biostudies-literatureDeng CNIDA NIH HHSNIA NIH HHSNIMH NIH HHSNHGRI NIH HHSNINDS NIH HHSNIGMS NIH HHSeadh0559https://www.ebi.ac.uk/biostudies/studies/S-EPMC12085231biostudies-literatureUnknown384(6698)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 comprScience (New York, N.Y.)Massively parallel characterization of regulatory elements in the developing human cortex.PMC12085231R21 MH105881U01 MH122678R01 MH116438R01 MH117406R56 MH114899DP2 MH122400U01 MH122592P30 AG066514U01 MH122590U01 MH122591UM1 HG011966R21 MH129817R01 MH117291R01 MH105898R01 MH117293R01 MH117292R01 MH126393R01 MH129301R01 MH116529U01 MH103365R21 MH103877R21 MH105853R01 MH110905T32 GM008042R01 NS123263U01 MH116438U01 MH122509R01 MH125516UF1 MH130700R01 NS079231R56 MH114911U01 MH116492U01 MH103339R21 MH102791R01 MH111721R01 MH109715R01 MH109677R01 MH121521U01 MH116489R01 MH105472R01 MH126459U01 MH116487U01 MH116488U01 MH116441R01 MH125246U01 MH116442R56 MH114901U01 MH103346U01 MH122681R01 MH110920R21 MH109956U01 MH103340R01 MH110927UM1 HG009408R01 MH110928R01 MH109907R01 MH094714R01 MH110926U01 MH103392P50 MH106934R01 MH110921U01 DA048279U01 MH122849U19 GM061390Ziffra RGaynor SLin XKawaguchi RReimonn TAkbarian STherrien KRuth MWhite KPAlmagro Armenteros JJSudhof TDavila-Velderrain JHe CYap CXMargolis MRozowsky JNairn ACPeters MAInoue FZeng BWylie DDursun CPage SCQuintero DSchneider JMXu SAhituv NHenry EGerstein MChampagne FAMeng RWuchty SSebra RSestan NStein JPollard KSNemeroff CBWei YDrusinsky SQin ZSRessler KJSnijders CZintel TMPhalke NBicks LRoss DMyers RMWeimer AKJajoo AChien JFHallmayer JBendl JKellis MWong WHuuki-Myers LADeng CHawken NPollen AMicallef CPjanic MMazariegos SSnyder MTsai LHClement ACrawford GEDiPietro CPChess AGoes FSMukamel EAArasappan DLou SPrzytycki PFGupta CVo DChen YChatterjee TKozlenkov ALi JDaskalakis NPCooper GMKundaje ALi MBharadwaj RASteyert MKleopoulos SPEdelstein JLiu JJiang LJourdon AMa SMa LSubburaju SShieh AWLiu SJensen MShin JHDeep-Soboslay AMing GLJops CPattni RMariani JVaccarino FMOmberg LPereira DASkarica MKleinman JEPatowary AShedd NFullard JFEmani PSZhang YHwang ALiu CZhang JMaynard KRChen HIGuo QHyde TMZhang PGalani KPsychENCODE Consortium‡Guo HKhullar SScuderi SMoore JEPertea GEagles NJHoffman GEJin PZhang CZhang BPochareddy SZeier ZRHadas YJin TChu ZHicks SCRuzicka WBHo LLHaroutunian VGirdhar KNorton Svan Bakel HWarrell JHan XPollen AACheng YLee DMohammadi SLee CShao ZGreenleaf WCheng LNowakowski TReach SMontgomery KSCollado-Torres LDuong DCapauto DBeliveau BJZhou XNi PChatzinakos CWang SHHuang YDai RClarke DMikhailova TKriegstein ADracheva SBrennand KNowakowski TJGrundman JWang DMoran JRWu FWu HVoloudakis GWang TWeng ZWen CWang YBerretta SRoussos PGaleev TLu DMonte EPark SPsychENCODE ConsortiumPratt HHo MPinto DSanders SJRajagopalan ASWamsley BWhalen SMartinowich KState MWUrban AEAbyzov AGeschwind DHRaj TWillsey AJWon HIatrou AGandal MJSong HDuan ZLoupe JMBhattacharya AQu PPPurmann CTao RWeinberger DRSeyfried NKundu SfalseMassively parallel characterization of regulatory elements in the developing human cortex.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 compr2024-01-01T00:00:00Z2024 May2026-06-02T20:54:33.941Z2026-05-28T03:06:37.734ZS-EPMC120852313878139010.1126/science.adh0559