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Ben-Simon Y, Hooper M, Narayan S, Daigle T, Dwivedi D, Way SW, Oster A, Stafford DA, Mich JK, Taormina MJ, Martinez RA, Opitz-Araya X, Roth JR, Allen S, Ayala A, Bakken TE, Barcelli T, Barta S, Bendrick J, Bertagnolli D, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, Chakka AB, Chakrabarty R, Chance RK, Chavan S, Departee M, Donadio N, Dotson N, Egdorf T, Gabitto M, Gary A, Gasperini M, Goldy J, Gore BB, Graybuck L, Greisman N, Haeseleer F, Halterman C, Helback O, Hockemeyer D, Huang C, Huff S, Hunker A, Johansen N, Juneau Z, Kalmbach B, Khem S, Kutsal R, Larsen R, Lee C, Lee AY, Leibly M, Lenz GH, Liang E, Lusk N, Malone J, Mollenkopf T, Morin E, Newman D, Ng L, Ngo K, Omstead V, Oyama A, Pham T, Pom CA, Potekhina L, Ransford S, Rette D, Rimorin C, Rocha D, Ruiz A, Sanchez RE, Sedeno-Cortes A, Sevigny JP, Shapovalova N, Shulga L, Sigler AR, Siverts LA, Somasundaram S, Stewart K, Tieu M, Trader C, van Velthoven CT, Walker M, Weed N, Wirthlin M, Wood T, Wynalda B, Yao Z, Zhou T, Ariza J, Dee N, Reding M, Ronellenfitch K, Mufti S, Sunkin SM, Smith KA, Esposito L, Waters J, Thyagarajan B, Yao S, Lein ES, Zeng H, Levi BP, Ngai J, Ting J, Tasic B. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597244. [PMID: 38915722 PMCID: PMC11195086 DOI: 10.1101/2024.06.10.597244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The mammalian cortex is comprised of cells with different morphological, physiological, and molecular properties that can be classified according to shared properties into cell types. Defining the contribution of each cell type to the computational and cognitive processes that are guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell type taxonomies from mice and humans to define marker genes and enhancers, and to build genetic tools for cortical cell types. Here, we present a large toolkit for selective targeting of cortical populations, including mouse transgenic lines and recombinant adeno-associated virus (AAV) vectors containing genomic enhancers. We report evaluation of fifteen new transgenic driver lines and over 680 different enhancer AAVs covering all major subclasses of cortical cells, with many achieving a high degree of specificity, comparable with existing transgenic lines. We find that the transgenic lines based on marker genes can provide exceptional specificity and completeness of cell type labeling, but frequently require generation of a triple-transgenic cross for best usability/specificity. On the other hand, enhancer AAVs are easy to screen and use, and can be easily modified to express diverse cargo, such as recombinases. However, their use depends on many factors, such as viral titer and route of administration. The tools reported here as well as the scaled process of tool creation provide an unprecedented resource that should enable diverse experimental strategies towards understanding mammalian cortex and brain function.
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Affiliation(s)
- Yoav Ben-Simon
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Marcus Hooper
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Sujatha Narayan
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Tanya Daigle
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | | | - Sharon W. Way
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Aaron Oster
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - John K. Mich
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Jada R. Roth
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Shona Allen
- University of California, Berkeley, Berkeley, CA 94720
| | - Angela Ayala
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Stuard Barta
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Sakshi Chavan
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Bryan B. Gore
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Noah Greisman
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | - Cindy Huang
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Sydney Huff
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Avery Hunker
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zoe Juneau
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shannon Khem
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Rana Kutsal
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Angus Y. Lee
- University of California, Berkeley, Berkeley, CA 94720
| | | | | | | | - Nicholas Lusk
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Elyse Morin
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Alana Oyama
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Shea Ransford
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dean Rette
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Dana Rocha
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | - Ana R. Sigler
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Kaiya Stewart
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Toren Wood
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Boaz P. Levi
- Allen Institute for Brain Science, Seattle, WA 98109
| | - John Ngai
- University of California, Berkeley, Berkeley, CA 94720
- Present affiliation: National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, WA 98109
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Trimbour R, Deutschmann IM, Cantini L. Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS. Bioinformatics 2024; 40:btae143. [PMID: 38460192 PMCID: PMC11065476 DOI: 10.1093/bioinformatics/btae143] [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: 08/28/2023] [Revised: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 03/11/2024] Open
Abstract
MOTIVATION The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation. RESULTS Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation. We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMuS in terms of transcription factor (TF) targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs. AVAILABILITY AND IMPLEMENTATION HuMMuS is available at https://github.com/cantinilab/HuMMuS.
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Affiliation(s)
- Remi Trimbour
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Ina Maria Deutschmann
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Laura Cantini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [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: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
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4
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Banks E, Gutekunst CA, Vargish GA, Eaton A, Pelkey KA, McBain CJ, Zheng JQ, Oláh VJ, Rowan MJM. An enhancer-AAV approach selectively targeting dentate granule cells of the mouse hippocampus. CELL REPORTS METHODS 2024; 4:100684. [PMID: 38211592 PMCID: PMC10831952 DOI: 10.1016/j.crmeth.2023.100684] [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: 05/18/2023] [Revised: 09/29/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024]
Abstract
The mammalian brain contains a diverse array of cell types, including dozens of neuronal subtypes with distinct anatomical and functional characteristics. The brain leverages these neuron-type specializations to perform diverse circuit operations and thus execute different behaviors properly. Through the use of Cre lines, access to specific neuron types has improved over past decades. Despite their extraordinary utility, development and cross-breeding of Cre lines is time consuming and expensive, presenting a significant barrier to entry for investigators. Furthermore, cell-based therapeutics developed in Cre mice are not clinically translatable. Recently, several adeno-associated virus (AAV) vectors utilizing neuron-type-specific regulatory transcriptional sequences (enhancer-AAVs) were developed that overcome these limitations. Using a publicly available RNA sequencing (RNA-seq) dataset, we evaluated the potential of several candidate enhancers for neuron-type-specific targeting in the hippocampus. Here, we demonstrate that a previously identified enhancer-AAV selectively targets dentate granule cells over other excitatory neuron types in the hippocampus of wild-type adult mice.
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Affiliation(s)
- Emmie Banks
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; GDBBS Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Claire-Anne Gutekunst
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Geoffrey A Vargish
- Section on Cellular and Synaptic Physiology, NICHD - Eunice Kennedy Shriver National Institute of Child Health, Bethesda, MD, USA
| | - Anna Eaton
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30322, USA; Human Development, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kenneth A Pelkey
- Section on Cellular and Synaptic Physiology, NICHD - Eunice Kennedy Shriver National Institute of Child Health, Bethesda, MD, USA
| | - Chris J McBain
- Section on Cellular and Synaptic Physiology, NICHD - Eunice Kennedy Shriver National Institute of Child Health, Bethesda, MD, USA
| | - James Q Zheng
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Viktor Janos Oláh
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Matthew J M Rowan
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA.
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5
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Zhu K, Bendl J, Rahman S, Vicari JM, Coleman C, Clarence T, Latouche O, Tsankova NM, Li A, Brennand KJ, Lee D, Yuan GC, Fullard JF, Roussos P. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. SCIENCE ADVANCES 2023; 9:eadg3754. [PMID: 37824614 PMCID: PMC10569714 DOI: 10.1126/sciadv.adg3754] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/01/2023] [Indexed: 10/14/2023]
Abstract
The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that is mediated, in part, by the spatiotemporal activity of cis-regulatory elements (CREs). We simultaneously profiled gene expression and chromatin accessibility in 45,549 cortical nuclei across six broad developmental time points from fetus to adult. We identified cell type-specific domains in which chromatin accessibility is highly correlated with gene expression. Differentiation pseudotime trajectory analysis indicates that chromatin accessibility at CREs precedes transcription and that dynamic changes in chromatin structure play a critical role in neuronal lineage commitment. In addition, we mapped cell type-specific and temporally specific genetic loci implicated in neuropsychiatric traits, including schizophrenia and bipolar disorder. Together, our results describe the complex regulation of cell composition at critical stages in lineage determination and shed light on the impact of spatiotemporal alterations in gene expression on neuropsychiatric disease.
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Affiliation(s)
- Kaiyi Zhu
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James M. Vicari
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Coleman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tereza Clarence
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ovaun Latouche
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Nadejda M. Tsankova
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aiqun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J. Brennand
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F. Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
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6
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Leyva-Díaz E. CUT homeobox genes: transcriptional regulation of neuronal specification and beyond. Front Cell Neurosci 2023; 17:1233830. [PMID: 37744879 PMCID: PMC10515288 DOI: 10.3389/fncel.2023.1233830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
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7
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Banks E, Gutekunst CA, Vargish GA, Eaton A, Pelkey KA, McBain CJ, Zheng JQ, Oláh VJ, Rowan MJ. A novel enhancer-AAV approach selectively targeting dentate granule cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527045. [PMID: 37214904 PMCID: PMC10197561 DOI: 10.1101/2023.02.03.527045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The mammalian brain contains the most diverse array of cell types of any organ, including dozens of neuronal subtypes with distinct anatomical and functional characteristics. The brain leverages these neuron-type-specializations to perform diverse circuit operations and thus execute different behaviors properly. Through the use of Cre lines, access to specific neuron types has steadily improved over past decades. Despite their extraordinary utility, development and cross-breeding of Cre lines is time-consuming and expensive, presenting a significant barrier to entry for many investigators. Furthermore, cell-based therapeutics developed in Cre mice are not clinically translatable. Recently, several AAV vectors utilizing neuron-type-specific regulatory transcriptional sequences (enhancer-AAVs) were developed which overcome these limitations. Using a publicly available RNAseq dataset, we evaluated the potential of several candidate enhancers for neuron-type-specific targeting in the hippocampus. Here we identified a promising enhancer-AAV for targeting dentate granule cells and validated its selectivity in wild-type adult mice.
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8
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Chan YC, Kienle E, Oti M, Di Liddo A, Mendez-Lago M, Aschauer DF, Peter M, Pagani M, Arnold C, Vonderheit A, Schön C, Kreuz S, Stark A, Rumpel S. An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo. Sci Rep 2023; 13:6745. [PMID: 37185990 PMCID: PMC10130037 DOI: 10.1038/s41598-023-33448-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3 Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease.
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Affiliation(s)
- Ya-Chien Chan
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Eike Kienle
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Oti
- Institute of Molecular Biology GmbH (IMB), Mainz, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | | | | | - Dominik F Aschauer
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manuel Peter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Cosmas Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Christian Schön
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | - Sebastian Kreuz
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany.
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9
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
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10
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Arzate-Mejia RG, Mansuy IM. Remembering through the genome: the role of chromatin states in brain functions and diseases. Transl Psychiatry 2023; 13:122. [PMID: 37041131 PMCID: PMC10090084 DOI: 10.1038/s41398-023-02415-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Chromatin is the physical substrate of the genome that carries the DNA sequence and ensures its proper functions and regulation in the cell nucleus. While a lot is known about the dynamics of chromatin during programmed cellular processes such as development, the role of chromatin in experience-dependent functions remains not well defined. Accumulating evidence suggests that in brain cells, environmental stimuli can trigger long-lasting changes in chromatin structure and tri-dimensional (3D) organization that can influence future transcriptional programs. This review describes recent findings suggesting that chromatin plays an important role in cellular memory, particularly in the maintenance of traces of prior activity in the brain. Inspired by findings in immune and epithelial cells, we discuss the underlying mechanisms and the implications for experience-dependent transcriptional regulation in health and disease. We conclude by presenting a holistic view of chromatin as potential molecular substrate for the integration and assimilation of environmental information that may constitute a conceptual basis for future research.
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Affiliation(s)
- Rodrigo G Arzate-Mejia
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty, University of Zurich, Zurich, Switzerland
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology Zürich (ETHZ), Zurich, Switzerland
- Center for Neuroscience Zürich, University Zürich and ETHZ, Zürich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty, University of Zurich, Zurich, Switzerland.
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology Zürich (ETHZ), Zurich, Switzerland.
- Center for Neuroscience Zürich, University Zürich and ETHZ, Zürich, Switzerland.
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11
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Lu T, Ang CE, Zhuang X. Spatially resolved epigenomic profiling of single cells in complex tissues. Cell 2022; 185:4448-4464.e17. [PMID: 36272405 PMCID: PMC9691621 DOI: 10.1016/j.cell.2022.09.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 08/22/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
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Affiliation(s)
- Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Cheen Euong Ang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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12
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Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nat Neurosci 2022; 25:1049-1058. [PMID: 35915179 PMCID: PMC9343253 DOI: 10.1038/s41593-022-01123-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022]
Abstract
Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
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13
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Zhang XL, Spencer WC, Tabuchi N, Kitt MM, Deneris ES. Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity. eLife 2022; 11:e75970. [PMID: 35471146 PMCID: PMC9098219 DOI: 10.7554/elife.75970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/12/2022] [Indexed: 12/02/2022] Open
Abstract
Assembly of transcriptomes encoding unique neuronal identities requires selective accessibility of transcription factors to cis-regulatory sequences in nucleosome-embedded postmitotic chromatin. Yet, the mechanisms controlling postmitotic neuronal chromatin accessibility are poorly understood. Here, we show that unique distal enhancers define the Pet1 neuron lineage that generates serotonin (5-HT) neurons in mice. Heterogeneous single-cell chromatin landscapes are established early in postmitotic Pet1 neurons and reveal the putative regulatory programs driving Pet1 neuron subtype identities. Distal enhancer accessibility is highly dynamic as Pet1 neurons mature, suggesting the existence of regulatory factors that reorganize postmitotic neuronal chromatin. We find that Pet1 and Lmx1b control chromatin accessibility to select Pet1-lineage-specific enhancers for 5-HT neurotransmission. Additionally, these factors are required to maintain chromatin accessibility during early maturation suggesting that postmitotic neuronal open chromatin is unstable and requires continuous regulatory input. Together, our findings reveal postmitotic transcription factors that reorganize accessible chromatin for neuron specialization.
