiong
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Translational Research Institute of Brain and Brain-Like Intelligence Affiliated to Tongji University School of Medicine, Shanghai Key Laboratory of Brain and Functional Modulation, Shanghai 200434, China
- Corresponding author at: Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Translational Research Institute of Brain and Brain-Like Intelligence Affiliated to Tongji University School of Medicine, Shanghai Key Laboratory of Brain and Functional Modulation, Shanghai 200434, China.
| | - Guanghou Zhao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
- Corresponding author.
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25
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EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release. Cell Rep 2022; 41:111830. [PMID: 36543143 PMCID: PMC9879271 DOI: 10.1016/j.celrep.2022.111830] [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: 08/18/2022] [Revised: 10/06/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
EKLF/Klf1 is a zinc-finger transcription activator essential for erythroid lineage commitment and terminal differentiation. Using ChIP-seq, we investigate EKLF DNA binding and transcription activation mechanisms during mouse embryonic erythropoiesis. We utilize the Nan/+ mouse that expresses the EKLF-E339D (Nan) variant mutated in its conserved zinc-finger region and address the mechanism of hypomorphic and neomorphic changes in downstream gene expression. First, we show that Nan-EKLF limits normal EKLF binding to a subset of its sites. Second, we find that ectopic binding of Nan-EKLF occurs largely at enhancers and activates transcription through pioneering activity. Third, we find that for a subset of ectopic targets, gene activation is achieved in Nan/+ only by Nan-EKLF binding to distal enhancers, leading to RNA polymerase II pause-release. These results have general applicability to understanding how a DNA binding variant factor confers dominant disruptive effects on downstream gene expression even in the presence of its normal counterpart.
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26
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Shu M, Hong D, Lin H, Zhang J, Luo Z, Du Y, Sun Z, Yin M, Yin Y, Liu L, Bao S, Liu Z, Lu F, Huang J, Dai J. Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse. Dev Cell 2022; 57:2761-2775.e6. [PMID: 36495874 DOI: 10.1016/j.devcel.2022.11.011] [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: 01/20/2022] [Revised: 06/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022]
Abstract
Spinal cord development is precisely orchestrated by spatiotemporal gene regulatory programs. However, the underlying epigenetic mechanisms remain largely elusive. Here, we profiled single-cell chromatin accessibility landscapes in mouse neural tubes spanning embryonic days 9.5-13.5. We identified neuronal-cell-cluster-specific cis-regulatory elements in neural progenitors and neurons. Furthermore, we applied a novel computational method, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression data and identify the hub enhancers within enhancer networks. It was experimentally validated in vivo for Atoh1 that knockout of the hub enhancers, but not the non-hub enhancers, markedly decreased Atoh1 expression and reduced dp1/dI1 cells. Together, our work provides insights into the epigenetic regulation of spinal cord development and a proof-of-concept demonstration of enhancer networks as a general mechanism in transcriptional regulation.
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Affiliation(s)
- Muya Shu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Danni Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongli Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengnan Luo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Man Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyun Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lifang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiyong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China.
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
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27
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Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022; 31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [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: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.
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Affiliation(s)
- Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
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28
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Apsley EJ, Becker EBE. Purkinje Cell Patterning-Insights from Single-Cell Sequencing. Cells 2022; 11:2918. [PMID: 36139493 PMCID: PMC9497131 DOI: 10.3390/cells11182918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022] Open
Abstract
Despite their homogeneous appearance, Purkinje cells are remarkably diverse with respect to their molecular phenotypes, physiological properties, afferent and efferent connectivity, as well as their vulnerability to insults. Heterogeneity in Purkinje cells arises early in development, with molecularly distinct embryonic cell clusters present soon after Purkinje cell specification. Traditional methods have characterized cerebellar development and cell types, including Purkinje cell subtypes, based on knowledge of selected markers. However, recent single-cell RNA sequencing studies provide vastly increased resolution of the whole cerebellar transcriptome. Here we draw together the results of multiple single-cell transcriptomic studies in developing and adult cerebellum in both mouse and human. We describe how this detailed transcriptomic data has increased our understanding of the intricate development and function of Purkinje cells and provides first clues into features specific to human cerebellar development.
