Cap analysis of gene expression (CAGE) and noncoding regulatory elements

Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

(2021) Yu H. Sun et al.   Nature Communications

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

(2021) Mathys Grapotte et al.   Nature Communications

Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease

(2020) Xinchen Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A brief history of human disease genetics

(2020) Melina Claussnitzer et al.   NATURE

A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine

(2020) Youqiong Ye et al.   TRENDS IN GENETICS

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers

(2020) Robin Steinhaus et al.   NUCLEIC ACIDS RESEARCH

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

(2020) Yupeng He et al.   NATURE

Landscape of cohesin-mediated chromatin loops in the human genome

(2020) Fabian Grubert et al.   NATURE

Occupancy maps of 208 chromatin-associated proteins in one human cell type

(2020) E. Christopher Partridge et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

(2020) Peng He et al.   NATURE

Enhancer RNAs are an important regulatory layer of the epigenome

(2020) Vittorio Sartorelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription imparts architecture, function and logic to enhancer units

(2020) Nathaniel D. Tippens et al.   NATURE GENETICS

Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

(2020) Vivek Chandra et al.   NATURE GENETICS

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

(2020) Katla Kristjánsdóttir et al.   Nature Communications

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

(2019) Tsukasa Kouno et al.   Nature Communications

Opportunities and challenges for transcriptome-wide association studies

(2019) Michael Wainberg et al.   NATURE GENETICS

Benefits and limitations of genome-wide association studies

(2019) Vivian Tam et al.   NATURE REVIEWS GENETICS

NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

(2019) Shigeki Hirabayashi et al.   NATURE GENETICS

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

(2018) Xian Adiconis et al.   NATURE METHODS

CTD-dependent and -independent mechanisms govern co-transcriptional capping of Pol II transcripts

(2018) Melvin Noe Gonzalez et al.   Nature Communications

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

(2018) Jacob M. Tome et al.   NATURE GENETICS

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme

(2018) Tinyi Chu et al.   NATURE GENETICS

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

(2017) Chung-Chau Hon et al.   NATURE

Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis

(2017) Kazuyoshi Ishigaki et al.   NATURE GENETICS

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

(2017) Julien Lagarde et al.   NATURE GENETICS

The effect of genetic variation on promoter usage and enhancer activity

(2017) Marco Garieri et al.   Nature Communications

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

(2017) J. Kenneth Baillie 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

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

The regulation and functions of the nuclear RNA exosome complex

(2016) Cornelia Kilchert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

mRNA capping: biological functions and applications

(2016) Anand Ramanathan et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

(2016) Yasuhiro Murakawa et al.   TRENDS IN GENETICS

High-density P300 enhancers control cell state transitions

(2015) Steven Witte et al.   BMC GENOMICS

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

(2015) Takayuki Nojima et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Molecular Basis of Transcription-Coupled Pre-mRNA Capping

(2015) Fuensanta W. Martinez-Rucobo et al.   MOLECULAR CELL

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Genome-guided transcript assembly by integrative analysis of RNA sequence data

(2014) Nathan Boley et al.   NATURE BIOTECHNOLOGY

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

(2014) T. Raj et al.   SCIENCE

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut 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

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Genomewide Association Studies — Illuminating Biologic Pathways

(2009) Joel N. Hirschhorn   NEW ENGLAND JOURNAL OF MEDICINE

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE