Search Results - "ECKER, R. R"

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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Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape by O’Malley, Ronan C., Huang, Shao-shan Carol, Song, Liang, Lewsey, Mathew G., Bartlett, Anna, Nery, Joseph R., Galli, Mary, Gallavotti, Andrea, Ecker, Joseph R.

“…The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific…”
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Non-CG Methylation in the Human Genome by He, Yupeng, Ecker, Joseph R

“…DNA methylation is a chemical modification that occurs predominantly on CG dinucleotides in mammalian genomes. However, recent studies have revealed that…”
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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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Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana by Sasaki, Eriko, Kawakatsu, Taiji, Ecker, Joseph R, Nordborg, Magnus

“…DNA cytosine methylation is an epigenetic mark associated with silencing of transposable elements (TEs) and heterochromatin formation. In plants, it occurs in…”
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Finding the fifth base: genome-wide sequencing of cytosine methylation by Lister, Ryan, Ecker, Joseph R

“…Complete sequences of myriad eukaryotic genomes, including several human genomes, are now available, and recent dramatic developments in DNA sequencing…”
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Dynamic DNA methylation reconfiguration during seed development and germination by Kawakatsu, Taiji, Nery, Joseph R, Castanon, Rosa, Ecker, Joseph R

“…Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene…”
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Integration of omic networks in a developmental atlas of maize by Walley, Justin W., Sartor, Ryan C., Shen, Zhouxin, Schmitz, Robert J., Wu, Kevin J., Urich, Mark A., Nery, Joseph R., Smith, Laurie G., Schnable, James C., Ecker, Joseph R., Briggs, Steven P.

“…Coexpression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting functional roles of individual genes at a system-wide…”
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Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism by Burko, Yogev, Seluzicki, Adam, Zander, Mark, Pedmale, Ullas V, Ecker, Joseph R, Chory, Joanne

“…The first exposure to light marks a crucial transition in plant development. This transition relies on the transcription factor HY5 controlling a complex…”
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Mapping genome-wide transcription-factor binding sites using DAP-seq by Bartlett, Anna, O'Malley, Ronan C, Huang, Shao-shan Carol, Galli, Mary, Nery, Joseph R, Gallavotti, Andrea, Ecker, Joseph R

“…This protocol describes DAP-seq, a transcription-factor binding site discovery assay that can be used to produce cistrome and epicistrome maps for any…”
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Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels by Salehin, Mohammad, Li, Baohua, Tang, Michelle, Katz, Ella, Song, Liang, Ecker, Joseph R., Kliebenstein, Daniel J., Estelle, Mark

“…A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions…”
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Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome by Vollmers, Christopher, Schmitz, Robert J., Nathanson, Jason, Yeo, Gene, Ecker, Joseph R., Panda, Satchidananda

“…In the mouse liver, circadian transcriptional rhythms are necessary for metabolic homeostasis. Whether dynamic epigenomic modifications are associated with…”
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Molecular Criteria for Defining the Naive Human Pluripotent State by Theunissen, Thorold W., Friedli, Marc, He, Yupeng, Planet, Evarist, O’Neil, Ryan C., Markoulaki, Styliani, Pontis, Julien, Wang, Haoyi, Iouranova, Alexandra, Imbeault, Michaël, Duc, Julien, Cohen, Malkiel A., Wert, Katherine J., Castanon, Rosa, Zhang, Zhuzhu, Huang, Yanmei, Nery, Joseph R., Drotar, Jesse, Lungjangwa, Tenzin, Trono, Didier, Ecker, Joseph R., Jaenisch, Rudolf

“…Recent studies have aimed to convert cultured human pluripotent cells to a naive state, but it remains unclear to what extent the resulting cells recapitulate…”
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Comprehensive analysis of single cell ATAC-seq data with SnapATAC by Fang, Rongxin, Preissl, Sebastian, Li, Yang, Hou, Xiaomeng, Lucero, Jacinta, Wang, Xinxin, Motamedi, Amir, Shiau, Andrew K., Zhou, Xinzhu, Xie, Fangming, Mukamel, Eran A., Zhang, Kai, Zhang, Yanxiao, Behrens, M. Margarita, Ecker, Joseph R., Ren, Bing

“…Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular…”
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The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas by Ecker, Joseph R., Geschwind, Daniel H., Kriegstein, Arnold R., Ngai, John, Osten, Pavel, Polioudakis, Damon, Regev, Aviv, Sestan, Nenad, Wickersham, Ian R., Zeng, Hongkui

“…A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of…”
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Environmental Surface Stability of the MAPbBr3 Single Crystal by Wang, Congcong, Ecker, Benjamin R, Wei, Haotong, Huang, Jinsong, Gao, Yongli

“…Organic–inorganic halide perovskites have emerged as a promising semiconductor family because of their remarkable performance in optoelectronic devices. On the…”
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High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell by Michael, Todd P., Jupe, Florian, Bemm, Felix, Motley, S. Timothy, Sandoval, Justin P., Lanz, Christa, Loudet, Olivier, Weigel, Detlef, Ecker, Joseph R.

“…The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench…”
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A transcription factor hierarchy defines an environmental stress response network by Song, Liang, Huang, Shao-shan Carol, Wise, Aaron, Castanon, Rosa, Nery, Joseph R., Chen, Huaming, Watanabe, Marina, Thomas, Jerushah, Bar-Joseph, Ziv, Ecker, Joseph R.

“…Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive transcription factor (TF)…”
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Chromatin architecture reorganization during stem cell differentiation by Dixon, Jesse R., Jung, Inkyung, Selvaraj, Siddarth, Shen, Yin, Antosiewicz-Bourget, Jessica E., Lee, Ah Young, Ye, Zhen, Kim, Audrey, Rajagopal, Nisha, Xie, Wei, Diao, Yarui, Liang, Jing, Zhao, Huimin, Lobanenkov, Victor V., Ecker, Joseph R., Thomson, James A., Ren, Bing

“…Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the…”
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MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing by Urich, Mark A, Nery, Joseph R, Lister, Ryan, Schmitz, Robert J, Ecker, Joseph R

“…This protocol describes how to prepare a sequencing library for MethylC-seq analysis, enabling the methylation status of cytosines in genomic DNA to be…”
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