4.8 Article

The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors

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

Phase separation of RNA-binding protein promotes polymerase binding and transcription

Wen Shao et al.

Summary: A new study suggests that RNA-binding proteins constitute half of the chromatin proteome in embryonic stem cells, with some colocalizing with RNA polymerase II at promoters and enhancers. These RNA-binding proteins inhibit premature release of Pol II and enhance the formation of transcription condensates using RNA as multivalent molecules, ultimately promoting polymerase engagement and activity. The study proposes a synergistic interplay between promoter-associated RNAs and their binding proteins to facilitate active transcription through phase separation of polymerase condensates.

NATURE CHEMICAL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates

Ryanggeun Lee et al.

Summary: CTCF plays a crucial role in RNA polymerase II (Pol II)-mediated chromatin interactions at super-enhancers, forming spatial clusters. CTCF clustering is resistant to liquid-liquid phase separation and has a significant instructive function in the formation of transcriptional condensates. Furthermore, depletion and restoration of CTCF affect the dissolution and reinstatement of Pol II, BRD4, and MED1 clusters, indicating the importance of CTCF in higher-order chromatin organization.

NUCLEIC ACIDS RESEARCH (2022)

Article Cell Biology

RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex

Xinxin Wang et al.

Summary: This study identified a novel protein, RPAP2, which plays an important regulatory role in transcription initiation and DNA replication. RPAP2 inhibits the assembly of the pre-initiation complex (PIC) by preventing the interaction between Pol II and TFIIF, thereby limiting the transcription initiation of genes. Loss of RPAP2 leads to the accumulation of TFIIF and Pol II at the promoter regions, affecting gene expression.

CELL REPORTS (2022)

Article Biochemistry & Molecular Biology

HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

Bidossessi Wilfried Hounkpe et al.

Summary: Housekeeping (HK) genes are crucial for maintaining basic cellular functions and the HRT Atlas database offers a more accurate and comprehensive resource for human and mouse HK genes and transcripts, addressing previous limitations in their identification. The database, generated from extensive RNA-seq data sets, also provides candidate reference transcripts for normalization of qPCR experiments and insights into gene expression modifiers.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

RNA-Mediated Feedback Control of Transcriptional Condensates

Jonathan E. Henninger et al.

Summary: This study discusses the mechanisms of feedback control in regulating biological processes, especially in transcription regulation. Research indicates that RNA in transcription initiation promotes condensate formation, while RNA produced during elongation stimulates condensate dissolution. Therefore, transcriptional regulation involves a feedback mechanism where transcribed RNA both stimulates and arrests the process.
Article Biochemistry & Molecular Biology

1,6-Hexanediol, commonly used to dissolve liquid-liquid phase separated condensates, directly impairs kinase and phosphatase activities

Robert Duester et al.

Summary: The widespread use of 1,6-hexanediol in phase separation studies may have significant effects on the activities of various enzymes, particularly kinases and phosphatases. This highlights the need for a reevaluation of the use of 1,6-hexanediol in research studies.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

Article Multidisciplinary Sciences

Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription

Linyu Zuo et al.

Summary: FUS/EWS/TAF15 (FET) fusion oncoproteins, containing low complexity domain, form biomolecular condensates that recruit RNA polymerase II, promoting gene transcription. Through the development of a single-molecule assay, a causal relationship between the formation of condensates on DNA and gene transcription is supported, along with the identification of a threshold number of fusion-binding DNA elements required for the formation of FET protein condensates.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Structural insights into preinitiation complex assembly on core promoters

Xizi Chen et al.

Summary: This study elucidates the assembly mechanism of human TFIID-based PIC, showing two tracks for modular reorganization and direct promoter deposition, converging at a holo PIC with around 50 subunits. TFIID stabilizes PIC organization and supports CAK-mediated phosphorylation of Pol II.

SCIENCE (2021)

Article Multidisciplinary Sciences

Structures of the human Mediator and Mediator-bound preinitiation complex

Xizi Chen et al.

Summary: This study investigates the mechanisms of TFIID and Mediator proteins in regulating transcription initiation and RNA polymerase activity, revealing their interactions and mutual regulation through structural analysis, as well as the phosphorylation process of Pol II CTD by CDK7.

SCIENCE (2021)

Article Multidisciplinary Sciences

Regulation of biomolecular condensates by interfacial protein clusters

Andrew W. Folkmann et al.

Summary: This study reveals that the dynamics of biomolecular condensates are regulated by protein clusters. Through experiments and theory, it is demonstrated that the assembly of P granules is controlled by MEG-3 protein, which helps lower surface tension and slow down coarsening.

SCIENCE (2021)

Article Multidisciplinary Sciences

Single-molecule Imaging of EWS-FLI1 Condensates Assembling on DNA

Linyu Zuo et al.

Summary: The article discusses the importance of fusion genes in tumors, as well as the mechanism of action of the EWS-FLI1 fusion gene in Ewing sarcoma, including the formation of biomolecular condensates to enhance gene transcription. The DNA Curtains method can be used to visualize the assembly process of EWS-FLI1 condensates.

JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2021)

Article Multidisciplinary Sciences

HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells

Haiyang Yu et al.

Summary: This study found that the RNA binding protein TDP-43 forms intranuclear or cytoplasmic aggregates in age-related neurodegenerative diseases. Through mathematical modeling, the primary components of TDP-43 liquid core were identified to be HSP70 family chaperones, and these structures converted to aggregates when ATP levels were reduced.

SCIENCE (2021)

Article Biochemistry & Molecular Biology

Guided nuclear exploration increases CTCF target search efficiency

Anders S. Hansen et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

Shaon Basu et al.

Article Cell Biology

Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals

Dapeng Ju et al.

SCIENCE TRANSLATIONAL MEDICINE (2020)

Article Biochemistry & Molecular Biology

Gene-Specific Control of tRNA Expression by RNA Polymerase II

Alan Gerber et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering

Mian Wei et al.

SCIENCE ADVANCES (2020)

Article Biochemistry & Molecular Biology

Hsp27 chaperones FUS phase separation under the modulation of stress-induced phosphorylation

Zhenying Liu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Review Cell Biology

Liquid-like interactions in heterochromatin: Implications for mechanism and regulation

Serena Sanulli et al.

CURRENT OPINION IN CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

MeCP2 links heterochromatin condensates and neurodevelopmental disease

Charles H. Li et al.

NATURE (2020)

Article Multidisciplinary Sciences

Hsp40 proteins phase separate to chaperone the assembly and maintenance of membraneless organelles

Jinge Gu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biotechnology & Applied Microbiology

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III

Yongpeng Jiang et al.

GENOME BIOLOGY (2020)

Review Multidisciplinary Sciences

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

Ralph Stadhouders et al.

NATURE (2019)

Article Genetics & Heredity

Liquid–Liquid Phase Separation in Disease

Simon Alberti et al.

Annual Review of Genetics (2019)

Review Multidisciplinary Sciences

Organization and regulation of gene transcription

Patrick Cramer

NATURE (2019)

Article Biochemistry & Molecular Biology

CB-6644 Is a Selective Inhibitor of the RUVBL1/2 Complex with Anticancer Activity

Victoria A. Assimon et al.

ACS CHEMICAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

GENCODE reference annotation for the human and mouse genomes

Adam Frankish et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase

Shinichiro Akichika et al.

SCIENCE (2019)

Review Biochemistry & Molecular Biology

A Solid-State Conceptualization of Information Transfer from Gene to Message to Protein

Masato Kato et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 87 (2018)

Article Multidisciplinary Sciences

Coactivator condensation at super-enhancers links phase separation and gene control

Benjamin R. Sabari et al.

SCIENCE (2018)

Article Biochemistry & Molecular Biology

RNA polymerase II clustering through carboxy-terminal domain phase separation

Marc Boehning et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Multidisciplinary Sciences

Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma

Otilia Menyhart et al.

ROYAL SOCIETY OPEN SCIENCE (2018)

Article Biochemistry & Molecular Biology

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

Shenglin Mei et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Cell Biology

Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones

Anna Malinova et al.

JOURNAL OF CELL BIOLOGY (2017)

Review Cell Biology

Biomolecular condensates: organizers of cellular biochemistry

Salman F. Banani et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

Zefang Tang et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

ATP as a biological hydrotrope

Avinash Patel et al.

SCIENCE (2017)

Review Multidisciplinary Sciences

Liquid phase condensation in cell physiology and disease

Yongdae Shin et al.

SCIENCE (2017)

Review Biochemistry & Molecular Biology

The Role of Pontin and Reptin in Cellular Physiology and Cancer Etiology

Yu-Qian Mao et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2017)

Review Physics, Applied

Visualizing biological reaction intermediates with DNA curtains

Yiling Zhao et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2017)

Review Biochemistry & Molecular Biology

A Phase Separation Model for Transcriptional Control

Denes Hnisz et al.

Article Chemistry, Multidisciplinary

Study of RNA Polymerase II Clustering inside Live-Cell Nuclei Using Bayesian Nanoscopy

Xuanze Chen et al.

ACS NANO (2016)

Article Biochemistry & Molecular Biology

Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR

Andrey Damianov et al.

Review Biochemistry & Molecular Biology

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

Denes Hnisz et al.

Article Biochemical Research Methods

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

Dig Bijay Mahat et al.

NATURE PROTOCOLS (2016)

Article Biochemistry & Molecular Biology

smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability

Nikolay Tsanov et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Sambamba: fast processing of NGS alignment formats

Artem Tarasov et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Pontin, a new mutant p53-binding protein, promotes gain-of-function of mutant p53

Y. Zhao et al.

CELL DEATH AND DIFFERENTIATION (2015)

Article Biochemistry & Molecular Biology

RuvbL1 and RuvbL2 enhance aggresome formation and disaggregate amyloid fibrils

Nava Zaarur et al.

EMBO JOURNAL (2015)

Article Biochemistry & Molecular Biology

Yeast Rvb1 and Rvb2 Proteins Oligomerize As a Conformationally Variable Dodecamer with Low Frequency

Ajitha Jeganathan et al.

JOURNAL OF MOLECULAR BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

Yuan Lin et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins

Jonathan Bizarro et al.

NUCLEIC ACIDS RESEARCH (2015)

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

Recruitment of Pontin/Reptin by E2f1 amplifies E2f transcriptional response during cancer progression

Amy Tarangelo et al.

NATURE COMMUNICATIONS (2015)

Article Biochemistry & Molecular Biology

TELP, a sensitive and versatile library construction method for next-generation sequencing

Xu Peng et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

CrossMap: a versatile tool for coordinate conversion between genome assemblies

Hao Zhao et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

Berenice A. Benayoun et al.

Article Cell Biology

RuvB-like ATPases Function in Chromatin Decondensation at the End of Mitosis

Adriana Magalska et al.

DEVELOPMENTAL CELL (2014)

Article Biochemistry & Molecular Biology

Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit

Murat A. Cevher et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Article Biochemistry & Molecular Biology

deepTools: a flexible platform for exploring deep-sequencing data

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

Shihao Shen 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

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Warren A. Whyte et al.

Article Biochemistry & Molecular Biology

Super-Enhancers in the Control of Cell Identity and Disease

Denes Hnisz et al.

Article Biochemistry & Molecular Biology

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

Jessica A. Hurt et al.

GENOME RESEARCH (2013)

Editorial Material Genetics & Heredity

The Genotype-Tissue Expression (GTEx) project

John Lonsdale et al.

NATURE GENETICS (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

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

Ibrahim I. Cisse et al.

SCIENCE (2013)

Article Biochemistry & Molecular Biology

The Emergence of the Conserved AAA plus ATPases Pontin and Reptin on the Signaling Landscape

Jean Rosenbaum et al.