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Affiliation(s)
- Xinrui L Zhang
- Department of Neurosciences, Case Western Reserve UniversityClevelandUnited States
| | - William C Spencer
- Department of Neurosciences, Case Western Reserve UniversityClevelandUnited States
| | - Nobuko Tabuchi
- Department of Neurosciences, Case Western Reserve UniversityClevelandUnited States
| | - Meagan M Kitt
- Department of Neurosciences, Case Western Reserve UniversityClevelandUnited States
| | - Evan S Deneris
- Department of Neurosciences, Case Western Reserve UniversityClevelandUnited States
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14
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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15
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Mauduit D, Taskiran II, Minnoye L, de Waegeneer M, Christiaens V, Hulselmans G, Demeulemeester J, Wouters J, Aerts S. Analysis of long and short enhancers in melanoma cell states. eLife 2021; 10:e71735. [PMID: 34874265 PMCID: PMC8691835 DOI: 10.7554/elife.71735] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
Understanding how enhancers drive cell-type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assays (MPRAs) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state-specific H3K27 acetylation close to differentially expressed genes. An in-depth evaluation of those regions was then pursued by investigating the activity of overlapping ATAC-seq peaks along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions, and we were able to precisely locate the active enhancers within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity. In contrast, SOX10 and MITF both influence MEL enhancer function with SOX10 being required to achieve high levels of activity. Overall, our MPRAs shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity across melanoma cell states.
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Affiliation(s)
- David Mauduit
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Ibrahim Ihsan Taskiran
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Liesbeth Minnoye
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Maxime de Waegeneer
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Valerie Christiaens
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Gert Hulselmans
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Jonas Demeulemeester
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
- Cancer Genomics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Jasper Wouters
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
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16
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Zhang H, Lu T, Liu S, Yang J, Sun G, Cheng T, Xu J, Chen F, Yen K. Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification. NAR Genom Bioinform 2021; 3:lqab094. [PMID: 34729473 PMCID: PMC8557372 DOI: 10.1093/nargab/lqab094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Tn5 transposase, which can efficiently tagment the genome, has been widely adopted as a molecular tool in next-generation sequencing, from short-read sequencing to more complex methods such as assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we systematically map Tn5 insertion characteristics across several model organisms, finding critical parameters that affect its insertion. On naked genomic DNA, we found that Tn5 insertion is not uniformly distributed or random. To uncover drivers of these biases, we used a machine learning framework, which revealed that DNA shape cooperatively works with DNA motif to affect Tn5 insertion preference. These intrinsic insertion preferences can be modeled using nucleotide dependence information from DNA sequences, and we developed a computational pipeline to correct for these biases in ATAC-seq data. Using our pipeline, we show that bias correction improves the overall performance of ATAC-seq peak detection, recovering many potential false-negative peaks. Furthermore, we found that these peaks are bound by transcription factors, underscoring the biological relevance of capturing this additional information. These findings highlight the benefits of an improved understanding and precise correction of Tn5 insertion preference.
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Affiliation(s)
- Houyu Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shan Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jianyu Yang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jin Xu
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Fangyao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Kuangyu Yen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
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17
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Loker R, Sanner JE, Mann RS. Cell-type-specific Hox regulatory strategies orchestrate tissue identity. Curr Biol 2021; 31:4246-4255.e4. [PMID: 34358443 PMCID: PMC8511240 DOI: 10.1016/j.cub.2021.07.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 07/13/2021] [Indexed: 01/25/2023]
Abstract
Hox proteins are homeodomain transcription factors that diversify serially homologous segments along the animal body axis, as revealed by the classic bithorax phenotype of Drosophila melanogaster, in which mutations in Ultrabithorax (Ubx) transform the third thoracic segment into the likeness of the second thoracic segment. To specify segment identity, we show that Ubx both increases and decreases chromatin accessibility, coinciding with its dual role as both an activator and repressor of transcription. However, the choice of transcriptional activity executed by Ubx is spatially regulated and depends on the availability of cofactors, with Ubx acting as a repressor in some populations and as an activator in others. Ubx-mediated changes to chromatin accessibility positively and negatively affect the binding of Scalloped (Sd), a transcription factor that is required for appendage development in both segments. These findings illustrate how a single Hox protein can modify complex gene regulatory networks to transform the identity of an entire tissue.
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Affiliation(s)
- Ryan Loker
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Jordyn E Sanner
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Department of Neuroscience, Columbia University Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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18
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Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development. Nat Commun 2021; 12:5685. [PMID: 34584102 PMCID: PMC8479071 DOI: 10.1038/s41467-021-25935-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
Chromatin remodeling and genomic alterations impact spatio-temporal regulation of gene expression, which is central to embryonic development. The analysis of mouse and chicken limb development provides important insights into the morphoregulatory mechanisms, however little is known about the regulatory differences underlying their morphological divergence. Here, we identify the underlying shared and species-specific epigenomic and genomic variations. In mouse forelimb buds, we observe striking synchrony between the temporal dynamics of chromatin accessibility and gene expression, while their divergence in chicken wing buds uncovers species-specific regulatory heterochrony. In silico mapping of transcription factor binding sites and computational footprinting establishes the developmental time-restricted transcription factor-DNA interactions. Finally, the construction of target gene networks for HAND2 and GLI3 transcriptional regulators reveals both conserved and species-specific interactions. Our analysis reveals the impact of genome evolution on the regulatory interactions orchestrating vertebrate limb bud morphogenesis and provides a molecular framework for comparative Evo-Devo studies. The vertebrate limb bud is a paradigm to uncover the fundamental mechanisms that govern embryogenesis and evolutionary diversification. Here the authors compare mouse and chicken limb bud development to study the impact of genome evolution on conserved and divergent gene regulatory interactions.
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19
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Multi-omics in mesial temporal lobe epilepsy with hippocampal sclerosis: Clues into the underlying mechanisms leading to disease. Seizure 2021; 90:34-50. [DOI: 10.1016/j.seizure.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
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20
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Mielnik CA, Binko MA, Chen Y, Funk AJ, Johansson EM, Intson K, Sivananthan N, Islam R, Milenkovic M, Horsfall W, Ross RA, Groc L, Salahpour A, McCullumsmith RE, Tripathy S, Lambe EK, Ramsey AJ. Consequences of NMDA receptor deficiency can be rescued in the adult brain. Mol Psychiatry 2021; 26:2929-2942. [PMID: 32807843 PMCID: PMC8505246 DOI: 10.1038/s41380-020-00859-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 07/11/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022]
Abstract
N-methyl-D-aspartate receptors (NMDARs) are required to shape activity-dependent connections in the developing and adult brain. Impaired NMDAR signalling through genetic or environmental insults causes a constellation of neurodevelopmental disorders that manifest as intellectual disability, epilepsy, autism, or schizophrenia. It is not clear whether the developmental impacts of NMDAR dysfunction can be overcome by interventions in adulthood. This question is paramount for neurodevelopmental disorders arising from mutations that occur in the GRIN genes, which encode NMDAR subunits, and the broader set of mutations that disrupt NMDAR function. We developed a mouse model where a congenital loss-of-function allele of Grin1 can be restored to wild type by gene editing with Cre recombinase. Rescue of NMDARs in adult mice yields surprisingly robust improvements in cognitive functions, including those that are refractory to treatment with current medications. These results suggest that neurodevelopmental disorders arising from NMDAR deficiency can be effectively treated in adults.
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Affiliation(s)
- Catharine A Mielnik
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mary A Binko
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Yuxiao Chen
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1L8, Canada
| | - Adam J Funk
- Department of Neurosciences, University of Toledo, Toledo, OH, 43614, USA
| | - Emily M Johansson
- Interdisciplinary Institute for NeuroScience (IINS) CNRS, Université Bordeaux Segalen, 33000, Bordeaux, France
| | - Katheron Intson
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Nirun Sivananthan
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Rehnuma Islam
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marija Milenkovic
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Wendy Horsfall
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ruth A Ross
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Laurent Groc
- Interdisciplinary Institute for NeuroScience (IINS) CNRS, Université Bordeaux Segalen, 33000, Bordeaux, France
| | - Ali Salahpour
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | - Shreejoy Tripathy
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1L8, Canada
| | - Evelyn K Lambe
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of OBGYN, University of Toronto, Toronto, ON, M5G 1E2, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1L8, Canada
| | - Amy J Ramsey
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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21
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Egervari G. Chromatin accessibility in neuropsychiatric disorders. Neurobiol Learn Mem 2021; 181:107438. [PMID: 33845131 DOI: 10.1016/j.nlm.2021.107438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Epigenetic mechanisms have recently emerged as critical regulators of brain function in health and disease. By controlling the accessibility and the expression of specific genes, these pathways can mediate transient and long-lasting changes in neuronal function in both physiological and pathological contexts. Due to the extreme complexity of the epigenetic regulatory landscape, emerging methods that directly assay chromatin accessibility are of particular interest. Here, I review recent insights gained on open and closed chromatin states in the brain, with emphasis on neuropsychiatric disorders. These advances generated an invaluable wealth of information that can help us better understand gene regulation in the brain and its impairments that contribute to the development of disease.
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Affiliation(s)
- Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.
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22
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Enhancer viruses for combinatorial cell-subclass-specific labeling. Neuron 2021; 109:1449-1464.e13. [PMID: 33789083 DOI: 10.1016/j.neuron.2021.03.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022]
Abstract
Rapid cell type identification by new genomic single-cell analysis methods has not been met with efficient experimental access to these cell types. To facilitate access to specific neural populations in mouse cortex, we collected chromatin accessibility data from individual cells and identified enhancers specific for cell subclasses and types. When cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, these enhancers drive transgene expression in specific cortical cell subclasses. We extensively characterized several enhancer AAVs to show that they label different projection neuron subclasses as well as a homologous neuron subclass in human cortical slices. We also show how coupling enhancer viruses expressing recombinases to a newly generated transgenic mouse, Ai213, enables strong labeling of three different neuronal classes/subclasses in the brain of a single transgenic animal. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.
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23
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Mich JK, Graybuck LT, Hess EE, Mahoney JT, Kojima Y, Ding Y, Somasundaram S, Miller JA, Kalmbach BE, Radaelli C, Gore BB, Weed N, Omstead V, Bishaw Y, Shapovalova NV, Martinez RA, Fong O, Yao S, Mortrud M, Chong P, Loftus L, Bertagnolli D, Goldy J, Casper T, Dee N, Opitz-Araya X, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Sunkin SM, Gradinaru V, Horwitz GD, Zeng H, Tasic B, Lein ES, Ting JT, Levi BP. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. Cell Rep 2021; 34:108754. [PMID: 33789096 PMCID: PMC8163032 DOI: 10.1016/j.celrep.2021.108754] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/07/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Viral genetic tools that target specific brain cell types could transform basic neuroscience and targeted gene therapy. Here, we use comparative open chromatin analysis to identify thousands of human-neocortical-subclass-specific putative enhancers from across the genome to control gene expression in adeno-associated virus (AAV) vectors. The cellular specificity of reporter expression from enhancer-AAVs is established by molecular profiling after systemic AAV delivery in mouse. Over 30% of enhancer-AAVs produce specific expression in the targeted subclass, including both excitatory and inhibitory subclasses. We present a collection of Parvalbumin (PVALB) enhancer-AAVs that show highly enriched expression not only in cortical PVALB cells but also in some subcortical PVALB populations. Five vectors maintain PVALB-enriched expression in primate neocortex. These results demonstrate how genome-wide open chromatin data mining and cross-species AAV validation can be used to create the next generation of non-species-restricted viral genetic tools.
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Affiliation(s)
- John K Mich
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | - Erik E Hess
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Yoshiko Kojima
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Yi Ding
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | - Bryan B Gore
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Luke Loftus
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ali Cetin
- Department of Biology and Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Ryder P Gwinn
- Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA, USA
| | | | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gregory D Horwitz
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA; Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA; Washington National Primate Research Center, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA.
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24
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Rocks D, Jaric I, Tesfa L, Greally JM, Suzuki M, Kundakovic M. Cell type-specific chromatin accessibility analysis in the mouse and human brain. Epigenetics 2021; 17:202-219. [PMID: 33775205 PMCID: PMC8865312 DOI: 10.1080/15592294.2021.1896983] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using ATAC-seq include a small amount of material needed, fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. With increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs. Here we tested three protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescence-activated nuclei sorting (FANS) and ATAC-seq. Our study shows that the cryopreservation method impacts the number of open chromatin regions identified from frozen brain tissue using ATAC-seq. However, we show that all protocols generate consistent and robust data and enable the identification of functional regulatory elements in neuronal cells. Our study implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. We also reveal additional challenges of doing chromatin analysis on post-mortem human brain tissue. Overall, ATAC-seq coupled with FANS is a powerful method to capture cell-type-specific chromatin accessibility information in mouse and human brain. Our study provides alternative brain preservation methods that generate high-quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in the brain.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Ivana Jaric
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Lydia Tesfa
- Flow Cytometry Core Facility, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
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25
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Thornton CA, Mulqueen RM, Torkenczy KA, Nishida A, Lowenstein EG, Fields AJ, Steemers FJ, Zhang W, McConnell HL, Woltjer RL, Mishra A, Wright KM, Adey AC. Spatially mapped single-cell chromatin accessibility. Nat Commun 2021; 12:1274. [PMID: 33627658 PMCID: PMC7904839 DOI: 10.1038/s41467-021-21515-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/28/2021] [Indexed: 12/27/2022] Open
Abstract
High-throughput single-cell epigenomic assays can resolve cell type heterogeneity in complex tissues, however, spatial orientation is lost. Here, we present single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, or sciMAP-ATAC, as a method for highly scalable, spatially resolved, single-cell profiling of chromatin states. sciMAP-ATAC produces data of equivalent quality to non-spatial sci-ATAC and retains the positional information of each cell within a 214 micron cubic region, with up to hundreds of tracked positions in a single experiment. We apply sciMAP-ATAC to assess cortical lamination in the adult mouse primary somatosensory cortex and in the human primary visual cortex, where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin accessibility single-cell datasets. Finally, we characterize the spatially progressive nature of cerebral ischemic infarction in the mouse brain using a model of transient middle cerebral artery occlusion. Spatial orientation of cells in an interconnected network is lost in high-throughput single-cell epigenomic assays. Here the authors present sciMAP-ATAC to produce spatially resolved single-cell ATAC-seq data.
