LncRNAs: Architectural Scaffolds or More Potential Roles in Phase Separation

Phase separation of the C. elegans Polycomb protein SOP-2 is modulated by RNA and sumoylation

(2020) Wenyan Qu et al.   Protein & Cell

The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability

(2019) Nicole Bettin et al.   Cells

Phase Separation, Transition, and Autophagic Degradation of Proteins in Development and Pathogenesis

(2019) Zheng Wang et al.   TRENDS IN CELL BIOLOGY

RNA Binding Antagonizes Neurotoxic Phase Transitions of TDP-43

(2019) Jacob R. Mann et al.   NEURON

Cytoplasmic TDP-43 De-mixing Independent of Stress Granules Drives Inhibition of Nuclear Import, Loss of Nuclear TDP-43, and Cell Death

(2019) Fatima Gasset-Rosa et al.   NEURON

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

(2019) Sreejith J. Nair et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality

(2019) Sethuramasundaram Pitchiaya et al.   MOLECULAR CELL

Phase separation drives X-chromosome inactivation: a hypothesis

(2019) Andrea Cerase et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Clustered telomeres in phase-separated nuclear condensates engage mitotic DNA synthesis through BLM and RAD52

(2019) Jaewon Min et al.   GENES & DEVELOPMENT

Developmental dynamics of lncRNAs across mammalian organs and species

(2019) Ioannis Sarropoulos et al.   NATURE

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression

(2019) Qingsong Hu et al.   NATURE IMMUNOLOGY

Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly

(2019) Xinrui Gui et al.   Nature Communications

Two distinct nuclear stress bodies containing different sets of RNA-binding proteins are formed with HSATIII architectural noncoding RNAs upon thermal stress exposure

(2019) Mahmoud Khamis Aly et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

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

Long non-coding RNAs and endometrial cancer

(2019) Hongyang Liu et al.   BIOMEDICINE & PHARMACOTHERAPY

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Interplay between ubiquitylation and SUMOylation: Empowered by phase separation

(2019) Jianping Jin   JOURNAL OF BIOLOGICAL CHEMISTRY

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

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression

(2019) Danfeng Cai et al.   NATURE CELL BIOLOGY

Chromosome-associated RNA–protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe

(2019) Da-Qiao Ding et al.   Nature Communications

FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions

(2018) Seema Qamar et al.   CELL

Tau protein liquid–liquid phase separation can initiate tau aggregation

(2018) Susanne Wegmann et al.   EMBO JOURNAL

Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior

(2018) Titus Franzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Role of RNA in Biological Phase Separations

(2018) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

RGG/RG Motif Regions in RNA Binding and Phase Separation

(2018) P. Andrew Chong et al.   JOURNAL OF MOLECULAR BIOLOGY

Ubiquitin Modulates Liquid-Liquid Phase Separation of UBQLN2 via Disruption of Multivalent Interactions

(2018) Thuy P. Dao et al.   MOLECULAR CELL

Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation

(2018) Veronica H. Ryan et al.   MOLECULAR CELL

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

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Paraspeckle factor turns TGF-β1 pro-metastatic

(2018) Fernando Salvador et al.   NATURE CELL BIOLOGY

A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer

(2018) Gabrijela Dumbović et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Shovamayee Maharana et al.   SCIENCE

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

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

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

TERRA recruitment of polycomb to telomeres is essential for histone trymethylation marks at telomeric heterochromatin

(2018) Juan J. Montero et al.   Nature Communications

The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2

(2018) Philipp Neumann et al.   Nature Communications

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

mTOR Regulates Phase Separation of PGL Granules to Modulate Their Autophagic Degradation

(2018) Gangming Zhang et al.   CELL

LncRNA CamK-A Regulates Ca2+-Signaling-Mediated Tumor Microenvironment Remodeling

