4.5 Article

CTCF blocks antisense transcription initiation at divergent promoters

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

Kirsten A. Reimer et al.

Summary: The study revealed tight coordination between co-transcriptional splicing and transcription elongation and 3' end formation in mammalian cells, with splicing delays possibly taking place between the two catalytic steps. Additionally, inefficient 3' end cleavage was associated with intron retention, highlighting the functional coupling between these co-transcriptional processes.

MOLECULAR CELL (2021)

Article Biochemistry & Molecular Biology

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Naoki Kubo et al.

Summary: CTCF, together with the cohesin complex, drives chromatin loops and topologically associating domains formation. Acute loss of CTCF affects transcription of genes that display promoter-proximal CTCF binding and are dependent on long-distance enhancers. Promoter-proximal CTCF binding is correlated with transcription of over 2,000 genes across diverse adult tissues.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Cell Biology

Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

Jing Luan et al.

Summary: CTCF, a conserved zinc finger transcription factor implicated in genome organization and transcription regulation, displays variable resistance to degradation at different binding sites. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and co-occupancy with cohesin are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, providing insights into architectural CTCF functions.

CELL REPORTS (2021)

Article Biochemical Research Methods

4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

Peter H. L. Krijger et al.

METHODS (2020)

Article Biochemistry & Molecular Biology

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

Apoorva Baluapuri et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping

Judith Hyle et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

R-Loops Promote Antisense Transcription across the Mammalian Genome

Sue Mei Tan-Wong et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

Geert Geeven et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor

Andrew C. K. Wu et al.

MOLECULAR CELL (2018)

Article Biochemistry & Molecular Biology

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals

Yong Xue et al.

MOLECULAR CELL (2017)

Article Biochemistry & Molecular Biology

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Sarah C. Hsu et al.

MOLECULAR CELL (2017)

Article Multidisciplinary Sciences

Two independent modes of chromatin organization revealed by cohesin removal

Wibke Schwarzer et al.

NATURE (2017)

Article Multidisciplinary Sciences

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

Georg A. Busslinger et al.

NATURE (2017)

Article Biochemistry & Molecular Biology

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Caroline R. Bartman et al.

MOLECULAR CELL (2016)

Review Genetics & Heredity

The Determinants of Directionally in Transcriptional Initiation

Dia N. Bagchi et al.

TRENDS IN GENETICS (2016)

Article Cell Biology

Formation of Chromosomal Domains by Loop Extrusion

Geoffrey Fudenberg et al.

CELL REPORTS (2016)

Article Hematology

Functions of BET proteins in erythroid gene expression

Aaron J. Stonestrom et al.

Article Biochemistry & Molecular Biology

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

Benjamin S. Scruggs et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Human Promoters Are Intrinsically Directional

Sascha H. C. Duttke et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Sense and antisense transcription are associated with distinct chromatin architectures across genes

Struan C. Murray et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Adrian L. Sanborn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Genetics & Heredity

A unified architecture of transcriptional regulatory elements

Robin Andersson et al.

TRENDS IN GENETICS (2015)

Correction Biochemistry & Molecular Biology

A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription (vol 157, pg 1712, 2014)

Sebastian Marquardt et al.

Article Multidisciplinary Sciences

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

Jessica Zuin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

Genome engineering using the CRISPR-Cas9 system

F. Ann Ran et al.

NATURE PROTOCOLS (2013)

Article Multidisciplinary Sciences

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Hojoong Kwak et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Genome-wide structure and organization of eukaryotic pre-initiation complexes

Ho Sung Rhee et al.

NATURE (2012)

Article Multidisciplinary Sciences

A map of the cis-regulatory sequences in the mouse genome

Yin Shen et al.

NATURE (2012)

Article Multidisciplinary Sciences

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Elphege P. Nora et al.

NATURE (2012)

Article Biochemical Research Methods

Robust 4C-seq data analysis to screen for regulatory DNA interactions

Harmen J. G. van de Werken et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Gene Loops Enhance Transcriptional Directionality

Sue Mei Tan-Wong et al.

SCIENCE (2012)

Article Multidisciplinary Sciences

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

Sanjeev Shukla et al.

NATURE (2011)

Article Multidisciplinary Sciences

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

E. L. van Dijk et al.

NATURE (2011)

Article Multidisciplinary Sciences

Variability in gene expression underlies incomplete penetrance

Arjun Raj et al.

NATURE (2010)

Review Biochemistry & Molecular Biology

CTCF: Master Weaver of the Genome

Jennifer E. Phillips et al.

Review Cell Biology

Divergent transcription A new feature of active promoters

Amy C. Seila et al.

CELL CYCLE (2009)

Article Multidisciplinary Sciences

Bidirectional promoters generate pervasive transcription in yeast

Zhenyu Xu et al.

NATURE (2009)

Article Multidisciplinary Sciences

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

Chunhui Hou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Divergent Transcription from Active Promoters

Amy C. Seila et al.

SCIENCE (2008)

Article Multidisciplinary Sciences

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Pascal Preker et al.

SCIENCE (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Multidisciplinary Sciences

RNA maps reveal new RNA classes and a possible function for pervasive transcription

Philipp Kapranov et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

Stochastic mRNA synthesis in mammalian cells

Arjun Raj et al.

PLOS BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Transcriptional pulsing of a developmental gene

JR Chubb et al.

CURRENT BIOLOGY (2006)

Review Biochemistry & Molecular Biology

Non-coding RNA

JS Mattick et al.

HUMAN MOLECULAR GENETICS (2006)

Article Biochemistry & Molecular Biology

Real-time kinetics of gene activity in individual bacteria

I Golding et al.

Article Biochemistry & Molecular Biology

An abundance of bidirectional promoters in the human genome

ND Trinklein et al.

GENOME RESEARCH (2004)

Article Biotechnology & Applied Microbiology

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

BJ Peter et al.

GENOME BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Effect of varying the supercoiling of DNA on transcription and its regulation

HM Lim et al.

BIOCHEMISTRY (2003)