Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu

Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation

(2018) Mario Hofweber et al.   CELL

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

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

(2018) Seema Qamar et al.   CELL

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

The Role of RNA in Biological Phase Separations

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

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

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis

(2018) Tatyana A. Shelkovnikova et al.   Molecular Neurodegeneration

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Shovamayee Maharana et al.   SCIENCE

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

(2018) Shasha Chong 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

Organization and Function of Non-dynamic Biomolecular Condensates

(2018) Jeffrey B. Woodruff et al.   TRENDS IN BIOCHEMICAL SCIENCES

Why Do Disordered and Structured Proteins Behave Differently in Phase Separation?

(2018) Huan-Xiang Zhou et al.   TRENDS IN BIOCHEMICAL SCIENCES

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

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

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

(2018) Akihide Takeuchi et al.   Cell Reports

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

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

(2018) Huasong Lu et al.   NATURE

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

(2018) Yang Wang et al.   NATURE CELL BIOLOGY

Long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) is critical for phenotypic switching of vascular smooth muscle cells

(2018) Abu Shufian Ishtiaq Ahmed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UPA-Seq: Prediction of Functional LncRNAs Using Differential Sensitivity to UV Crosslinking

(2018) Komatsu Taiwa et al.   RNA

Neat1 is a p53-inducible lincRNA essential for transformation suppression

(2017) Stephano S. Mello et al.   GENES & DEVELOPMENT

Genetic mutations in RNA-binding proteins and their roles in ALS

(2017) Katannya Kapeli et al.   HUMAN GENETICS

Long non-coding RNA NEAT1 is a transcriptional target of p53 and modulates p53-induced transactivation and tumor-suppressor function

(2017) Masashi Idogawa et al.   INTERNATIONAL JOURNAL OF CANCER

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

(2017) Julia Joung et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

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

Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development

(2017) Swapna Thomas-Jinu et al.   NEURON

Functional dissection of NEAT1 using genome editing reveals substantial localization of the NEAT1_1 isoform outside paraspeckles

(2017) Ruohan Li et al.   RNA

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

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

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

High expression of long non-coding RNA NEAT1 indicates poor prognosis of human cancer

(2017) Jian Fang et al.   Oncotarget

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

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

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

(2016) Zhipeng Lu et al.   CELL

The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL

(2016) Taro Mannen et al.   JOURNAL OF CELL BIOLOGY

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

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

Decoding ALS: from genes to mechanism

(2016) J. Paul Taylor et al.   NATURE

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

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold

(2016) Gavin J. Knott et al.   NUCLEIC ACIDS RESEARCH

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

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

(2016) Manon Torres et al.   eLife

Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA

(2016) Aparna Anantharaman et al.   Scientific Reports

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus

(2015) Shi-Bin Hu et al.   GENES & DEVELOPMENT

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

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

SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies

(2015) Tetsuya Kawaguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging Roles of Disordered Sequences in RNA-Binding Proteins

(2015) Sara Calabretta et al.   TRENDS IN BIOCHEMICAL SCIENCES

PSF: nuclear busy-body or nuclear facilitator?

(2015) Christopher A. Yarosh et al.   Wiley Interdisciplinary Reviews-RNA

The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice

(2014) S. Nakagawa et al.   DEVELOPMENT

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

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

The long noncoding RNA Neat1 is required for mammary gland development and lactation

(2014) Laura Standaert et al.   RNA

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer

(2014) Dimple Chakravarty et al.   Nature Communications

Compromised paraspeckle formation as a pathogenic factor in FUSopathies

(2013) Tatyana A. Shelkovnikova et al.   HUMAN MOLECULAR GENETICS

Whole-genome screening identifies proteins localized to distinct nuclear bodies

(2013) Ka-wing Fong et al.   JOURNAL OF CELL BIOLOGY

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

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

Exome sequencing to identify de novo mutations in sporadic ALS trios

(2013) Alessandra Chesi et al.   NATURE NEUROSCIENCE

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

The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease

(2012) Oliver D. King et al.   BRAIN RESEARCH

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

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

(2012) Takao Naganuma et al.   EMBO JOURNAL

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

(2012) J. E. Wilusz et al.   GENES & DEVELOPMENT

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

(2012) H. Tani et al.   GENOME RESEARCH

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

Evaluating the role of the FUS/TLS-related gene EWSR1 in amyotrophic lateral sclerosis

(2012) Julien Couthouis et al.   HUMAN MOLECULAR GENETICS

Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MEN  noncoding RNAs

(2012) J. A. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

(2011) Shinichi Nakagawa et al.   JOURNAL OF CELL BIOLOGY

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies

(2010) Sylvie Souquere et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

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

TDP-43 expression in mouse models of amyotrophic lateral sclerosis and spinal muscular atrophy

(2008) Bradley J Turner et al.   BMC NEUROSCIENCE

The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus

(2008) Christine Mayer et al.   EMBO REPORTS

MEN  /  nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

(2008) H. Sunwoo et al.   GENOME RESEARCH