Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain-Reference-Cited by-同舟云学术

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

Published:2024-05-24 Issue:6698 Volume:384 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Wen Cindy¹²³^ORCID,Margolis Michael²³^ORCID,Dai Rujia⁴^ORCID,Zhang Pan²³^ORCID,Przytycki Pawel F.⁵^ORCID,Vo Daniel D.²³⁶⁷^ORCID,Bhattacharya Arjun⁸⁹^ORCID,Matoba Nana¹⁰¹¹^ORCID,Tang Miao⁶⁷,Jiao Chuan⁴¹²^ORCID,Kim Minsoo²³,Tsai Ellen²³^ORCID,Hoh Celine²³^ORCID,Aygün Nil¹⁰¹¹^ORCID,Walker Rebecca L.¹²³^ORCID,Chatzinakos Christos¹³¹⁴¹⁵,Clarke Declan¹⁶^ORCID,Pratt Henry¹⁷^ORCID, ,Peters Mette A.¹⁸^ORCID,Gerstein Mark¹⁶¹⁹²⁰²¹^ORCID,Daskalakis Nikolaos P.¹³¹⁴¹⁵^ORCID,Weng Zhiping¹⁷^ORCID,Jaffe Andrew E.²²²³²⁴²⁵²⁶^ORCID,Kleinman Joel E.²²²³^ORCID,Hyde Thomas M.²²²³²⁷^ORCID,Weinberger Daniel R.²²²³²⁴²⁵²⁷^ORCID,Bray Nicholas J.²⁸^ORCID,Sestan Nenad²⁹³⁰^ORCID,Geschwind Daniel H.³³¹³²^ORCID,Roeder Kathryn³³³⁴^ORCID,Gusev Alexander³⁵³⁶³⁷³⁸^ORCID,Pasaniuc Bogdan¹³⁸³²³⁹,Stein Jason L.¹⁰¹¹^ORCID,Love Michael I.¹⁰⁴⁰,Pollard Katherine S.⁵⁴¹⁴²^ORCID,Liu Chunyu⁴⁴³^ORCID,Gandal Michael J.¹²³⁶⁷^ORCID,Akbarian Schahram,Abyzov Alexej,Ahituv Nadav,Arasappan Dhivya,Almagro Armenteros Jose Juan,Beliveau Brian J.,Bendl Jaroslav,Berretta Sabina,Bharadwaj Rahul A.,Bicks Lucy,Brennand Kristen,Capauto Davide,Champagne Frances A.,Chatterjee Tanima,Chatzinakos Chris,Chen Yuhang,Chen H. Isaac,Cheng Yuyan,Cheng Lijun,Chess Andrew,Chien Jo-fan,Chu Zhiyuan,Clement Ashley,Collado-Torres Leonardo,Cooper Gregory M.,Crawford Gregory E.,Davila-Velderrain Jose,Deep-Soboslay Amy,Deng Chengyu,DiPietro Christopher P.,Dracheva Stella,Drusinsky Shiron,Duan Ziheng,Duong Duc,Dursun Cagatay,Eagles Nicholas J.,Edelstein Jonathan,Emani Prashant S.,Fullard John F.,Galani Kiki,Galeev Timur,Gaynor Sophia,Girdhar Kiran,Goes Fernando S.,Greenleaf William,Grundman Jennifer,Guo Hanmin,Guo Qiuyu,Gupta Chirag,Hadas Yoav,Hallmayer Joachim,Han Xikun,Haroutunian Vahram,Hawken Natalie,He Chuan,Henry Ella,Hicks Stephanie C.,Ho Marcus,Ho Li-Lun,Hoffman Gabriel E.,Huang Yiling,Huuki-Myers Louise A.,Hwang Ahyeon,Iatrou Artemis,Inoue Fumitaka,Jajoo Aarti,Jensen Matthew,Jiang Lihua,Jin Peng,Jin Ting,Jops Connor,Jourdon Alexandre,Kawaguchi Riki,Kellis Manolis,Kleopoulos Steven P.,Kozlenkov Alex,Kriegstein Arnold,Kundaje Anshul,Kundu Soumya,Lee Cheyu,Lee Donghoon,Li Junhao,Li Mingfeng,Lin Xiao,Liu Shuang,Liu Jason,Liu Jianyin,Liu Shuang,Lou Shaoke,Loupe Jacob M.,Lu Dan,Ma Shaojie,Ma Liang,Mariani Jessica,Martinowich Keri,Maynard Kristen R.,Mazariegos Samantha,Meng Ran,Myers Richard M.,Micallef Courtney,Mikhailova Tatiana,Ming Guo-li,Mohammadi Shahin,Monte Emma,Montgomery Kelsey S.,Moore Jill E.,Moran Jennifer R.,Mukamel Eran A.,Nairn Angus C.,Nemeroff Charles B.,Ni Pengyu,Norton Scott,Nowakowski Tomasz,Omberg Larsson,Page Stephanie C.,Park Saejeong,Patowary Ashok,Pattni Reenal,Pertea Geo,Phalke Nishigandha,Pinto Dalila,Pjanic Milos,Pochareddy Sirisha,Pollen Alex,Purmann Carolin,Qin Zhaohui S.,Qu Ping-Ping,Quintero Diana,Raj Towfique,Rajagopalan Ananya S.,Reach Sarah,Reimonn Thomas,Ressler Kerry J.,Ross Deanna,Roussos Panos,Rozowsky Joel,Ruth Misir,Ruzicka W. Brad,Sanders Stephan J.,Schneider Juliane M.,Scuderi Soraya,Sebra Robert,Seyfried Nicholas,Shao Zhiping,Shedd Nicole,Shieh Annie W.,Shin Joo Heon,Skarica Mario,Snijders Clara,Song Hongjun,State Matthew W.,Steyert Marilyn,Subburaju Sivan,Sudhof Thomas,Snyder Michael,Tao Ran,Therrien Karen,Tsai Li-Huei,Urban Alexander E.,Vaccarino Flora M.,van Bakel Harm,Voloudakis Georgios,Wamsley Brie,Wang Tao,Wang Sidney H.,Wang Daifeng,Wang Yifan,Warrell Jonathan,Wei Yu,Weimer Annika K.,Whalen Sean,White Kevin P.,Willsey A. Jeremy,Won Hyejung,Wong Wing,Wu Hao,Wu Feinan,Wuchty Stefan,Wylie Dennis,Xu Siwei,Yap Chloe X.,Zeng Biao,Zhang Chunling,Zhang Bin,Zhang Jing,Zhang Yanqiong,Zhou Xiao,Ziffra Ryan,Zeier Zane R.,Zintel Trisha M.

