Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq

Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae

(2019) Zhaolian Lu et al.   GENOME RESEARCH

MAPCap allows high-resolution detection and differential expression analysis of transcription start sites

(2019) Vivek Bhardwaj et al.   Nature Communications

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

(2019) Deniz Demircioğlu et al.   CELL

Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other

(2019) Madalee G. Wulf et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

(2019) Tianshun Gao et al.   NUCLEIC ACIDS RESEARCH

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

(2018) Gemma B. Danks et al.   BMC GENOMICS

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

(2018) Xian Adiconis et al.   NATURE METHODS

Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq

(2018) Charles Cole et al.   NUCLEIC ACIDS RESEARCH

Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression inArabidopsis

(2018) Yukio Kurihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

(2018) Mette Boyd et al.   Nature Communications

NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA

(2018) Michael A. Schon et al.   GENOME RESEARCH

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

(2018) Nevena Cvetesic et al.   GENOME RESEARCH

The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters

(2017) Long Vo ngoc et al.   GENES & DEVELOPMENT

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

(2017) Alejandro Reyes et al.   NUCLEIC ACIDS RESEARCH

Systematic analysis of transcription start sites in avian development

(2017) Marina Lizio et al.   PLOS BIOLOGY

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals

(2016) Xi Wang et al.   Molecular Systems Biology

Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

(2016) Samir Rahman et al.   NUCLEIC ACIDS RESEARCH

Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

(2016) Daniel A. Nissley et al.   Nature Communications

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

(2015) Jason S. Cumbie et al.   BMC GENOMICS

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

(2014) H. Kawaji et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Leighton J Core et al.   NATURE GENETICS

Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements

(2014) Daechan Park et al.   NUCLEIC ACIDS RESEARCH

Paired-End Analysis of Transcription Start Sites inArabidopsisReveals Plant-Specific Promoter Signatures

(2014) Taj Morton et al.   PLANT CELL

Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases

(2014) Pawel Zajac et al.   PLoS One

Capture and Amplification by Tailing and Switching (CATS)

(2014) Andrey Turchinovich et al.   RNA Biology

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

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

(2012) P. Batut et al.   GENOME RESEARCH

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response

(2012) Assaf Weiner et al.   PLOS BIOLOGY

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

(2011) Kasper Thorsen et al.   BMC GENOMICS

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples

(2010) Jeremy Kapteyn et al.   BMC GENOMICS

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

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

(2010) Charles Plessy et al.   NATURE METHODS

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS