The activity of human enhancers is modulated by the splicing of their associated lncRNAs

U1 snRNP regulates chromatin retention of noncoding RNAs

(2020) Yafei Yin et al.   NATURE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Exon-Mediated Activation of Transcription Starts

(2019) Ana Fiszbein et al.   CELL

Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity

(2018) Noa Gil et al.   Cell Systems

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

cis -Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

(2017) Jennifer Yihong Tan et al.   Cell Reports

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data

(2017) Lingfei Wang et al.   PLoS Computational Biology

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy

(2017) Pin Tong et al.   PLoS Genetics

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

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

(2016) Jesse M. Engreitz et al.   NATURE

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

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

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci

(2015) Wilfried Haerty et al.   RNA

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

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

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

(2014) Suhas S.P. Rao et al.   CELL

Purifying Selection on Splice-Related Motifs, Not Expression Level nor RNA Folding, Explains Nearly All Constraint on Human lincRNAs

(2014) Andreas Schüler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Non-coding RNA derived from the region adjacent to the human HO-1 E2 enhancer selectively regulates HO-1 gene induction by modulating Pol II binding

(2014) Atsushi Maruyama et al.   NUCLEIC ACIDS RESEARCH

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes

(2014) Nicholas E. Ilott et al.   Nature Communications

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Mutations within lncRNAs are effectively selected against in fruitfly but not in human

(2013) Wilfried Haerty et al.   GENOME BIOLOGY

The evolution, impact and properties of exonic splice enhancers

(2013) Eva Cáceres et al.   GENOME BIOLOGY

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

Intron-centric estimation of alternative splicing from RNA-seq data

(2012) D. D. Pervouchine et al.   BIOINFORMATICS

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data

(2012) Boyko Kakaradov et al.   BMC BIOINFORMATICS

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

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Critical reasoning on causal inference in genome-wide linkage and association studies

(2010) Yang Li et al.   TRENDS IN GENETICS

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

A 5′ Splice Site Enhances the Recruitment of Basal Transcription Initiation Factors In Vivo

(2008) Christian Kroun Damgaard et al.   MOLECULAR CELL