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Affiliation(s)
- Casey A Thornton
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Ryan M Mulqueen
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Kristof A Torkenczy
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Andrew Nishida
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Eve G Lowenstein
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Andrew J Fields
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | | | - Wenri Zhang
- Anesthesiology and Peri-Operative Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Heather L McConnell
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health & Science University, Portland, OR, USA
| | - Randy L Woltjer
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Anusha Mishra
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health & Science University, Portland, OR, USA.,Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Kevin M Wright
- The Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Andrew C Adey
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA. .,Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA. .,CEDAR, Oregon Health & Science University, Portland, OR, USA. .,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
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26
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Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay. Genome Res 2020; 30:1468-1480. [PMID: 32973041 PMCID: PMC7605270 DOI: 10.1101/gr.263228.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
A key mechanism in cellular regulation is the ability of the transcriptional machinery to physically access DNA. Transcription factors interact with DNA to alter the accessibility of chromatin, which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native genome because every genomic site is distinct in multiple ways. Here we introduce the multiplexed integrated accessibility assay (MIAA), an assay that measures chromatin accessibility of synthetic oligonucleotide sequence libraries integrated into a controlled genomic context with low native accessibility. We apply MIAA to measure the effects of sequence motifs on cell type-specific accessibility between mouse embryonic stem cells and embryonic stem cell-derived definitive endoderm cells, screening 7905 distinct DNA sequences. MIAA recapitulates differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions, identifying E-box motifs common to epithelial-mesenchymal transition driver transcription factors in stem cell-specific accessible regions that become repressed in endoderm. We show that a single binding motif for a key regulatory transcription factor is sufficient to open chromatin, and classify sets of stem cell-specific, endoderm-specific, and shared accessibility-modifying transcription factor motifs. We also show that overexpression of two definitive endoderm transcription factors, T and Foxa2, results in changes to accessibility in DNA sequences containing their respective DNA-binding motifs and identify preferential motif arrangements that influence accessibility.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Budhaditya Banerjee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Hubrecht Institute, 3584 CT Utrecht, Netherlands
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27
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Laukoter S, Pauler FM, Beattie R, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex. Neuron 2020; 107:1160-1179.e9. [PMID: 32707083 PMCID: PMC7523403 DOI: 10.1016/j.neuron.2020.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/20/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.
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Affiliation(s)
- Susanne Laukoter
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Florian M Pauler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Robert Beattie
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Andi H Hansen
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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28
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Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes. Proc Natl Acad Sci U S A 2020; 117:25074-25084. [PMID: 32948690 DOI: 10.1073/pnas.2008013117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We are only just beginning to catalog the vast diversity of cell types in the cerebral cortex. Such categorization is a first step toward understanding how diversification relates to function. All cortical projection neurons arise from a uniform pool of progenitor cells that lines the ventricles of the forebrain. It is still unclear how these progenitor cells generate the more than 50 unique types of mature cortical projection neurons defined by their distinct gene-expression profiles. Moreover, exactly how and when neurons diversify their function during development is unknown. Here we relate gene expression and chromatin accessibility of two subclasses of projection neurons with divergent morphological and functional features as they develop in the mouse brain between embryonic day 13 and postnatal day 5 in order to identify transcriptional networks that diversify neuron cell fate. We compare these gene-expression profiles with published profiles of single cells isolated from similar populations and establish that layer-defined cell classes encompass cell subtypes and developmental trajectories identified using single-cell sequencing. Given the depth of our sequencing, we identify groups of transcription factors with particularly dense subclass-specific regulation and subclass-enriched transcription factor binding motifs. We also describe transcription factor-adjacent long noncoding RNAs that define each subclass and validate the function of Myt1l in balancing the ratio of the two subclasses in vitro. Our multidimensional approach supports an evolving model of progressive restriction of cell fate competence through inherited transcriptional identities.
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29
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Liu J, Wang M, Sun L, Pan NC, Zhang C, Zhang J, Zuo Z, He S, Wu Q, Wang X. Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1. Protein Cell 2020; 11:417-432. [PMID: 32350740 PMCID: PMC7251024 DOI: 10.1007/s13238-020-00720-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/09/2020] [Indexed: 01/09/2023] Open
Abstract
Vision formation is classically based on projections from retinal ganglion cells (RGC) to the lateral geniculate nucleus (LGN) and the primary visual cortex (V1). Neurons in the mouse V1 are tuned to light stimuli. Although the cellular information of the retina and the LGN has been widely studied, the transcriptome profiles of single light-stimulated neuron in V1 remain unknown. In our study, in vivo calcium imaging and whole-cell electrophysiological patch-clamp recording were utilized to identify 53 individual cells from layer 2/3 of V1 as light-sensitive (LS) or non-light-sensitive (NS) by single-cell light-evoked calcium evaluation and action potential spiking. The contents of each cell after functional tests were aspirated in vivo through a patch-clamp pipette for mRNA sequencing. Moreover, the three-dimensional (3-D) morphological characterizations of the neurons were reconstructed in a live mouse after the whole-cell recordings. Our sequencing results indicated that V1 neurons with a high expression of genes related to transmission regulation, such as Rtn4r and Rgs7, and genes involved in membrane transport, such as Na+/K+ ATPase and NMDA-type glutamatergic receptors, preferentially responded to light stimulation. Furthermore, an antagonist that blocks Rtn4r signals could inactivate the neuronal responses to light stimulation in live mice. In conclusion, our findings of the vivo-seq analysis indicate the key role of the strength of synaptic transmission possesses neurons in V1 of light sensory.
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Affiliation(s)
- Jianwei Liu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Sun
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Clara Pan
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changjiang Zhang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjing Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
| | - Zhentao Zuo
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sheng He
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, Beijing, 100069, China.
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30
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Hook PW, McCallion AS. Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia. Genome Res 2020; 30:528-539. [PMID: 32303558 PMCID: PMC7197474 DOI: 10.1101/gr.256578.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies have implicated thousands of noncoding variants across common human phenotypes. However, they cannot directly inform the cellular context in which disease-associated variants act. Here, we use open chromatin profiles from discrete mouse cell populations to address this challenge. We applied stratified linkage disequilibrium score regression and evaluated heritability enrichment in 64 genome-wide association studies, emphasizing schizophrenia. We provide evidence that mouse-derived human open chromatin profiles can serve as powerful proxies for difficult to obtain human cell populations, facilitating the illumination of common disease heritability enrichment across an array of human phenotypes. We demonstrate that signatures from discrete subpopulations of cortical excitatory and inhibitory neurons are significantly enriched for schizophrenia heritability with maximal enrichment in cortical layer V excitatory neurons. We also show that differences between schizophrenia and bipolar disorder are concentrated in excitatory neurons in cortical layers II-III, IV, and V, as well as the dentate gyrus. Finally, we leverage these data to fine-map variants in 177 schizophrenia loci nominating variants in 104/177. We integrate these data with transcription factor binding site, chromatin interaction, and validated enhancer data, placing variants in the cellular context where they may modulate risk.
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Affiliation(s)
- Paul W Hook
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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31
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Nakagawa T, Wada Y, Katada S, Kishi Y. Epigenetic regulation for acquiring glial identity by neural stem cells during cortical development. Glia 2020; 68:1554-1567. [PMID: 32163194 DOI: 10.1002/glia.23818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/09/2020] [Accepted: 03/02/2020] [Indexed: 12/16/2022]
Abstract
The nervous system consists of several hundred neuronal subtypes and glial cells that show specific gene expression and are generated from common ancestors, neural stem cells (NSCs). As the experimental techniques and molecular tools to analyze epigenetics and chromatin structures are rapidly advancing, the comprehensive events and genome-wide states of DNA methylation, histone modifications, and chromatin accessibility in developing NSCs are gradually being unveiled. Here, we review recent advances in elucidating the role of epigenetic and chromatin regulation in NSCs, especially focusing on the acquisition of glial identity and how epigenetic regulation enables the temporal regulation of NSCs during murine cortical development.
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Affiliation(s)
- Takumi Nakagawa
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshikuni Wada
- Laboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sayako Katada
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusuke Kishi
- Laboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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32
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Poor Concordance of Floxed Sequence Recombination in Single Neural Stem Cells: Implications for Cell Autonomous Studies. eNeuro 2020; 7:ENEURO.0470-19.2020. [PMID: 32079584 PMCID: PMC7086402 DOI: 10.1523/eneuro.0470-19.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 11/24/2022] Open
Abstract
To manipulate target gene function in specific adult cell populations, tamoxifen (TAM)-dependent CreERT2 is widely used to drive inducible, site-specific recombination of loxP flanked sequences. In studies of cell autonomous target gene function, it is common practice to combine these CreERT2-lox systems with a ubiquitously expressed stop-floxed fluorescent reporter gene to identify single cells supposedly undergoing target gene recombination. Here, we studied the reliability of using Cre-induced recombination of one gene to predict recombination in another gene at the single-cell level in adult hippocampal neural stem and progenitor cells (NSPCs). Using both probabilistic predictions in a generic experimental paradigm, as well as a mouse model with two separate stop-floxed reporters plus a Nestin promoter-driven CreERT2, we found that, in individual cells, recombination of one gene was a poor predictor of recombination in another. This poor concordance in floxed sequence recombination across genes suggests that use of stop-floxed reporters to investigate cell autonomous gene function may not be universally reliable and could lead to false conclusions.
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33
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Cadwell CR, Bhaduri A, Mostajo-Radji MA, Keefe MG, Nowakowski TJ. Development and Arealization of the Cerebral Cortex. Neuron 2019; 103:980-1004. [PMID: 31557462 PMCID: PMC9245854 DOI: 10.1016/j.neuron.2019.07.009] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/15/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Adult cortical areas consist of specialized cell types and circuits that support unique higher-order cognitive functions. How this regional diversity develops from an initially uniform neuroepithelium has been the subject of decades of seminal research, and emerging technologies, including single-cell transcriptomics, provide a new perspective on area-specific molecular diversity. Here, we review the early developmental processes that underlie cortical arealization, including both cortex intrinsic and extrinsic mechanisms as embodied by the protomap and protocortex hypotheses, respectively. We propose an integrated model of serial homology whereby intrinsic genetic programs and local factors establish early transcriptomic differences between excitatory neurons destined to give rise to broad "proto-regions," and activity-dependent mechanisms lead to progressive refinement and formation of sharp boundaries between functional areas. Finally, we explore the potential of these basic developmental processes to inform our understanding of the emergence of functional neural networks and circuit abnormalities in neurodevelopmental disorders.
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Affiliation(s)
- Cathryn R Cadwell
- Department of Anatomic Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94122, USA; The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mohammed A Mostajo-Radji
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94122, USA; The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew G Keefe
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at the University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA.
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34
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Hickey SL, Berto S, Konopka G. Chromatin Decondensation by FOXP2 Promotes Human Neuron Maturation and Expression of Neurodevelopmental Disease Genes. Cell Rep 2019; 27:1699-1711.e9. [PMID: 31067457 PMCID: PMC6794152 DOI: 10.1016/j.celrep.2019.04.044] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 03/08/2019] [Accepted: 04/08/2019] [Indexed: 01/06/2023] Open
Abstract
Forkhead box P2 (FOXP2) is a transcription factor expressed in the human brain that peaks during fetal development, and disruption in its ability to regulate downstream target genes leads to vulnerability to neurodevelopmental disorders. However, the mechanisms by which FOXP2 exerts regulatory control over targets during neuronal maturation have not been fully elucidated. Here, we use genome-wide chromatin accessibility assays and transcriptome-wide expression analyses in differentiating human neurons to show that FOXP2 represses proliferation-promoting genes in a DNA-binding-dependent manner. In contrast, FOXP2 and its cofactors, NFIA and NFIB, activate neuronal maturation genes in a manner that does not require FOXP2 to interact with DNA directly. Moreover, comparisons with expression data from the developing human brain suggest that FOXP2 and NFIA- or NFIB-dependent chromatin alterations drive maturation of excitatory cortical neurons. Thus, FOXP2 and its NFI cofactors may be specifically important for the development of cortical circuits underlying neurodevelopmental disorders.