Affiliation:

1. Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA.

2. Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

3. Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

4. Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA.

5. Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA.

6. Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

7. Lifespan Brain Institute, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA.

8. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

9. Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

10. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

11. UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

12. Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Team Krebs, 75014 Paris, France.

13. Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.

14. McLean Hospital, Belmont, MA 02478, USA.

15. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

16. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

17. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

18. CNS Data Coordination Group, Sage Bionetworks, Seattle, WA 98109, USA.

19. Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

20. Department of Computer Science, Yale University, New Haven, CT 06520, USA.

21. Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA.

22. Lieber Institute for Brain Development, Baltimore, MD 21205, USA.

23. Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

24. Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

25. Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

26. Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

27. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

28. MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine, Cardiff CF24 4HQ, UK.

29. Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.

30. Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.

31. Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

32. Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA.

33. Department of Statistics & Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

34. Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

35. Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

36. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

37. Harvard Medical School, Boston, MA 02215, USA.

38. Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02215, USA.

39. Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

40. Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

41. Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA.

42. Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

43. Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.

Abstract

Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.

Publisher

American Association for the Advancement of Science (AAAS)

Link

https://www.science.org/doi/pdf/10.1126/science.adh0829

Reference121 articles.

1. Mapping genomic loci implicates genes and synaptic biology in schizophrenia

2. Identification of common genetic risk variants for autism spectrum disorder

3. The road to precision psychiatry: translating genetics into disease mechanisms

4. Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

5. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Cited by 4 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Reconstructing human-specific regulatory functions in model systems;Current Opinion in Genetics & Development;2024-12

2. Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis;The American Journal of Human Genetics;2024-09

3. Genetic Implication of Prenatal GABAergic and Cholinergic Neuron Development in Susceptibility to Schizophrenia;Schizophrenia Bulletin;2024-06-13

4. Transcriptomic analysis of the human habenula in schizophrenia;2024-02-27