Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP
Published 2022 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP
Authors
Keywords
DANCE-MaP, ensemble deconvolution, noncoding RNA, transcriptional regulation, cancer, HIV
Journal
MOLECULAR CELL
Volume 82, Issue 9, Pages 1708-1723.e10
Publisher
Elsevier BV
Online
2022-03-23
DOI
10.1016/j.molcel.2022.02.009
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions
- (2021) Le Luo et al. JOURNAL OF MOLECULAR BIOLOGY
- Genome-scale deconvolution of RNA structure ensembles
- (2021) Edoardo Morandi et al. NATURE METHODS
- Interaction of 7SK with the Smn complex modulates snRNP production
- (2021) Changhe Ji et al. Nature Communications
- SHAPE Directed Discovery of New Functions in Large RNAs
- (2021) Kevin M. Weeks ACCOUNTS OF CHEMICAL RESEARCH
- The 7SK/P-TEFb snRNP controls ultraviolet radiation-induced transcriptional reprogramming
- (2021) Cécilia Studniarek et al. Cell Reports
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids
- (2021) Bei Liu et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Curing HIV: Seeking to Target and Clear Persistent Infection
- (2020) David M. Margolis et al. CELL
- Discovery of a High Affinity, Orally Bioavailable Macrocyclic FXIa Inhibitor with Antithrombotic Activity in Preclinical Species
- (2020) Wu Yang et al. JOURNAL OF MEDICINAL CHEMISTRY
- Determination of RNA structural diversity and its role in HIV-1 RNA splicing
- (2020) Phillip J. Tomezsko et al. NATURE
- DDX5 potentiates HIV-1 transcription as a co-factor of Tat
- (2020) Nyaradzai Sithole et al. Retrovirology
- Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA
- (2020) Jeffrey E. Ehrhardt et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Advances in RNA 3D Structure Modeling Using Experimental Data
- (2020) Bing Li et al. Frontiers in Genetics
- Rfam 14: expanded coverage of metagenomic, viral and microRNA families
- (2020) Ioanna Kalvari et al. NUCLEIC ACIDS RESEARCH
- DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples
- (2019) Laurence M. Shaw et al. Scientific Reports
- Entry of Polarized Effector Cells into Quiescence Forces HIV Latency
- (2019) Curtis Dobrowolski et al. mBio
- P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress
- (2019) Andrii Bugai et al. MOLECULAR CELL
- Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation
- (2019) Leighton Core et al. GENES & DEVELOPMENT
- Intrinsic checkpoint deficiency during cell cycle re-entry from quiescence
- (2019) Jacob Peter Matson et al. JOURNAL OF CELL BIOLOGY
- Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells
- (2019) Arnab Sengupta et al. PLOS BIOLOGY
- RNA base-pairing complexity in living cells visualized by correlated chemical probing
- (2019) Anthony M. Mustoe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- RNA Splicing by the Spliceosome
- (2019) Max E. Wilkinson et al. Annual Review of Biochemistry
- Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7
- (2018) Catherine D. Eichhorn et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping
- (2018) Siqi Tian et al. eLife
- Structural basis of 7SK RNA 5′-γ-phosphate methylation and retention by MePCE
- (2018) Yuan Yang et al. Nature Chemical Biology
- Pervasive tertiary structure in the dengue virus RNA genome
- (2018) Elizabeth A. Dethoff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Carbodiimide reagents for the chemical probing of RNA structure in cells
- (2018) Peter Y. Wang et al. RNA
- Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation
- (2017) Calla M Olson et al. Nature Chemical Biology
- Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy
- (2017) Sven Warhaut et al. NUCLEIC ACIDS RESEARCH
- Reconstitution of a functional 7SK snRNP
- (2017) John E. Brogie et al. NUCLEIC ACIDS RESEARCH
- Ribosome dynamics during decoding
- (2017) Marina V. Rodnina et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- RNA structure inference through chemical mapping after accidental or intentional mutations
- (2017) Clarence Y. Cheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Detailed secondary structure models of invertebrate 7SK RNAs
- (2017) Ali M. Yazbeck et al. RNA Biology
- Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2
- (2017) Steven Busan et al. RNA
- The Molecular Basis for Human Immunodeficiency Virus Latency
- (2017) Uri Mbonye et al. Annual Review of Virology
- Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV‐1 transcription and escape from latency
- (2016) Yang Zhao et al. EMBO REPORTS
- Molecular mechanisms of HIV latency
- (2016) Daniele C. Cary et al. JOURNAL OF CLINICAL INVESTIGATION
- Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma
- (2016) Justin L. Tan et al. MOLECULAR CELL
- A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs
- (2016) Elena Rivas et al. NATURE METHODS
- 7SK-BAF axis controls pervasive transcription at enhancers
- (2016) Ryan A Flynn et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb
- (2016) Alexandre J. C. Quaresma et al. NUCLEIC ACIDS RESEARCH
- Direct identification of base-paired RNA nucleotides by correlated chemical probing
- (2016) Andrey Krokhotin et al. RNA
- Latency reversal and viral clearance to cure HIV-1
- (2016) D. M. Margolis et al. SCIENCE
- 7SK-BAF axis controls pervasive transcription at enhancers
- (2016) Ryan A Flynn et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Detection of RNA–Protein Interactions in Living Cells with SHAPE
- (2015) Matthew J. Smola et al. BIOCHEMISTRY
- Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis
- (2015) Matthew J Smola et al. Nature Protocols
- The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones
- (2014) Thomas R. Cech et al. CELL
- Release of Positive Transcription Elongation Factor b (P-TEFb) from 7SK Small Nuclear Ribonucleoprotein (snRNP) Activates Hexamethylene Bisacetamide-inducible Protein (HEXIM1) Transcription
- (2014) Pingyang Liu et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Visualization of Positive Transcription Elongation Factor b (P-TEFb) Activation in Living Cells
- (2014) Koh Fujinaga et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Genetic Analysis of the Structure and Function of 7SK Small Nuclear Ribonucleoprotein (snRNP) in Cells
- (2014) Koh Fujinaga et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- RNA helicase DDX21 coordinates transcription and ribosomal RNA processing
- (2014) Eliezer Calo et al. NATURE
- RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
- (2014) Nathan A Siegfried et al. NATURE METHODS
- Single-molecule correlated chemical probing of RNA
- (2014) P. J. Homan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Contact inhibition and high cell density deactivate the mammalian target of rapamycin pathway, thus suppressing the senescence program
- (2014) O. V. Leontieva et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration
- (2014) Jinwei Zhang et al. STRUCTURE
- LARP7 suppresses P-TEFb activity to inhibit breast cancer progression and metastasis
- (2014) Xiaodan Ji et al. eLife
- SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase
- (2013) Xiong Ji et al. CELL
- Three-state mechanism couples ligand and temperature sensing in riboswitches
- (2013) Anke Reining et al. NATURE
- Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria
- (2013) Yang Fu et al. NUCLEIC ACIDS RESEARCH
- RNA elements directing in vivo assembly of the 7SK/MePCE/Larp7 transcriptional regulatory snRNP
- (2013) L. Muniz et al. NUCLEIC ACIDS RESEARCH
- Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
- (2013) C. E. Hajdin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells
- (2013) Gonçalo Castelo-Branco et al. GENOME BIOLOGY
- Bromodomain and Extra-terminal (BET) Bromodomain Inhibition Activate Transcription via Transient Release of Positive Transcription Elongation Factor b (P-TEFb) from 7SK Small Nuclear Ribonucleoprotein
- (2012) Koen Bartholomeeusen et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- LARP7 is a potential tumor suppressor gene in gastric cancer
- (2012) Yulan Cheng et al. LABORATORY INVESTIGATION
- Functional complexity and regulation through RNA dynamics
- (2012) Elizabeth A. Dethoff et al. NATURE
- 7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription
- (2011) B. Matija Peterlin et al. Wiley Interdisciplinary Reviews-RNA
- RNAstructure: software for RNA secondary structure prediction and analysis
- (2010) Jessica S Reuter et al. BMC BIOINFORMATICS
- Nuclear Organization and Dynamics of 7SK RNA in Regulating Gene Expression
- (2010) Kannanganattu V. Prasanth et al. MOLECULAR BIOLOGY OF THE CELL
- 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation
- (2010) S. Eilebrecht et al. NUCLEIC ACIDS RESEARCH
- HEXIM1 targets a repeated GAUC motif in the riboregulator of transcription 7SK and promotes base pair rearrangements
- (2010) Isabelle Lebars et al. NUCLEIC ACIDS RESEARCH
- The Mechanism of Release of P-TEFb and HEXIM1 from the 7SK snRNP by Viral and Cellular Activators Includes a Conformational Change in 7SK
- (2010) Brian J. Krueger et al. PLoS One
- Riboswitches and the RNA World
- (2010) R. R. Breaker Cold Spring Harbor Perspectives in Biology
- The Structural and Functional Diversity of Metabolite-Binding Riboswitches
- (2009) Adam Roth et al. Annual Review of Biochemistry
- The Centrality of RNA
- (2009) Phillip A. Sharp CELL
- Specificity of Hexim1 and Hexim2 Complex Formation with Cyclin T1/T2, Importin α and 7SK snRNA
- (2009) Nadine Czudnochowski et al. JOURNAL OF MOLECULAR BIOLOGY
- Evolution of 7SK RNA and Its Protein Partners in Metazoa
- (2009) M. Marz et al. MOLECULAR BIOLOGY AND EVOLUTION
- 7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development
- (2009) M. Barboric et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A stress-responsive RNA switch regulates VEGFA expression
- (2008) Partho Sarothi Ray et al. NATURE
- LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated
- (2008) B. J. Krueger et al. NUCLEIC ACIDS RESEARCH
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now