Massively parallel characterization of regulatory elements in the developing human cortex
Authors: Deng Chengyu , Whalen Sean , Steyert Marilyn , Ziffra Ryan , Przytycki Pawel F. , Inoue Fumitaka , Pereira Daniela A. , Capauto Davide , Norton Scott , Vaccarino Flora M. ,   PsychENCODE Consortium‡, Pollen Alex A. , Nowakowski Tomasz J. , Ahituv Nadav , Pollard Katherine S. , Akbarian Schahram , Abyzov Alexej , Ahituv Nadav , Arasappan Dhivya , Almagro Armenteros Jose Juan , Beliveau Brian J. , Bendl Jaroslav , Berretta Sabina , Bharadwaj Rahul A. , Bhattacharya Arjun , 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 , Clarke Declan , Clement Ashley , Collado-Torres Leonardo , Cooper Gregory M. , Crawford Gregory E. , Dai Rujia , Daskalakis Nikolaos P. , 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 , Gandal Michael J. , Gaynor Sophia , Gerstein Mark , Geschwind Daniel H. , 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 , Hyde Thomas M. , Iatrou Artemis , Inoue Fumitaka , Jajoo Aarti , Jensen Matthew , Jiang Lihua , Jin Peng , Jin Ting , Jops Connor , Jourdon Alexandre , Kawaguchi Riki , Kellis Manolis , Khullar Saniya , Kleinman Joel E. , 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 Chunyu , Liu Shuang , Lou Shaoke , Loupe Jacob M. , Lu Dan , Ma Shaojie , Ma Liang , Margolis Michael , 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 , Peters Mette A. , Phalke Nishigandha , Pinto Dalila , Pjanic Milos , Pochareddy Sirisha , Pollard Katherine S. , Pollen Alex , Pratt Henry , Przytycki Pawel F. , 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 , Sestan Nenad , Seyfried Nicholas , Shao Zhiping , Shedd Nicole , Shieh Annie W. , Shin Joo Heon , Skarica Mario , Snijders Clara , Song Hongjun , State Matthew W. , Stein Jason , Steyert Marilyn , Subburaju Sivan , Sudhof Thomas , Snyder Michael , Tao Ran , Therrien Karen , Tsai Li-Huei , Urban Alexander E. , Vaccarino Flora M. , van Bakel Harm , Vo Daniel , Voloudakis Georgios , Wamsley Brie , Wang Tao , Wang Sidney H. , Wang Daifeng , Wang Yifan , Warrell Jonathan , Wei Yu , Weimer Annika K. , Weinberger Daniel R. , Wen Cindy , Weng Zhiping , 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 Pan , Zhang Chunling , Zhang Bin , Zhang Jing , Zhang Yanqiong , Zhou Xiao , Ziffra Ryan , Zeier Zane R. , Zintel Trisha M. 
Published: May 2024

Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type–specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.