Substoichiometric action of long noncoding RNAs

Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome

(2022) Joanna W. Jachowicz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long noncoding RNA NIHCOLE promotes ligation efficiency of DNA double-strand breaks in hepatocellular carcinoma

(2021) Juan P. Unfried et al.   CANCER RESEARCH

A phosphatidic acid-binding lncRNA SNHG9 facilitates LATS1 liquid–liquid phase separation to promote oncogenic YAP signaling

(2021) Rui-Hua Li et al.   CELL RESEARCH

Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses

(2021) Florian Geiger et al.   EMBO JOURNAL

NORAD-induced Pumilio phase separation is required for genome stability

(2021) Mahmoud M. Elguindy et al.   NATURE

Mechanistic dissection of increased enzymatic rate in a phase-separated compartment

(2021) William Peeples et al.   Nature Chemical Biology

Nuclear compartmentalization as a mechanism of quantitative control of gene expression

(2021) Prashant Bhat et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Long noncoding RNA and protein abundance in lncRNPs

(2021) Man Wu et al.   RNA

lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription

(2021) Man Wu et al.   SCIENCE

Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading

(2021) Lisa Rodermund et al.   SCIENCE

Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution

(2021) Guido Pacini et al.   Nature Communications

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Xist nucleates local protein gradients to propagate silencing across the X chromosome

(2021) Yolanda Markaki et al.   CELL

Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins

(2021) Lu Li et al.   GENES & DEVELOPMENT

RNA multimerization as an organizing force for liquid–liquid phase separation

(2021) Philip C. Bevilacqua et al.   RNA

SPEN is required for Xist upregulation during initiation of X chromosome inactivation

(2021) Teresa Robert-Finestra et al.   Nature Communications

Activation by substoichiometric inhibition

(2020) Melisa Merdanovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules

(2020) Peiguo Yang et al.   CELL

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation

(2020) Lukas Frank et al.   JOURNAL OF MOLECULAR BIOLOGY

Composition-dependent thermodynamics of intracellular phase separation

(2020) Joshua A. Riback et al.   NATURE

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

(2020) Zhenying Liu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment

(2020) David Colognori et al.   DEVELOPMENTAL CELL

CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies

(2020) Woonyung Hur et al.   DEVELOPMENTAL CELL

Progress toward understanding chromosome silencing by Xist RNA

(2020) Neil Brockdorff et al.   GENES & DEVELOPMENT

RNA contributions to the form and function of biomolecular condensates

(2020) Christine Roden et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A protein assembly mediates Xist localization and gene silencing

(2020) Amy Pandya-Jones et al.   NATURE

Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA

(2020) Chase A. Weidmann et al.   NATURE BIOTECHNOLOGY

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

(2020) Kaveh Daneshvar et al.   NATURE CELL BIOLOGY

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Gene regulation by long non-coding RNAs and its biological functions

(2020) Luisa Statello et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural modularity of the XIST ribonucleoprotein complex

(2020) Zhipeng Lu et al.   Nature Communications

Stochasticity of Biological Soft Matter: Emerging Concepts in Intrinsically Disordered Proteins and Biological Phase Separation

(2019) Konstantin K. Turoverov et al.   TRENDS IN BIOCHEMICAL SCIENCES

lncRNA-Induced Spread of Polycomb Controlled by Genome Architecture, RNA Abundance, and CpG Island DNA

(2019) Megan D. Schertzer et al.   MOLECULAR CELL

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis

(2019) Brian Reichholf et al.   MOLECULAR CELL

PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments

(2019) Chen-Yu Wang et al.   Nature Communications

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

Global analyses of the dynamics of mammalian microRNA metabolism

(2019) Elena Kingston et al.   GENOME RESEARCH

Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway

(2019) Tina Uroda et al.   MOLECULAR CELL

Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors

(2019) Fabio Pessina et al.   NATURE CELL BIOLOGY

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

(2019) David T. McSwiggen et al.   GENES & DEVELOPMENT

The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

(2019) Xiangru Huo et al.   MOLECULAR CELL

Different Heat Shock Proteins Bind α-Synuclein With Distinct Mechanisms and Synergistically Prevent Its Amyloid Aggregation

(2019) Chunyu Jia et al.   Frontiers in Neuroscience

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

(2018) Benjamin Kleaveland et al.   CELL

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

MicroRNA degradation by a conserved target RNA regulates animal behavior

(2018) Angelo Bitetti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

mRNA structure determines specificity of a polyQ-driven phase separation

(2018) Erin M. Langdon et al.   SCIENCE

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

(2018) Archa H. Fox et al.   TRENDS IN BIOCHEMICAL SCIENCES

MicroRNA degradation by a conserved target RNA regulates animal behavior

(2018) Angelo Bitetti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of microRNA function in animals

(2018) Luca F. R. Gebert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation

(2018) Francesco Ghini et al.   Nature Communications

Stress-Induced Low Complexity RNA Activates Physiological Amyloidogenesis

(2018) Miling Wang et al.   Cell Reports

Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds

(2018) Dan Bracha et al.   CELL

Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development

(2018) Matthias Reisser et al.   Nature Communications

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

(2017) Greta Pintacuda et al.   MOLECULAR CELL

An Argonaute phosphorylation cycle promotes microRNA-mediated silencing

(2017) Ryan J. Golden et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

(2017) Monika Piwecka et al.   SCIENCE

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

(2016) Sungyul Lee et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression

(2016) Rémy Denzler et al.   MOLECULAR CELL

High resolution atomic force microscopy of double-stranded RNA

(2016) Pablo Ares et al.   Nanoscale

Do nucleic acids moonlight as molecular chaperones?

(2016) Brianne E. Docter et al.   NUCLEIC ACIDS RESEARCH

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

(2016) Ailone Tichon et al.   Nature Communications

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells

(2015) Hongjae Sunwoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells

(2015) Asun Monfort et al.   Cell Reports

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

(2014) Rémy Denzler et al.   MOLECULAR CELL

Endogenous miRNA and Target Concentrations Determine Susceptibility to Potential ceRNA Competition

(2014) Andrew D. Bosson et al.   MOLECULAR CELL

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

(2014) Eliezer Calo et al.   NATURE

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

(2013) Matthew D. Simon et al.   NATURE

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA

(2010) D. Cazalla et al.   SCIENCE

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE