Search Results - "Ecker, Joseph 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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis by Zhang, Xiaoyu, Yazaki, Junshi, Sundaresan, Ambika, Cokus, Shawn, Chan, Simon W.-L., Chen, Huaming, Henderson, Ian R., Shinn, Paul, Pellegrini, Matteo, Jacobsen, Steve E., Ecker, Joseph R.

“…Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification…”
Get full text

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…”
Get full text

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)…”
Get full text

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light by Pedmale, Ullas V., Huang, Shao-shan Carol, Zander, Mark, Cole, Benjamin J., Hetzel, Jonathan, Ljung, Karin, Reis, Pedro A.B., Sridevi, Priya, Nito, Kazumasa, Nery, Joseph R., Ecker, Joseph R., Chory, Joanne

“…Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs)…”
Get full text

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…”
Get full text