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Affiliation(s)
- Stephanie L Hickey
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stefano Berto
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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35
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Bravo González-Blas C, Minnoye L, Papasokrati D, Aibar S, Hulselmans G, Christiaens V, Davie K, Wouters J, Aerts S. cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data. Nat Methods 2019; 16:397-400. [PMID: 30962623 DOI: 10.1038/s41592-019-0367-1] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 12/17/2022]
Abstract
We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data ( http://github.com/aertslab/cistopic ). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity in cell populations.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Liesbeth Minnoye
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dafni Papasokrati
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kristofer Davie
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
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36
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Starks RR, Biswas A, Jain A, Tuteja G. Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. Epigenetics Chromatin 2019; 12:16. [PMID: 30795793 PMCID: PMC6385419 DOI: 10.1186/s13072-019-0260-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The assay for transposase-accessible chromatin (ATAC-seq) is a powerful method to examine chromatin accessibility. While many studies have reported a positive correlation between gene expression and promoter accessibility, few have investigated the genes that deviate from this trend. In this study, we aimed to understand the relationship between gene expression and promoter accessibility in multiple cell types while also identifying gene regulatory networks in the placenta, an understudied organ that is critical for a successful pregnancy. RESULTS We started by assaying the open chromatin landscape in the mid-gestation placenta, when the fetal vasculature has started developing. After incorporating transcriptomic data generated in the placenta at the same time point, we grouped genes based on their expression levels and ATAC-seq promoter coverage. We found that the genes with the strongest correlation (high expression and high coverage) are likely involved in housekeeping functions, whereas tissue-specific genes were highly expressed and had only medium-low coverage. We also predicted that genes with medium-low expression and high promoter coverage were actively repressed. Within this group, we extracted a protein-protein interaction network enriched for neuronal functions, likely preventing the cells from adopting a neuronal fate. We further confirmed that a repressive histone mark is bound to the promoters of genes in this network. Finally, we ran our pipeline using ATAC-seq and RNA-seq data generated in ten additional cell types. We again found that genes with the strongest correlation are enriched for housekeeping functions and that genes with medium-low promoter coverage and high expression are more likely to be tissue-specific. These results demonstrate that only two data types, both of which require relatively low starting material to generate and are becoming more commonly available, can be integrated to understand multiple aspects of gene regulation. CONCLUSIONS Within the placenta, we identified an active placenta-specific gene network as well as a repressed neuronal network. Beyond the placenta, we demonstrate that ATAC-seq data and RNA-seq data can be integrated to identify tissue-specific genes and actively repressed gene networks in multiple cell types.
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Affiliation(s)
- Rebekah R. Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011 USA
| | - Anilisa Biswas
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Molecular, Cellular, and Developmental Biology, Iowa State University, Ames, IA 50011 USA
| | - Ashish Jain
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011 USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011 USA
- Molecular, Cellular, and Developmental Biology, Iowa State University, Ames, IA 50011 USA
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37
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Michaelson SD, Ozkan ED, Aceti M, Maity S, Llamosas N, Weldon M, Mizrachi E, Vaissiere T, Gaffield MA, Christie JM, Holder JL, Miller CA, Rumbaugh G. SYNGAP1 heterozygosity disrupts sensory processing by reducing touch-related activity within somatosensory cortex circuits. Nat Neurosci 2018; 21:1-13. [PMID: 30455457 PMCID: PMC6309426 DOI: 10.1038/s41593-018-0268-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/02/2018] [Indexed: 01/08/2023]
Abstract
In addition to cognitive impairments, neurodevelopmental disorders often result in sensory processing deficits. However, the biological mechanisms that underlie impaired sensory processing associated with neurodevelopmental disorders are generally understudied and poorly understood. We found that SYNGAP1 haploinsufficiency in humans, which causes a sporadic neurodevelopmental disorder defined by cognitive impairment, autistic features, and epilepsy, also leads to deficits in tactile-related sensory processing. In vivo neurophysiological analysis in Syngap1 mouse models revealed that upper-lamina neurons in somatosensory cortex weakly encode information related to touch. This was caused by reduced synaptic connectivity and impaired intrinsic excitability within upper-lamina somatosensory cortex neurons. These results were unexpected, given that Syngap1 heterozygosity is known to cause circuit hyperexcitability in brain areas more directly linked to cognitive functions. Thus, Syngap1 heterozygosity causes a range of circuit-specific pathologies, including reduced activity within cortical neurons required for touch processing, which may contribute to sensory phenotypes observed in patients.
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Affiliation(s)
| | - Emin D Ozkan
- Department of Neuroscience, Scripps Florida, Jupiter, FL, USA
| | - Massimiliano Aceti
- Department of Neuroscience, Scripps Florida, Jupiter, FL, USA
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Nerea Llamosas
- Department of Neuroscience, Scripps Florida, Jupiter, FL, USA
| | - Monica Weldon
- Bridge-the-GAP Educational Research Foundation, Cyprus, TX, USA
| | - Elisa Mizrachi
- Department of Neuroscience, Scripps Florida, Jupiter, FL, USA
| | | | | | | | - J Lloyd Holder
- Jan and Dan Duncan Neurological Research Institute and Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Courtney A Miller
- Department of Neuroscience, Scripps Florida, Jupiter, FL, USA
- Department of Molecular Medicine, Scripps Florida, Jupiter, Fl, USA
| | - Gavin Rumbaugh
- Department of Neuroscience, Scripps Florida, Jupiter, FL, USA.
- Department of Molecular Medicine, Scripps Florida, Jupiter, Fl, USA.
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38
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Venkatesh I, Mehra V, Wang Z, Califf B, Blackmore MG. Developmental Chromatin Restriction of Pro-Growth Gene Networks Acts as an Epigenetic Barrier to Axon Regeneration in Cortical Neurons. Dev Neurobiol 2018; 78:960-977. [PMID: 29786967 PMCID: PMC6204296 DOI: 10.1002/dneu.22605] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/01/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022]
Abstract
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility. When applied to the developing cortex, this pipeline detected overall closure of chromatin in sub-networks of genes associated with axon growth. We next analyzed mature CNS neurons that were supplied with various pro-regenerative transcription factors. Unlike prior results with SOX11 and KLF7, here we found that neither JUN nor an activated form of STAT3 promoted substantial corticospinal tract regeneration. Correspondingly, chromatin accessibility in JUN or STAT3 target genes was substantially lower than in predicted targets of SOX11 and KLF7. Finally, we used the pipeline to predict pioneer factors that could potentially relieve chromatin constraints at growth-associated loci. Overall this integrated analysis substantiates the hypothesis that dynamic chromatin accessibility contributes to the developmental decline in axon growth ability and influences the efficacy of pro-regenerative interventions in the adult, while also pointing toward selected pioneer factors as high-priority candidates for future combinatorial experiments. © 2018 Wiley Periodicals, Inc. Develop Neurobiol 00: 000-000, 2018.
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Affiliation(s)
| | - Vatsal Mehra
- Department of Biomedical Sciences, Marquette University, 53201
| | - Zimei Wang
- Department of Biomedical Sciences, Marquette University, 53201
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39
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Chang M, Suzuki N, Kawai HD. Laminar specific gene expression reveals differences in postnatal laminar maturation in mouse auditory, visual, and somatosensory cortex. J Comp Neurol 2018; 526:2257-2284. [DOI: 10.1002/cne.24481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/03/2018] [Accepted: 05/21/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Minzi Chang
- Department of Bioinformatics; Graduate School of Engineering; Hachioji Tokyo 192-8577 Japan
| | - Nobuko Suzuki
- Department of Bioinformatics; Graduate School of Engineering; Hachioji Tokyo 192-8577 Japan
| | - Hideki Derek Kawai
- Department of Bioinformatics; Graduate School of Engineering; Hachioji Tokyo 192-8577 Japan
- Department of Science and Engineering for Sustainable Innovation; Faculty of Science and Engineering; Hachioji Tokyo 192-8577 Japan
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40
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Blankvoort S, Witter MP, Noonan J, Cotney J, Kentros C. Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression. Curr Biol 2018; 28:2103-2114.e5. [PMID: 30008330 DOI: 10.1016/j.cub.2018.05.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 04/27/2018] [Accepted: 05/04/2018] [Indexed: 10/28/2022]
Abstract
Understanding neural circuit function requires individually addressing their component parts: specific neuronal cell types. However, not only do the precise genetic mechanisms specifying neuronal cell types remain obscure, access to these neuronal cell types by transgenic techniques also remains elusive. Whereas most genes are expressed in the brain, the vast majority are expressed in many different kinds of neurons, suggesting that promoters alone are not sufficiently specific to distinguish cell types. However, there are orders of magnitude more distal genetic cis-regulatory elements controlling transcription (i.e., enhancers), so we screened for enhancer activity in microdissected samples of mouse cortical subregions. This identified thousands of novel putative enhancers, many unique to particular cortical subregions. Pronuclear injection of expression constructs containing such region-specific enhancers resulted in transgenic lines driving expression in distinct sets of cells specifically in the targeted cortical subregions, even though the parent gene's promoter was relatively non-specific. These data showcase the promise of utilizing the genetic mechanisms underlying the specification of diverse neuronal cell types for the development of genetic tools potentially capable of targeting any neuronal circuit of interest, an approach we call enhancer-driven gene expression (EDGE).
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Affiliation(s)
- Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - James Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT, USA
| | - Justin Cotney
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Centre, Farmington, CT, USA.
| | - Cliff Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway; Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
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41
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Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences. J Neurosci 2018; 38:5441-5455. [PMID: 29798890 DOI: 10.1523/jneurosci.0150-18.2018] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/25/2022] Open
Abstract
Neocortical pyramidal neurons with somata in layers 5 and 6 are among the most visually striking and enigmatic neurons in the brain. These deep-layer pyramidal neurons (DLPNs) integrate a plethora of cortical and extracortical synaptic inputs along their impressive dendritic arbors. The pattern of cortical output to both local and long-distance targets is sculpted by the unique physiological properties of specific DLPN subpopulations. Here we revisit two broad DLPN subpopulations: those that send their axons within the telencephalon (intratelencephalic neurons) and those that project to additional target areas outside the telencephalon (extratelencephalic neurons). While neuroscientists across many subdisciplines have characterized the intrinsic and synaptic physiological properties of DLPN subpopulations, our increasing ability to selectively target and manipulate these output neuron subtypes advances our understanding of their distinct functional contributions. This Viewpoints article summarizes our current knowledge about DLPNs and highlights recent work elucidating the functional differences between DLPN subpopulations.
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42
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Tosches MA, Yamawaki TM, Naumann RK, Jacobi AA, Tushev G, Laurent G. Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles. Science 2018; 360:881-888. [DOI: 10.1126/science.aar4237] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/12/2018] [Indexed: 12/14/2022]
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43
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Manoli DS, Tollkuhn J. Gene regulatory mechanisms underlying sex differences in brain development and psychiatric disease. Ann N Y Acad Sci 2018; 1420:26-45. [PMID: 29363776 PMCID: PMC5991992 DOI: 10.1111/nyas.13564] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/26/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
Abstract
The sexual differentiation of the mammalian nervous system requires the precise coordination of the temporal and spatial regulation of gene expression in diverse cell types. Sex hormones act at multiple developmental time points to specify sex-typical differentiation during embryonic and early development and to coordinate subsequent responses to gonadal hormones later in life by establishing sex-typical patterns of epigenetic modifications across the genome. Thus, mutations associated with neuropsychiatric conditions may result in sexually dimorphic symptoms by acting on different neural substrates or chromatin landscapes in males and females. Finally, as stress hormone signaling may directly alter the molecular machinery that interacts with sex hormone receptors to regulate gene expression, the contribution of chronic stress to the pathogenesis or presentation of mental illness may be additionally different between the sexes. Here, we review the mechanisms that contribute to sexual differentiation in the mammalian nervous system and consider some of the implications of these processes for sex differences in neuropsychiatric conditions.
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Affiliation(s)
- Devanand S. Manoli
- Department of Psychiatry and Weill Institute for Neuroscience, University of California, San Francisco, San Francisco, California
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44
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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci 2018; 21:432-439. [PMID: 29434377 DOI: 10.1038/s41593-018-0079-3] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/27/2017] [Indexed: 01/23/2023]
Abstract
Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.
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45
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de la Torre-Ubieta L, Stein JL, Won H, Opland CK, Liang D, Lu D, Geschwind DH. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. Cell 2018; 172:289-304.e18. [PMID: 29307494 PMCID: PMC5924568 DOI: 10.1016/j.cell.2017.12.014] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 09/14/2017] [Accepted: 12/07/2017] [Indexed: 01/19/2023]
Abstract
Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. We link distal regulatory elements (DREs) to their cognate gene(s) together with chromatin interaction data and show that target genes of human-gained enhancers (HGEs) regulate cortical neurogenesis and are enriched in outer radial glia, a cell type linked to human cortical evolution. We experimentally validate the regulatory effects of predicted enhancers for FGFR2 and EOMES. We observe that common genetic variants associated with educational attainment, risk for neuropsychiatric disease, and intracranial volume are enriched within regulatory elements involved in cortical neurogenesis, demonstrating the importance of this early developmental process for adult human cognitive function.
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Affiliation(s)
- Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason L Stein
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hyejung Won
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carli K Opland
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daning Lu
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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46
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Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron 2017; 96:542-557. [PMID: 29096072 PMCID: PMC5689454 DOI: 10.1016/j.neuron.2017.10.007] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 10/25/2022]
Abstract
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.
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Affiliation(s)
- Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nenad Sestan
- Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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47
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Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 2017; 14:959-962. [PMID: 28846090 PMCID: PMC5623106 DOI: 10.1038/nmeth.4396] [Citation(s) in RCA: 1295] [Impact Index Per Article: 185.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Abstract
We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.
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Affiliation(s)
- M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandro E Trevino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA
| | - Emily G Hamilton
- Program in Cancer Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA
| | | | - Sam Vesuna
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Arwa Kathiria
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Maya Kasowski
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa A Orloff
- Department of Otolaryngology Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
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