Chongyuan Luo, Ph.D.
Assistant Professor, Human Genetics
Member, Bioinformatics GPB Home Area, Gene Regulation GPB Home Area, Genetics & Genomics GPB Home Area
Research Interests

We are interested in studying how gene regulatory mechanisms contribute to human diseases including neurodevelopmental disorders. Many genome-wide association studies (GWAS) of diseases have identified the enrichment of non-coding risk variants in regulatory elements such as enhancers, highlighting the contribution of regulatory mechanisms to complex traits. In addition, epigenetic variants, such as cytosine methylation (5mC), have been reported to associate with diseases and can be driven by genetic, environmental or stochastic factors. We are developing and applying new genomic and genetic technologies to address long-standing questions in human diseases including the causal cell type(s) of diseases and the functions of non-coding genetic variants. Two major areas of research in my group are described below.

Developing new epigenomic technologies. Genomic profiling of epigenomic signatures (e.g. DNA methylation, histone modifications) enables the study of gene regulatory events on a global scale. In previous work, we have developed single-cell epigenomic and multi-omic technologies, and use these methods to study the gene regulatory diversity in the brain. We developed a high-throughput single-cell methylome profiling method snmC-seq and its major update snmC-seq2 that have enabled cell-type classification and the identification of cell-type-specific regulatory elements across cortical neuron subtypes in mouse and human (Luo et al., 2017. Science; Luo et al., 2018. Nature Communications). More recently we have developed two single-cell multi-omic methods that allow the multi-modal integration of transcriptome, DNA methylome, chromatin accessibility and chromatin conformation (Luo et al., 2018. bioRxiv; Lee*, Luo*, Zhou* et al., 2019. Nature Methods), providing a near-comprehensive epigenomic characterization of individual brain cells.

Genetic basis of neurodevelopmental disorders. Psychiatric neurodevelopmental disorders such as schizophrenia and autism spectrum disorders (ASD) are highly heritable. Regulatory mechanisms play an important role in both diseases and schizophrenia risk variants are enriched in bulk brain tissue enhancers and immune cell types. Importantly, ASD can be contributed by epigenetic regulation by 5mC. Rett syndrome is a type of ASD and is caused by mutations in MECP2 (methyl-CpG binding protein 2) that recognize 5mC. Neurodevelopmental disorders are likely contributed by multiple cell types in developing and adult brains. We will use a combination of single-cell multi-epigenomics and population genetics approaches to address the contribution of aberrant gene regulations in neurodevelopmental disorders.


Dr. Chongyuan Luo received his B.Sc. degree in Biology (Honors Program in Life Sciences) from China Agricultural University, in 2006. Dr. Luo received his Ph.D. degree in Plant Biology from Rutgers University in 2012. During his Ph.D. study, he studied histone modifications of the model plant species Arabidopsis thaliana using high-throughput sequencing approaches. After completing his postdoctoral training in Joe Ecker’s lab at the Salk Institute for Biological Studies, Dr. Luo joined the Department of Human Genetics at UCLA as an Assistant Professor in 2019.


A selected list of publications:

Gao Chao, Liu Jialin, Kriebel April R, Preissl Sebastian, Luo Chongyuan, Castanon Rosa, Sandoval Justin, Rivkin Angeline, Nery Joseph R, Behrens Margarita M, Ecker Joseph R, Ren Bing, Welch Joshua D   Iterative single-cell multi-omic integration using online learning Nature biotechnology, 2021; .
Evrony Gilad D, Hinch Anjali Gupta, Luo Chongyuan   Applications of Single-Cell DNA Sequencing Annual review of genomics and human genetics, 2021; 109(1): 11-26.
Armand Ethan J, Li Junhao, Xie Fangming, Luo Chongyuan, Mukamel Eran A   Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes Neuron, 2021; 109(1): 11-26.
He Yupeng, Hariharan Manoj, Gorkin David U, Dickel Diane E, Luo Chongyuan, Castanon Rosa G, Nery Joseph R, Lee Ah Young, Zhao Yuan, Huang Hui, Williams Brian A, Trout Diane, Amrhein Henry, Fang Rongxin, Chen Huaming, Li Bin, Visel Axel, Pennacchio Len A, Ren Bing, Ecker Joseph R   Spatiotemporal DNA methylome dynamics of the developing mouse fetus Nature, 2020; 583(7818): 752-759.
Lavery Laura A, Ure Kerstin, Wan Ying-Wooi, Luo Chongyuan, Trostle Alexander J, Wang Wei, Jin Haijing, Lopez Joanna, Lucero Jacinta, Durham Mark A, Castanon Rosa, Nery Joseph R, Liu Zhandong, Goodell Margaret, Ecker Joseph R, Behrens M Margarita, Zoghbi Huda Y   Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome eLife, 2020; 9: .
Lee Dong-Sung, Luo Chongyuan, Zhou Jingtian, Chandran Sahaana, Rivkin Angeline, Bartlett Anna, Nery Joseph R, Fitzpatrick Conor, O'Connor Carolyn, Dixon Jesse R, Ecker Joseph R   Simultaneous profiling of 3D genome structure and DNA methylation in single human cells Nature methods, 2019; 16(10): 999-1006.
Luo Chongyuan, Lee Qian Yi, Wapinski Orly, Castanon Rosa, Nery Joseph R, Mall Moritz, Kareta Michael S, Cullen Sean M, Goodell Margaret A, Chang Howard Y, Wernig Marius, Ecker Joseph R   Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons eLife, 2019; 8(10): 999-1006.
Luo Chongyuan, Hajkova Petra, Ecker Joseph R   Dynamic DNA methylation: In the right place at the right time Science (New York, N.Y.), 2018; 361(6409): 1336-1340.
Luo Chongyuan, Rivkin Angeline, Zhou Jingtian, Sandoval Justin P, Kurihara Laurie, Lucero Jacinta, Castanon Rosa, Nery Joseph R, Pinto-Duarte António, Bui Brian, Fitzpatrick Conor, O'Connor Carolyn, Ruga Seth, Van Eden Marc E, Davis David A, Mash Deborah C, Behrens M Margarita, Ecker Joseph R   Robust single-cell DNA methylome profiling with snmC-seq2 Nature communications, 2018; 9(1): 3824.
Sabbagh Mark F, Heng Jacob S, Luo Chongyuan, Castanon Rosa G, Nery Joseph R, Rattner Amir, Goff Loyal A, Ecker Joseph R, Nathans Jeremy   Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells eLife, 2018; 7(1): 3824.
Luo Chongyuan, Keown Christopher L, Kurihara Laurie, Zhou Jingtian, He Yupeng, Li Junhao, Castanon Rosa, Lucero Jacinta, Nery Joseph R, Sandoval Justin P, Bui Brian, Sejnowski Terrence J, Harkins Timothy T, Mukamel Eran A, Behrens M Margarita, Ecker Joseph R   Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex Science (New York, N.Y.), 2017; 357(6351): 600-604.
Luo Chongyuan, Lancaster Madeline A, Castanon Rosa, Nery Joseph R, Knoblich Juergen A, Ecker Joseph R   Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain Cell reports, 2016; 17(12): 3369-3384.
Chin Chen-Shan, Peluso Paul, Sedlazeck Fritz J, Nattestad Maria, Concepcion Gregory T, Clum Alicia, Dunn Christopher, O'Malley Ronan, Figueroa-Balderas Rosa, Morales-Cruz Abraham, Cramer Grant R, Delledonne Massimo, Luo Chongyuan, Ecker Joseph R, Cantu Dario, Rank David R, Schatz Michael C   Phased diploid genome assembly with single-molecule real-time sequencing Nature methods, 2016; 13(12): 1050-1054.
