Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments

Deciphering molecular interactions by proximity labeling

(2021) Wei Qin et al.   NATURE METHODS

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing

(2021) Simon Alberti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation

(2021) Xianzhi Lin et al.   RNA Biology

RIC-seq for global in situ profiling of RNA–RNA spatial interactions

(2020) Zhaokui Cai et al.   NATURE

Nuclear hubs built on RNAs and clustered organization of the genome

(2020) Kelly P. Smith et al.   CURRENT OPINION IN CELL BIOLOGY

RNA contributions to the form and function of biomolecular condensates

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

The nucleolus as a multiphase liquid condensate

(2020) Denis L. J. Lafontaine et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting

(2020) Shuo Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Expanding APEX2 Substrates for Proximity-Dependent Labeling of Nucleic Acids and Proteins in Living Cells

(2019) Ying Zhou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

β-Actin mRNA interactome mapping by proximity biotinylation

(2019) Joyita Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

(2019) Alejandro Padrón et al.   MOLECULAR CELL

Regulation of gene expression by cis-acting long non-coding RNAs

(2019) Noa Gil et al.   NATURE REVIEWS GENETICS

snoDB: an interactive database of human snoRNA sequences, abundance and interactions

(2019) Philia Bouchard-Bourelle et al.   NUCLEIC ACIDS RESEARCH

RNA Splicing by the Spliceosome

(2019) Max E. Wilkinson et al.   Annual Review of Biochemistry

Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA–Protein Complexes

(2018) Ying Li et al.   BIOCHEMISTRY

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

Dynamic regulation of nucleolar architecture

(2018) Attila Németh et al.   CURRENT OPINION IN CELL BIOLOGY

RNA–protein interaction detection in living cells

(2018) Muthukumar Ramanathan et al.   NATURE METHODS

Proteome-wide identification of ubiquitin interactions using UbIA-MS

(2018) Xiaofei Zhang et al.   Nature Protocols

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

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

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Interchromosomal interactions: A genomic love story of kissing chromosomes

(2018) Philipp G. Maass et al.   JOURNAL OF CELL BIOLOGY

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

(2018) Yang Wang et al.   NATURE CELL BIOLOGY

Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing

(2018) Iain A. Sawyer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

(2018) Daniel Benhalevy et al.   NATURE METHODS

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Neat1 is a p53-inducible lincRNA essential for transformation suppression

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

Biotinylation by antibody recognition—a method for proximity labeling

(2017) Daniel Z Bar et al.   NATURE METHODS

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

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

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

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

(2017) Pornchai Kaewsapsak et al.   eLife

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Unique features of long non-coding RNA biogenesis and function

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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA

(2016) Aparna Anantharaman et al.   Scientific Reports

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

High-Resolution Structure of the Eukaryotic 80S Ribosome

(2014) Gulnara Yusupova et al.   Annual Review of Biochemistry

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

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

Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome

(2014) Annelyse Thévenin et al.   NUCLEIC ACIDS RESEARCH

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization

(2013) Jean Ollion et al.   BIOINFORMATICS

The shared genomic architecture of human nucleolar organizer regions

(2013) I. Floutsakou et al.   GENOME RESEARCH

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

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

(2012) Takao Naganuma et al.   EMBO JOURNAL

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Biogenesis and function of nuclear bodies

(2011) Yuntao S. Mao et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

The Perinucleolar Compartment

(2010) C. Pollock et al.   Cold Spring Harbor Perspectives in Biology

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies

(2009) Prabhakar Rajan et al.   BMC 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