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

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

(2013) Matthew D. Simon et al.   NATURE

XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

(2013) Céline Vallot et al.   NATURE GENETICS

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

(2013) Syuzo Kaneko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long noncoding RNAs regulate adipogenesis

(2013) Lei Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding

(2013) Saskia Delpretti et al.   Cell Reports

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Cytotopic localization by long noncoding RNAs

(2012) Pedro J Batista et al.   CURRENT OPINION IN CELL BIOLOGY

New and Xisting regulatory mechanisms of X chromosome inactivation

(2012) Yesu Jeon et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Genome-wide Studies of CCCTC-binding Factor (CTCF) and Cohesin Provide Insight into Chromatin Structure and Regulation: FIGURE 1.

(2012) Bum-Kyu Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A misplaced lncRNA causes brachydactyly in humans

(2012) Philipp G. Maass et al.   JOURNAL OF CLINICAL INVESTIGATION

Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation

(2012) Rui Xiao et al.   MOLECULAR CELL

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins

(2012) Stephanie C. Huelga et al.   Cell Reports

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

SAF-A Has a Role in Transcriptional Regulation of Oct4 in ES Cells Through Promoter Binding

(2011) Dzeneta Vizlin-Hodzic et al.   Cellular Reprogramming

Effect of Peucedanum japonicum Thunb on the Expression of Obesity-Related Genes in Mice on a High-Fat Diet

(2011) Natthanan Nukitrangsan et al.   Journal of Oleo Science

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Large non-coding RNAs: missing links in cancer?

(2010) M. Huarte et al.   HUMAN MOLECULAR GENETICS

miR-130 Suppresses Adipogenesis by Inhibiting Peroxisome Proliferator-Activated Receptor   Expression

(2010) E. K. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

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

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

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Atf4 Regulates Obesity, Glucose Homeostasis, and Energy Expenditure

(2009) J. Seo et al.   DIABETES

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

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

The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

(2009) Mary E. Donohoe et al.   NATURE

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme

(2008) David Umlauf et al.   BIOLOGICAL CHEMISTRY

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

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

(2008) J. Zhao et al.   SCIENCE