The emerging molecular biology toolbox for the study of long noncoding RNA biology

Biallelic insertion of a transcriptional terminator via the CRISPR/Cas9 system efficiently silences expression of protein-coding and non-coding RNA genes

(2017) Yangyang Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unlinking an lncRNA from Its Associated cis Element

(2016) Vikram R. Paralkar et al.   MOLECULAR CELL

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

(2016) Jesse M. Engreitz et al.   NATURE

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

From profiles to function in epigenomics

(2016) Stefan H. Stricker et al.   NATURE REVIEWS GENETICS

Unique features of long non-coding RNA biogenesis and function

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

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) S. John Liu et al.   SCIENCE

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

(2016) Emily J. Hawkes et al.   Cell Reports

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

(2015) Estel Aparicio-Prat et al.   BMC GENOMICS

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

(2015) Evangelos Pefanis et al.   CELL

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

(2015) Yafei Yin et al.   Cell Stem Cell

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

(2015) Jens Durruthy-Durruthy et al.   NATURE GENETICS

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides

(2015) Kim A. Lennox et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

(2014) Yul W Yang et al.   eLife

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE