Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

BRAFV600Eremodels the melanocyte transcriptome and inducesBANCRto regulate melanoma cell migration

(2012) Ross J. Flockhart et al.   GENOME RESEARCH

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

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

(2012) Satish Sati et al.   NUCLEIC ACIDS RESEARCH

The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type

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

Dark Matter RNA: Existence, Function, and Controversy

(2012) Philipp Kapranov et al.   Frontiers in Genetics

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk

(2011) Guangfu Jin et al.   CARCINOGENESIS

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Identification of intergenic trans-regulatory RNAs containing a disease-linked SNP sequence and targeting cell cycle progression/differentiation pathways in multiple common human disorders

(2011) Anna B. Glinskii et al.   CELL CYCLE

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

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

Response to “The Reality of Pervasive Transcription”

(2011) Harm van Bakel et al.   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

The uniqueome: a mappability resource for short-tag sequencing

(2010) Ryan Koehler et al.   BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

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

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

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

(2009) Mitchell Guttman et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

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

(2008) Jeremy E. Wilusz et al.   CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology