Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP

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