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Affiliation(s)
- Elizabeth J. Apsley
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Esther B. E. Becker
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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29
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Joyner AL, Bayin NS. Cerebellum lineage allocation, morphogenesis and repair: impact of interplay amongst cells. Development 2022; 149:dev185587. [PMID: 36172987 PMCID: PMC9641654 DOI: 10.1242/dev.185587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The cerebellum has a simple cytoarchitecture consisting of a folded cortex with three cell layers that surrounds a nuclear structure housing the output neurons. The excitatory neurons are generated from a unique progenitor zone, the rhombic lip, whereas the inhibitory neurons and astrocytes are generated from the ventricular zone. The growth phase of the cerebellum is driven by lineage-restricted progenitor populations derived from each zone. Research during the past decade has uncovered the importance of cell-to-cell communication between the lineages through largely unknown signaling mechanisms for regulating the scaling of cell numbers and cell plasticity during mouse development and following injury in the neonatal (P0-P14) cerebellum. This Review focuses on how the interplay between cell types is key to morphogenesis, production of robust neural circuits and replenishment of cells after injury, and ends with a discussion of the implications of the greater complexity of the human cerebellar progenitor zones for development and disease.
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Affiliation(s)
- Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - N. Sumru Bayin
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge CB2 1NQ, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
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30
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Hain D, Gallego-Flores T, Klinkmann M, Macias A, Ciirdaeva E, Arends A, Thum C, Tushev G, Kretschmer F, Tosches MA, Laurent G. Molecular diversity and evolution of neuron types in the amniote brain. Science 2022; 377:eabp8202. [PMID: 36048944 DOI: 10.1126/science.abp8202] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The existence of evolutionarily conserved regions in the vertebrate brain is well established. The rules and constraints underlying the evolution of neuron types, however, remain poorly understood. To compare neuron types across brain regions and species, we generated a cell type atlas of the brain of a bearded dragon and compared it with mouse datasets. Conserved classes of neurons could be identified from the expression of hundreds of genes, including homeodomain-type transcription factors and genes involved in connectivity. Within these classes, however, there are both conserved and divergent neuron types, precluding a simple categorization of the brain into ancestral and novel areas. In the thalamus, neuronal diversification correlates with the evolution of the cortex, suggesting that developmental origin and circuit allocation are drivers of neuronal identity and evolution.
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Affiliation(s)
- David Hain
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | - Tatiana Gallego-Flores
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Angeles Macias
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Elena Ciirdaeva
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Anja Arends
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Christina Thum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gilles Laurent
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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31
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Ramirez M, Badayeva Y, Yeung J, Wu J, Abdalla-Wyse A, Yang E, Trost B, Scherer SW, Goldowitz D. Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions. eLife 2022; 11:74207. [PMID: 35942939 PMCID: PMC9398453 DOI: 10.7554/elife.74207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
We have identified active enhancers in the mouse cerebellum at embryonic and postnatal stages which provides a view of novel enhancers active during cerebellar development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Furthermore, by comparing our data with relevant brain development ENCODE histone profiles and cerebellar single-cell datasets we have been able to generalize and expand on the presented analyses, respectively. We have made the results of our analyses available online in the Developing Mouse Cerebellum Enhancer Atlas (https://goldowitzlab.shinyapps.io/developing_mouse_cerebellum_enhancer_atlas/), where our dataset can be efficiently queried, curated and exported by the scientific community to facilitate future research efforts. Our study provides a valuable resource for studying the dynamics of gene expression regulation by enhancers in the developing cerebellum and delivers a rich dataset of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Yuliya Badayeva
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Erin Yang
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | -
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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32
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Histone Deacetylase 3 Inhibitor Alleviates Cerebellar Defects in Perinatal Hypothyroid Mice by Stimulating Histone Acetylation and Transcription at Thyroid Hormone-Responsive Gene Loci. Int J Mol Sci 2022; 23:ijms23147869. [PMID: 35887216 PMCID: PMC9319938 DOI: 10.3390/ijms23147869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 01/27/2023] Open
Abstract
Perinatal hypothyroidism impairs cerebellar organogenesis and results in motor coordination defects. The thyroid hormone receptor binds to corepressor complexes containing histone deacetylase (HDAC) 3 in the absence of ligands and acts as a transcriptional repressor. Although histone acetylation status is strongly correlated with transcriptional regulation, its role in cerebellar development remains largely unknown. We aimed to study whether the cerebellar developmental defects induced by perinatal hypothyroidism can be rescued by treatment with a specific HDAC3 inhibitor, RGFP966. Motor coordination was analyzed using three behavioral tests. The cerebella were subjected to RT-qPCR and chromatin immunoprecipitation assays for acetylated histone H3. The treatment with RGFP966 partially reversed the cerebellar morphological defects in perinatal hypothyroid mice. These findings were associated with the alleviation of motor coordination defects in these mice. In addition, the RGFP966 administration increased the mRNA levels of cerebellar thyroid hormone-responsive genes. These increases were accompanied by augmented histone acetylation status at these gene loci. These findings indicate that HDAC3 plays an important role in the cerebellar developmental defects induced by perinatal hypothyroidism. The HDAC3 inhibitor might serve as a novel therapeutic agent for hypothyroidism-induced cerebellar defects by acetylating histone tails and stimulating transcription at thyroid hormone-responsive gene loci.
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33
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Qu J, Yang F, Zhu T, Wang Y, Fang W, Ding Y, Zhao X, Qi X, Xie Q, Chen M, Xu Q, Xie Y, Sun Y, Chen D. A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys. Nat Commun 2022; 13:4069. [PMID: 35831300 PMCID: PMC9279386 DOI: 10.1038/s41467-022-31770-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
Non-human primates are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium of cell types across multiple organs in cynomolgus monkeys (Macaca fascicularis) using both single-cell chromatin accessibility and RNA sequencing data. The integrated cell map enables in-depth dissection and comparison of molecular dynamics, cell-type compositions and cellular heterogeneity across multiple tissues and organs. Using single-cell transcriptomic data, we infer pseudotime cell trajectories and cell-cell communications to uncover key molecular signatures underlying their cellular processes. Furthermore, we identify various cell-specific cis-regulatory elements and construct organ-specific gene regulatory networks at the single-cell level. Finally, we perform comparative analyses of single-cell landscapes among mouse, monkey and human. We show that cynomolgus monkey has strikingly higher degree of similarities in terms of immune-associated gene expression patterns and cellular communications to human than mouse. Taken together, our study provides a valuable resource for non-human primate cell biology. Non-human primates are attractive laboratory animal models that can accurately reflect some developmental and pathological features of humans. Here the authors chart a reference cell map of cynomolgus monkeys using both scATAC-seq and scRNA-seq data across multiple organs, providing insights into the molecular dynamics and cellular heterogeneity of this organism.
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Affiliation(s)
- Jiao Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Fa Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yingshuo Wang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Wen Fang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yan Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xianjia Qi
- Shanghai XuRan Biotechnology Co., Ltd., 1088 Zhongchun Road, 201109, Shanghai, China
| | - Qiangmin Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yicheng Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China.
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China.
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34
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Haldipur P, Millen KJ, Aldinger KA. Human Cerebellar Development and Transcriptomics: Implications for Neurodevelopmental Disorders. Annu Rev Neurosci 2022; 45:515-531. [PMID: 35440142 PMCID: PMC9271632 DOI: 10.1146/annurev-neuro-111020-091953] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Developmental abnormalities of the cerebellum are among the most recognized structural brain malformations in human prenatal imaging. Yet reliable information regarding their cause in humans is sparse, and few outcome studies are available to inform prognosis. We know very little about human cerebellar development, in stark contrast to the wealth of knowledge from decades of research on cerebellar developmental biology of model organisms, especially mice. Recent studies show that multiple aspects of human cerebellar development significantly differ from mice and even rhesus macaques, a nonhuman primate. These discoveries challenge many current mouse-centric models of normal human cerebellar development and models regarding the pathogenesis of several neurodevelopmental phenotypes affecting the cerebellum, including Dandy-Walker malformation and medulloblastoma. Since we cannot model what we do not know, additional normative and pathological human developmental data are essential, and new models are needed.
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Affiliation(s)
- Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA; .,Department of Pediatrics, Division of Medical Genetics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
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35
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Detecting signatures of selection on gene expression. Nat Ecol Evol 2022; 6:1035-1045. [PMID: 35551249 DOI: 10.1038/s41559-022-01761-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.
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Khouri-Farah N, Guo Q, Morgan K, Shin J, Li JYH. Integrated single-cell transcriptomic and epigenetic study of cell state transition and lineage commitment in embryonic mouse cerebellum. SCIENCE ADVANCES 2022; 8:eabl9156. [PMID: 35363520 PMCID: PMC10938588 DOI: 10.1126/sciadv.abl9156] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Recent studies using single-cell RNA-sequencing have revealed cellular heterogeneity in the developing mammalian cerebellum, yet the regulatory logic underlying this cellular diversity remains to be elucidated. Using integrated single-cell RNA and ATAC analyses, we resolved developmental trajectories of cerebellar progenitors and identified putative trans- and cis-elements that control cell state transition. We reverse engineered gene regulatory networks (GRNs) of each cerebellar cell type. Through in silico simulations and in vivo experiments, we validated the efficacy of GRN analyses and uncovered the molecular control of a posterior transitory zone (PTZ), a distinct progenitor zone residing immediately anterior to the morphologically defined rhombic lip (RL). We showed that perturbing cell fate specification in the PTZ and RL causes posterior cerebellar vermis hypoplasia, the most common cerebellar birth defect in humans. Our study provides a foundation for comprehensive studies of developmental programs of the mammalian cerebellum.
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Affiliation(s)
- Nagham Khouri-Farah
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Qiuxia Guo
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Kerry Morgan
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Jihye Shin
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - James Y. H. Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
- Institute for Systems Genomics, University of Connecticut, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
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Karthik S, Huang D, Delgado Y, Laing JJ, Peltekian L, Iverson GN, Grady F, Miller RL, McCann CM, Fritzsch B, Iskusnykh IY, Chizhikov VV, Geerling JC. Molecular ontology of the parabrachial nucleus. J Comp Neurol 2022; 530:1658-1699. [PMID: 35134251 PMCID: PMC9119955 DOI: 10.1002/cne.25307] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/07/2022]
Abstract
This article has been removed because of a technical problem in the rendering of the PDF. 11 February 2022.
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Affiliation(s)
| | - Dake Huang
- Department of NeurologyUniversity of IowaIowa CityIowaUSA
| | | | | | - Lila Peltekian
- Department of NeurologyUniversity of IowaIowa CityIowaUSA
| | | | - Fillan Grady
- Department of NeurologyUniversity of IowaIowa CityIowaUSA
| | - Rebecca L. Miller
- Department of Anatomy and NeurobiologyWashington University School of MedicineSaint LouisMissouriUSA
| | - Corey M. McCann
- Department of Anatomy and NeurobiologyWashington University School of MedicineSaint LouisMissouriUSA
| | - Bernd Fritzsch
- Iowa Neuroscience InstituteIowa CityIowaUSA
- Department of BiologyUniversity of IowaIowa CityIowaUSA
| | - Igor Y. Iskusnykh
- Department of Anatomy and NeurobiologyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Victor V. Chizhikov
- Department of Anatomy and NeurobiologyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Joel C. Geerling
- Department of NeurologyUniversity of IowaIowa CityIowaUSA
- Iowa Neuroscience InstituteIowa CityIowaUSA
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Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza DF, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, Blackshaw S. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina. Cell Rep 2021; 37:109994. [PMID: 34788628 PMCID: PMC8642835 DOI: 10.1016/j.celrep.2021.109994] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. This study inventories cis- and trans-acting factors that control retinal development and can guide cell-based therapies aimed at replacing retinal neurons lost to disease.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric D Thomas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Megan Gimmen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nguyet Le
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Siqi Chen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David F Espinoza
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ariel E Telger
- Department of Ophthalmology and Visual Sciences, Brotman Baty Institute, Seattle, WA 98195, USA
| | - Kurt Weir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Brian S Clark
- Department of Ophthalmology and Visual Sciences, Brotman Baty Institute, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute, Seattle, WA 98195, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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