4.5 Review Book Chapter

An emerging role of chromatin-interacting RNA-binding proteins in transcription regulation

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

Danling Zhu et al.

MOLECULAR PLANT (2020)

Article Multidisciplinary Sciences

SPEN integrates transcriptional and epigenetic control of X-inactivation

Francois Dossin et al.

NATURE (2020)

Review Biochemistry & Molecular Biology

How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms

Meredith Corley et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

A large-scale binding and functional map of human RNA-binding proteins

Eric L. Van Nostrand et al.

NATURE (2020)

Review Multidisciplinary Sciences

Transcription factors and 3D genome conformation in cell-fate decisions

Ralph Stadhouders et al.

NATURE (2019)

Review Genetics & Heredity

Chromatin-associated RNAs as facilitators of functional genomic interactions

Xiao Li et al.

NATURE REVIEWS GENETICS (2019)

Article Multidisciplinary Sciences

CUT&Tag for efficient epigenomic profiling of small samples and single cells

Hatice S. Kaya-Okur et al.

NATURE COMMUNICATIONS (2019)

Review Biochemistry & Molecular Biology

Mechanisms of Interplay between Transcription Factors and the 3D Genome

Seungsoo Kim et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

Ricardo Saldana-Meyer et al.

MOLECULAR CELL (2019)

Review Genetics & Heredity

Nascent RNA analyses: tracking transcription and its regulation

Erin M. Wissink et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemistry & Molecular Biology

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

Jakob Trendel et al.

Article Biotechnology & Applied Microbiology

Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)

Rayner M. L. Queiroz et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes

Hui Fan et al.

GENOME RESEARCH (2018)

Article Biochemical Research Methods

Capturing the interactome of newly transcribed RNA

Xichen Bao et al.

NATURE METHODS (2018)

Article Multidisciplinary Sciences

Structure of paused transcription complex Pol II-DSIF-NELF

Seychelle M. Vos et al.

NATURE (2018)

Article Multidisciplinary Sciences

Structure of a pre-catalytic spliceosome

Clemens Plaschka et al.

NATURE (2017)

Article Biotechnology & Applied Microbiology

GRID-seq reveals the global RNA-chromatin interactome

Xiao Li et al.

NATURE BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

Abraham S. Weintraub et al.

Article Biotechnology & Applied Microbiology

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

Giulia Babbi et al.

BMC GENOMICS (2017)

Article Biochemistry & Molecular Biology

RNA Binding to CBP Stimulates Histone Acetylation and Transcription

Daniel A. Bose et al.

Review Biochemistry & Molecular Biology

On the Dependency of Cellular Protein Levels on mRNA Abundance

Yansheng Liu et al.

Review Biochemistry & Molecular Biology

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

Hannah K. Long et al.

Review Cell Biology

The new (dis)order in RNA regulation

Aino I. Jaervelin et al.

CELL COMMUNICATION AND SIGNALING (2016)

Article Biochemistry & Molecular Biology

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes

Kristopher W. Brannan et al.

MOLECULAR CELL (2016)

Article Biochemical Research Methods

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

Eric L. Van Nostrand et al.

NATURE METHODS (2016)

Review Multidisciplinary Sciences

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

Nick J. Proudfoot

SCIENCE (2016)

Review Genetics & Heredity

Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors

Muhammad A. Zabidi et al.

TRENDS IN GENETICS (2016)

Article Mathematical & Computational Biology

ATtRACT-a database of RNA-binding proteins and associated motifs

Girolamo Giudice et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)

Article Biotechnology & Applied Microbiology

Widespread RNA binding by chromatin-associated proteins

David G. Hendrickson et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Structural Snapshots of Actively Translating Human Ribosomes

Elmar Behrmann et al.

Article Multidisciplinary Sciences

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

Xiong Ji et al.

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

Article Multidisciplinary Sciences

Transcription factor trapping by RNA in gene regulatory elements

Alla A. Sigova et al.

SCIENCE (2015)

Review Biochemistry & Molecular Biology

Emerging Roles of Disordered Sequences in RNA-Binding Proteins

Sara Calabretta et al.

TRENDS IN BIOCHEMICAL SCIENCES (2015)

Article Cell Biology

Enhancer RNAs: A Class of Long Noncoding RNAs Synthesized at Enhancers

Tae-Kyung Kim et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)

Article Multidisciplinary Sciences

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

Benedikt M. Beckmann et al.

NATURE COMMUNICATIONS (2015)

Article Biochemistry & Molecular Biology

Regulatory Interactions between RNA and Polycomb Repressive Complex 2

Catherine Cifuentes-Rojas et al.

MOLECULAR CELL (2014)

Article Biochemistry & Molecular Biology

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

Jason A. West et al.

MOLECULAR CELL (2014)

Article Multidisciplinary Sciences

R-loops induce repressive chromatin marks over mammalian gene terminators

Konstantina Skourti-Stathaki et al.

NATURE (2014)

Review Genetics & Heredity

Context-dependent control of alternative splicing by RNA-binding proteins

Xiang-Dong Fu et al.

NATURE REVIEWS GENETICS (2014)

Review Genetics & Heredity

Coupling mRNA processing with transcription in time and space

David L. Bentley

NATURE REVIEWS GENETICS (2014)

Review Genetics & Heredity

A census of human RNA-binding proteins

Stefanie Gerstberger et al.

NATURE REVIEWS GENETICS (2014)

Review Cell Biology

A day in the life of the spliceosome

A. Gregory Matera et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

Article Mathematical & Computational Biology

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

Janos X. Binder et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2014)

Article Biotechnology & Applied Microbiology

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

Gilad Fuchs et al.

GENOME BIOLOGY (2014)

Review Biochemistry & Molecular Biology

The RNA polymerase II preinitiation complex Through what pathway is the complex assembled?

Donal S. Luse

TRANSCRIPTION-AUSTIN (2014)

Article Biochemistry & Molecular Biology

Circular Intronic Long Noncoding RNAs

Yang Zhang et al.

MOLECULAR CELL (2013)

Review Genetics & Heredity

RNA-binding proteins in Mendelian disease

Alfredo Castello et al.

TRENDS IN GENETICS (2013)

Article Biochemistry & Molecular Biology

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

Alfredo Castello et al.

Article Cell Biology

FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2

Jacob C. Schwartz et al.

GENES & DEVELOPMENT (2012)

Review Cell Biology

The RNA polymerase II CTD coordinates transcription and RNA processing

Jing-Ping Hsin et al.

GENES & DEVELOPMENT (2012)

Article Biochemistry & Molecular Biology

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

Alexander G. Baltz et al.

MOLECULAR CELL (2012)

Article Multidisciplinary Sciences

Landscape of transcription in human cells

Sarah Djebali et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

Karen Adelman et al.

NATURE REVIEWS GENETICS (2012)

Article Cell Biology

From Cis-Regulatory Elements to Complex RNPs and Back

Fatima Gebauer et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2012)

Review Cell Biology

Identification of RNA-protein interaction networks using PAR-CLIP

Manuel Ascano et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2012)

Article Biochemistry & Molecular Biology

Promoter Elements Regulate Cytoplasmic mRNA Decay

Almog Bregman et al.

Article Biochemistry & Molecular Biology

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Ho Sung Rhee et al.

Review Biochemistry & Molecular Biology

Molecular Mechanisms of Long Noncoding RNAs

Kevin C. Wang et al.

MOLECULAR CELL (2011)

Article Biochemistry & Molecular Biology

RBPDB: a database of RNA-binding specificities

Kate B. Cook et al.

NUCLEIC ACIDS RESEARCH (2011)

Review Cell Biology

Small RNA and transcriptional upregulation

Victoria Portnoy et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2011)

Article Biochemistry & Molecular Biology

c-Myc Regulates Transcriptional Pause Release

Peter B. Rahl et al.

Article Biochemistry & Molecular Biology

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

Julian Koenig et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Review Multidisciplinary Sciences

Defining mechanisms that regulate RNA polymerase II transcription in vivo

Nicholas J. Fuda et al.

NATURE (2009)

Review Genetics & Heredity

ChIP-seq: advantages and challenges of a maturing technology

Peter J. Park

NATURE REVIEWS GENETICS (2009)

Review Biochemistry & Molecular Biology

Structure and function of KH domains

Roberto Valverde et al.

FEBS JOURNAL (2008)

Article Multidisciplinary Sciences

Promoter-driven splicing regulation in fission yeast

Alberto Moldon et al.

NATURE (2008)

Review Cell Biology

A structural understanding of the dynamic ribosome machine

Thomas A. Steitz

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

The splicing factor SC35 has an active role in transcriptional elongation

Shengrong Lin et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2008)

Article Multidisciplinary Sciences

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Leighton J. Core et al.

SCIENCE (2008)

Review Genetics & Heredity

RNA-binding proteins in human genetic disease

Kiven E. Lukong et al.

TRENDS IN GENETICS (2008)

Review Cell Biology

RNA-binding proteins: modular design for efficient function

Bradley M. Lunde et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

Article Biochemical Research Methods

How repetitive are genomes?

Bernhard Haubold et al.

BMC BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells

Imke Listerman et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast

SA Lacadie et al.

MOLECULAR CELL (2005)

Article Biochemistry & Molecular Biology

Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex

J Görnemann et al.

MOLECULAR CELL (2005)

Article Biochemistry & Molecular Biology

Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II

H Meka et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II

SC Schroeder et al.

MOLECULAR CELL (2004)

Article Biochemistry & Molecular Biology

Newly initiated RNA encounters a factor involved in splicing immediately upon emerging from within RNA polymerase II

A Ujvári et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Zinc finger proteins: new insights into structural and functional diversity

JH Laity et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2001)