SCIENCE SIGNALING (2013)

Article Biochemical Research Methods

RSeQC: quality control of RNA-seq experiments

Liguo Wang et al.

BIOINFORMATICS (2012)

Review Cell Biology

Transcription factories: genetic programming in three dimensions

Lucas Brandon Edelman et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2012)

Article Biochemical Research Methods

Rational design of true monomeric and bright photoactivatable fluorescent proteins

Mingshu Zhang et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Conformational transitions regulate the exposure of a DNA-binding domain in the RuvBL1-RuvBL2 complex

Andres Lopez-Perrote et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Statistics & Probability

MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS

Qunhua Li et al.

ANNALS OF APPLIED STATISTICS (2011)

Article Biochemical Research Methods

FIMO: scanning for occurrences of a given motif

Charles E. Grant et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

John H. Morris et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Review Biochemistry & Molecular Biology

Hallmarks of Cancer: The Next Generation

Douglas Hanahan et al.

Letter Biotechnology & Applied Microbiology

Integrative genomics viewer

James T. Robinson et al.

NATURE BIOTECHNOLOGY (2011)

Article Biochemical Research Methods

The proteomes of transcription factories containing RNA polymerases I, II or III

Svitlana Melnik et al.

NATURE METHODS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Review Biochemistry & Molecular Biology

A Model for all Genomes: The Role of Transcription Factories

Peter R. Cook

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

HSP90 and Its R2TP/Prefoldin-like Cochaperone Are Involved in the Cytoplasmic Assembly of RNA Polymerase II

Severine Boulon et al.

MOLECULAR CELL (2010)

Article Biochemistry & Molecular Biology

AAA plus Proteins RUVBL1 and RUVBL2 Coordinate PIKK Activity and Function in Nonsense-Mediated mRNA Decay

Natsuko Izumi et al.

SCIENCE SIGNALING (2010)

Review Biochemistry & Molecular Biology

RVB1/RVB2: Running Rings around Molecular Biology

Sudhakar Jha et al.

MOLECULAR CELL (2009)

Review Genetics & Heredity

Transcription factories: gene expression in unions?

Heidi Sutherland et al.

NATURE REVIEWS GENETICS (2009)

Review Oncology

Pontin and Reptin, two related ATPases with multiple roles in cancer

Otmar Huber et al.

CANCER RESEARCH (2008)

Article Biochemistry & Molecular Biology

Identification of ATPases pontin and reptin as telomerase components essential for holoenzyme assembly

Andrew S. Venteicher et al.

Article Biochemistry & Molecular Biology

Dynamic regulation of nucleosome positioning in the human genome

Dustin E. Schones et al.

Article Biochemical Research Methods

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

Arnauld Serge et al.

NATURE METHODS (2008)

Article Biochemical Research Methods

Highly inclined thin illumination enables clear single-molecule imaging in cells

Makio Tokunaga et al.

NATURE METHODS (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo

Marc A. Schwabish et al.

MOLECULAR AND CELLULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

In vivo dynamics of RNA polymerase II transcription

Xavier Darzacq et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

SR proteins function in coupling RNAP II transcription to pre-mRNA splicing

Rita Das et al.

MOLECULAR CELL (2007)

Review Cell Biology

Control of transcription by pontin and reptin

Peter Gallant

TRENDS IN CELL BIOLOGY (2007)

Article Multidisciplinary Sciences

Myc interacts genetically with Tip48/Reptin and Tip49/Pontin to control growth and proliferation during Drosophila development

P Bellosta et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

From silencing to gene expression: Real-time analysis in single cells

SM Janicki et al.

Article Biochemistry & Molecular Biology

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

A Sandelin et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

Pontin52 and Reptin52 function as antagonistic regulators of β-catenin signalling activity

A Bauer et al.

EMBO JOURNAL (2000)

Article Biochemistry & Molecular Biology

An ATPase/helicase complex is an essential cofactor for oncogenic transformation by c-Myc

MA Wood et al.

MOLECULAR CELL (2000)