(2018) Ling-jie Sang et al.   MOLECULAR CELL

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

(2018) Mathias Munschauer et al.   NATURE

A mitochondria–paraspeckle crosstalk

(2018) Archa H. Fox   NATURE CELL BIOLOGY

Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria

(2018) Yang Wang et al.   NATURE CELL BIOLOGY

Stress-Induced Low Complexity RNA Activates Physiological Amyloidogenesis

(2018) Miling Wang et al.   Cell Reports

CARM1 and Paraspeckles Regulate Pre-implantation Mouse Embryo Development

(2018) Anna Hupalowska et al.   CELL

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival

(2018) Karen Yap et al.   MOLECULAR CELL

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

(2017) Jin-Zhou Huang et al.   MOLECULAR CELL

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

A ROR1–HER3–lncRNA signalling axis modulates the Hippo–YAP pathway to regulate bone metastasis

(2017) Chunlai Li et al.   NATURE CELL BIOLOGY

The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors

(2017) Aifu Lin et al.   NATURE CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

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

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Direct observation of structure and dynamics during phase separation of an elastomeric protein

(2017) Sean E. Reichheld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies

(2016) Takeshi Chujo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Long Noncoding RNAs in Cancer Pathways

(2016) Adam M. Schmitt et al.   CANCER CELL

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

(2016) Sungyul Lee et al.   CELL

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

Mechanisms of long noncoding RNA function in development and disease

(2016) Sandra U. Schmitz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Liquid–liquid phase separation in cellular signaling systems

(2016) P Andrew Chong et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

(2016) Jason A. West et al.   JOURNAL OF CELL BIOLOGY

Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins

(2016) Huang Wu et al.   MOLECULAR CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

The LINK-A lncRNA activates normoxic HIF1α signalling in triple-negative breast cancer

(2016) Aifu Lin et al.   NATURE CELL BIOLOGY

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches

(2016) Julia Beermann et al.   PHYSIOLOGICAL REVIEWS

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain

(2016) Alexander E. Conicella et al.   STRUCTURE

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

(2016) Ailone Tichon et al.   Nature Communications

Circadian RNA expression elicited by 3’-UTR IRAlu-paraspeckle associated elements

(2016) Manon Torres et al.   eLife

Distinct stages in stress granule assembly and disassembly

(2016) Joshua R Wheeler et al.   eLife

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

(2015) Evangelos Pefanis et al.   CELL

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

(2015) Yanying Wang et al.   Cell Stem Cell

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

(2015) Sven Hennig et al.   JOURNAL OF CELL BIOLOGY

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function

(2015) Tetsuro Murakami et al.   NEURON

RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene

(2015) Lilach Pnueli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing

(2015) Benoit Moindrot et al.   Cell Reports

Liquid-Liquid Phase Separation in Biology

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

lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals

(2014) Zhen Xing et al.   CELL

Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex

(2014) Zhijie Liu et al.   CELL

The ways of action of long non-coding RNAs in cytoplasm and nucleus

(2014) Kun Zhang et al.   GENE

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

(2014) Katsutoshi Imamura et al.   MOLECULAR CELL

RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells

(2014) Rajika Arora et al.   Nature Communications

Meiotic long non-coding meiRNA accumulates as a dot at its genetic locus facilitated by Mmi1 and plays as a decoy to lure Mmi1

(2014) Y. Shichino et al.   Open Biology

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

(2013) Per Johnsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Regulation of Telomere Length by G-Quadruplex Telomere DNA- and TERRA-Binding Protein TLS/FUS

(2013) Kentaro Takahama et al.   CHEMISTRY & BIOLOGY

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

(2013) Tetsuro Hirose et al.   MOLECULAR BIOLOGY OF THE CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS

(2013) Hong Joo Kim et al.   NATURE

The long non-coding RNA nuclear-enriched abundant transcript 1_2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis

(2013) Yoshinori Nishimoto et al.   Molecular Brain

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

Cis-acting noncoding RNAs: friends and foes

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Nucleation of nuclear bodies by RNA

(2011) Sergey P. Shevtsov et al.   NATURE CELL BIOLOGY

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

The long and the short of noncoding RNAs

(2009) Christopher A Brosnan et al.   CURRENT OPINION IN CELL BIOLOGY

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres

(2009) Zhong Deng et al.   MOLECULAR CELL

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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