biostudies-literatureUnknownChang LThe basal ganglia play essential roles in motor control, emotion, learning and reward processing. Their dysfunction contributes to many neurological and psychiatric disorders. However, the gene regulatory programs defining basal ganglia cell-type identity and function remain poorly understood, limiting interpretation of disease-associated non-coding variants. Here, we present the first single-cell multiome atlas of histone modifications and transcriptomes across eight basal ganglia regions from neurotypical adult human donors. Joint profiling reveals cell-type-specific deployment of active and repressive <i>cis</i> -regulatory elements and gene regulatory networks, and suggests a combinatorial homeobox transcription factor code underlying cell identity. Integration with matched spatial trabioRxiv : the preprint server for biology2026.02.03.703645https://www.ebi.ac.uk/biostudies/studies/S-EPMC12893060biostudies-literatureSingle-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia.PMC12893060Behrens MMManning ACYoung CKBerry JHodge RDDong KWang TZemke NRBikkina AO'Connor CSanchez YWang ZMonell ABakken TEXie YLi DKern JCRink JAKnutson KWBoone EWillier JKLi KJohansen NRusso KGFlores JLoe TZhong GGao XXu XBarcoma ASLein ESAlt SNLiu JOwens WFu YZhao ZDing WBaez-Becerra CTArzavala JIndralingam HSLiem MOsgood EEcker JRCho SBarragan CSchenker-Ahmed NMarrin MVChang LZu SOlness JLie ARose CRen BZhu CZhang WKlein ASundaram GVLiu DKeene CDZhu QfalseSingle-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia.The basal ganglia play essential roles in motor control, emotion, learning and reward processing. Their dysfunction contributes to many neurological and psychiatric disorders. However, the gene regulatory programs defining basal ganglia cell-type identity and function remain poorly understood, limiting interpretation of disease-associated non-coding variants. Here, we present the first single-cell multiome atlas of histone modifications and transcriptomes across eight basal ganglia regions from neurotypical adult human donors. Joint profiling reveals cell-type-specific deployment of active and repressive <i>cis</i> -regulatory elements and gene regulatory networks, and suggests a combinatorial homeobox transcription factor code underlying cell identity. Integration with matched spatial tra2026-01-01T00:00:00Z2026 Feb2026-07-12T03:17:56.35Z2026-07-12T03:11:31.831ZS-EPMC128930604168493010.64898/2026.02.03.703645