Mo Alisa, Luo Chongyuan, Davis Fred P, Mukamel Eran A, Henry Gilbert L, Nery Joseph R, Urich Mark A, Picard Serge, Lister Ryan, Eddy Sean R, Beer Michael A, Ecker Joseph R, Nathans Jeremy   Epigenomic landscapes of retinal rods and cones eLife, 2016; 5(12): e11613.
Luo Chongyuan, Ecker Joseph R   Epigenetics. Exceptional epigenetics in the brain Science (New York, N.Y.), 2015; 348(6239): 1094-5.
Mo Alisa, Mukamel Eran A, Davis Fred P, Luo Chongyuan, Henry Gilbert L, Picard Serge, Urich Mark A, Nery Joseph R, Sejnowski Terrence J, Lister Ryan, Eddy Sean R, Ecker Joseph R, Nathans Jeremy   Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain Neuron, 2015; 86(6): 1369-84.
Wu Jun, Okamura Daiji, Li Mo, Suzuki Keiichiro, Luo Chongyuan, Ma Li, He Yupeng, Li Zhongwei, Benner Chris, Tamura Isao, Krause Marie N, Nery Joseph R, Du Tingting, Zhang Zhuzhu, Hishida Tomoaki, Takahashi Yuta, Aizawa Emi, Kim Na Young, Lajara Jeronimo, Guillen Pedro, Campistol Josep M, Esteban Concepcion Rodriguez, Ross Pablo J, Saghatelian Alan, Ren Bing, Ecker Joseph R, Izpisua Belmonte Juan Carlos   An alternative pluripotent state confers interspecies chimaeric competency Nature, 2015; 521(7552): 316-21.
Luo Chongyuan, Lam Eric   Quantitatively profiling genome-wide patterns of histone modifications in Arabidopsis thaliana using ChIP-seq Methods in molecular biology (Clifton, N.J.), 2014; 1112(1): 177-93.
Widiez Thomas, Symeonidi Aikaterini, Luo Chongyuan, Lam Eric, Lawton Michael, Rensing Stefan A   The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress The Plant journal : for cell and molecular biology, 2014; 79(1): 67-81.
Luo Chongyuan, Dong Juan, Zhang Yi, Lam Eric   Decoding the role of chromatin architecture in development: coming closer to the end of the tunnel Frontiers in plant science, 2014; 5(7552): 374.
Luo Chongyuan, Sidote David J, Zhang Yi, Kerstetter Randall A, Michael Todd P, Lam Eric   Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production The Plant journal : for cell and molecular biology, 2013; 73(1): 77-90.
Vaquero-Sedas María I, Luo Chongyuan, Vega-Palas Miguel A   Analysis of the epigenetic status of telomeres by using ChIP-seq data Nucleic acids research, 2012; 40(21): e163.
Amini Aniça, Luo Chongyuan, Lam Eric   Chromatin beacons: global sampling of chromatin physical properties using chromatin charting lines Methods in molecular biology (Clifton, N.J.), 2011; 701(21): 301-14.
Luo Chongyuan, Lam Eric   ANCORP: a high-resolution approach that generates distinct chromatin state models from multiple genome-wide datasets The Plant journal : for cell and molecular biology, 2010; 63(2): 339-51.
Luo Chongyuan, Durgin Brittany G, Watanabe Naohide, Lam Eric   Defining the functional network of epigenetic regulators in Arabidopsis thaliana Molecular plant, 2009; 2(4): 661-674.
Lam Eric, Luo Chongyuan, Watanabe Naohide   Charting functional and physical properties of chromatin in living cells Current opinion in genetics & development, 2009; 19(2): 135-41.
Luo Chongyuan, Lam Eric   Chromatin charting: global mapping of epigenetic effects Methods in molecular biology (Clifton, N.J.), 2009; 553(2): 127-39.
Rotter David, Bharti Arvind K, Li Huaijun Michael, Luo Chongyuan, Bonos Stacy A, Bughrara Suleiman, Jung Geunhwa, Messing Joachim, Meyer William A, Rudd Stephen, Warnke Scott E, Belanger Faith C   Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses Molecular genetics and genomics : MGG, 2007; 278(2): 197-209.