Distinct properties and functions of CTCF revealed by a rapidly inducible degron system
出版年份 2021 全文链接
标题
Distinct properties and functions of CTCF revealed by a rapidly inducible degron system
作者
关键词
CTCF, cohesin, degradation dynamics, chromatin architecture, transcription elongation stalling, residence time, PRO-seq, single-molecule tracking
出版物
Cell Reports
Volume 34, Issue 8, Pages 108783
出版商
Elsevier BV
发表日期
2021-02-24
DOI
10.1016/j.celrep.2021.108783
参考文献
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data
- (2020) Guanjue Xiang et al. NUCLEIC ACIDS RESEARCH
- Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
- (2020) Amanda Khoury et al. Nature Communications
- Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers
- (2020) Michiel J. Thiecke et al. Cell Reports
- Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping
- (2019) Judith Hyle et al. NUCLEIC ACIDS RESEARCH
- Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription
- (2019) Vivek Behera et al. Cell Reports
- The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse
- (2019) Lucas J.T. Kaaij et al. CELL
- RNA Interactions Are Essential for CTCF-Mediated Genome Organization
- (2019) Ricardo Saldaña-Meyer et al. MOLECULAR CELL
- cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression
- (2019) Jason A. Watts et al. AMERICAN JOURNAL OF HUMAN GENETICS
- Chromatin structure dynamics during the mitosis-to-G1 phase transition
- (2019) Haoyue Zhang et al. NATURE
- Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos
- (2018) Bin Gu et al. NATURE BIOTECHNOLOGY
- Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility
- (2018) Vivek Behera et al. Nature Communications
- Transcription Elongation Can Affect Genome 3D Structure
- (2018) Sven Heinz et al. CELL
- Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers
- (2018) Jacob M. Tome et al. NATURE GENETICS
- TrackMate: An open and extensible platform for single-particle tracking
- (2017) Jean-Yves Tinevez et al. METHODS
- R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters
- (2017) Liang Chen et al. MOLECULAR CELL
- Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl
- (2017) Georg A. Busslinger et al. NATURE
- CDK9-dependent RNA polymerase II pausing controls transcription initiation
- (2017) Saskia Gressel et al. eLife
- CTCF and cohesin regulate chromatin loop stability with distinct dynamics
- (2017) Anders S Hansen et al. eLife
- CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals
- (2017) Mariana Ruiz-Velasco et al. Cell Systems
- CTCF: making the right connections
- (2016) Rodolfo Ghirlando et al. GENES & DEVELOPMENT
- Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation
- (2016) Dig B. Mahat et al. MOLECULAR CELL
- Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)
- (2016) Dig Bijay Mahat et al. Nature Protocols
- Formation of Chromosomal Domains by Loop Extrusion
- (2016) Geoffrey Fudenberg et al. Cell Reports
- Synthesis of a Far-Red Photoactivatable Silicon-Containing Rhodamine for Super-Resolution Microscopy
- (2015) Jonathan B. Grimm et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Functions of BET proteins in erythroid gene expression
- (2015) Aaron J. Stonestrom et al. BLOOD
- Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
- (2015) Andreas Mayer et al. CELL
- A general method to improve fluorophores for live-cell and single-molecule microscopy
- (2015) Jonathan B Grimm et al. NATURE METHODS
- Identification of active transcriptional regulatory elements from GRO-seq data
- (2015) Charles G Danko et al. NATURE METHODS
- Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I
- (2015) Rodrigo Peña-Hernández et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
- (2015) Adrian L. Sanborn et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A review of progress in single particle tracking: from methods to biophysical insights
- (2015) Carlo Manzo et al. REPORTS ON PROGRESS IN PHYSICS
- Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe
- (2014) Takeshi Mizuguchi et al. NATURE
- CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
- (2013) R. N. Plasschaert et al. NUCLEIC ACIDS RESEARCH
- Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
- (2013) J. Zuin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
- (2013) H. Kwak et al. SCIENCE
- An expanded tool kit for the auxin-inducible degron system in budding yeast
- (2013) Magdalena Morawska et al. YEAST
- A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
- (2013) Hirotaka Nakahashi et al. Cell Reports
- Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index
- (2012) Sur Herrera Paredes et al. BIOINFORMATICS
- Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
- (2012) Tom Sexton et al. CELL
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Spatial partitioning of the regulatory landscape of the X-inactivation centre
- (2012) Elphège P. Nora et al. NATURE
- NIH Image to ImageJ: 25 years of image analysis
- (2012) Caroline A Schneider et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- A benchmark for chromatin binding measurements in live cells
- (2012) Davide Mazza et al. NUCLEIC ACIDS RESEARCH
- CHANCE: comprehensive software for quality control and validation of ChIP-seq data
- (2012) Aaron Diaz et al. GENOME BIOLOGY
- MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
- (2012) Zhen Shao et al. GENOME BIOLOGY
- ViennaRNA Package 2.0
- (2011) Ronny Lorenz et al. Algorithms for Molecular Biology
- MEME-ChIP: motif analysis of large DNA datasets
- (2011) Philip Machanick et al. BIOINFORMATICS
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- FLASH: fast length adjustment of short reads to improve genome assemblies
- (2011) T. Magoc et al. BIOINFORMATICS
- Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
- (2011) Ho Sung Rhee et al. CELL
- Dynamic long-range chromatin interactions controlMybproto-oncogene transcription during erythroid development
- (2011) Ralph Stadhouders et al. EMBO JOURNAL
- Mechanism of Glycyrrhizic Acid Inhibition of Kaposi's Sarcoma-Associated Herpesvirus: Disruption of CTCF-Cohesin-Mediated RNA Polymerase II Pausing and Sister Chromatid Cohesion
- (2011) H. Kang et al. JOURNAL OF VIROLOGY
- Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability
- (2011) Hannah E. Mischo et al. MOLECULAR CELL
- Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination
- (2011) Konstantina Skourti-Stathaki et al. MOLECULAR CELL
- CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
- (2011) Sanjeev Shukla et al. NATURE
- Fast and accurate long-read alignment with Burrows–Wheeler transform
- (2010) Heng Li et al. BIOINFORMATICS
- High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
- (2010) A. P. Boyle et al. GENOME RESEARCH
- Mechanisms and implications of transcription blockage by guanine-rich DNA sequences
- (2010) B. P. Belotserkovskii et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- CTCF: Master Weaver of the Genome
- (2009) Jennifer E. Phillips et al. CELL
- An auxin-based degron system for the rapid depletion of proteins in nonplant cells
- (2009) Kohei Nishimura et al. NATURE METHODS
- Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms
- (2008) Vania Parelho et al. CELL
- Cohesin mediates transcriptional insulation by CCCTC-binding factor
- (2008) Kerstin S. Wendt et al. NATURE
- Highly inclined thin illumination enables clear single-molecule imaging in cells
- (2008) Makio Tokunaga et al. NATURE METHODS
- CTCF physically links cohesin to chromatin
- (2008) E. D. Rubio et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Divergent Transcription from Active Promoters
- (2008) Amy C. Seila et al. SCIENCE
- Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
- (2008) Leighton J. Core et al. SCIENCE
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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