Search Results - "Luo, Chongyuan"

Dynamic DNA methylation: In the right place at the right time by Luo, Chongyuan, Hajkova, Petra, Ecker, Joseph R

“…The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive…”
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Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes by Armand, Ethan J, Li, Junhao, Xie, Fangming, Luo, Chongyuan, Mukamel, Eran A

“…Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of…”
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Applications of Single-Cell DNA Sequencing by Evrony, Gilad D, Hinch, Anjali Gupta, Luo, Chongyuan

“…Over the past decade, genomic analyses of single cells-the fundamental units of life-have become possible. Single-cell DNA sequencing has shed light on…”
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Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells by Sabbagh, Mark F, Heng, Jacob S, Luo, Chongyuan, Castanon, Rosa G, Nery, Joseph R, Rattner, Amir, Goff, Loyal A, Ecker, Joseph R, Nathans, Jeremy

“…Vascular endothelial cell (EC) function depends on appropriate organ-specific molecular and cellular specializations. To explore genomic mechanisms that…”
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Iterative single-cell multi-omic integration using online learning by 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.

“…Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches…”
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Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex by 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.

“…The mammalian brain contains diverse neuronal types, yet we lack single-cell epigenomic assays that are able to identify and characterize them. DNA methylation…”
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Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain by Luo, Chongyuan, Lancaster, Madeline A., Castanon, Rosa, Nery, Joseph R., Knoblich, Juergen A., Ecker, Joseph R.

“…Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of the human brain, but whether they establish the…”
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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain by 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

“…Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate…”
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Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD by Gandal, Michael J., Haney, Jillian R., Wamsley, Brie, Yap, Chloe X., Parhami, Sepideh, Emani, Prashant S., Chang, Nathan, Chen, George T., Hoftman, Gil D., de Alba, Diego, Ramaswami, Gokul, Hartl, Christopher L., Bhattacharya, Arjun, Luo, Chongyuan, Jin, Ting, Wang, Daifeng, Kawaguchi, Riki, Quintero, Diana, Ou, Jing, Wu, Ye Emily, Parikshak, Neelroop N., Swarup, Vivek, Belgard, T. Grant, Gerstein, Mark, Pasaniuc, Bogdan, Geschwind, Daniel H.

“…Neuropsychiatric disorders classically lack defining brain pathologies, but recent work has demonstrated dysregulation at the molecular level, characterized by…”
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Robust single-cell DNA methylome profiling with snmC-seq2 by 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.

“…Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader…”
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Epigenomic landscapes of retinal rods and cones by 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

“…Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide…”
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Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons by 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

“…Direct reprogramming of fibroblasts to neurons induces widespread cellular and transcriptional reconfiguration. Here, we characterized global epigenomic…”
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Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production by Luo, Chongyuan, Sidote, David J, Zhang, Yi, Kerstetter, Randall A, Michael, Todd P, Lam, Eric

“…Genome‐wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the…”
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Spatiotemporal DNA methylome dynamics of the developing mouse fetus by 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.

“…Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited 1…”
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chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress by Widiez, Thomas, Symeonidi, Aikaterini, Luo, Chongyuan, Lam, Eric, Lawton, Michael, Rensing, Stefan A

“…The moss Physcomitrella patens is an important model organism for evo‐devo studies. Here, we determined the genome‐wide chromatin landscape of five important…”
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Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome by 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

“…Methylated cytosine is an effector of epigenetic gene regulation. In the brain, Dnmt3a is the sole 'writer' of atypical non-CpG methylation (mCH), and MeCP2 is…”
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Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3 by Li, Junhao, Pinto-Duarte, Antonio, Zander, Mark, Cuoco, Michael S, Lai, Chi-Yu, Osteen, Julia, Fang, Linjing, Luo, Chongyuan, Lucero, Jacinta D, Gomez-Castanon, Rosa, Nery, Joseph R, Silva-Garcia, Isai, Pang, Yan, Sejnowski, Terrence J, Powell, Susan B, Ecker, Joseph R, Mukamel, Eran A, Behrens, M Margarita

“…Two epigenetic pathways of transcriptional repression, DNA methylation and polycomb repressive complex 2 (PRC2), are known to regulate neuronal development and…”
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ANCORP: a high‐resolution approach that generates distinct chromatin state models from multiple genome‐wide datasets by Luo, Chongyuan, Lam, Eric

“…Summary Chromatin components can be extensively modified and dynamically regulated by a plethora of catalytic complexes. The numerous modifications may form a…”
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Exceptional epigenetics in the brain by Luo, Chongyuan, Ecker, Joseph R

“…Non-CG DNA methylation modulates gene expression in the adult brain Cytosine (C) methylation, or mC, is a modification of DNA that regulates gene expression in…”
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Quantitatively profiling genome-wide patterns of histone modifications in Arabidopsis thaliana using ChIP-seq by Luo, Chongyuan, Lam, Eric

“…Genome-wide quantitative profiling of chromatin modifications is a critical experimental approach to study epigenetic and transcriptional control mechanisms…”
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