4.3 Article

RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants

Related references

Note: Only part of the references are listed.
Article Plant Sciences

An inferred fitness consequence map of the rice genome

Zoe Joly-Lopez et al.

NATURE PLANTS (2020)

Article Plant Sciences

Widespread long-range cis-regulatory elements in the maize genome

William A. Ricci et al.

NATURE PLANTS (2019)

Review Biochemistry & Molecular Biology

Emerging roles of transcriptional enhancers in chromatin looping and promoter-proximal pausing of RNA polymerase II

Huan Meng et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2018)

Editorial Material Plant Sciences

Adaptation in plant genomes: Bigger is different

Wenbin Mei et al.

AMERICAN JOURNAL OF BOTANY (2018)

Article Multidisciplinary Sciences

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast

Gregory T. Booth et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

Karl A. G. Kremling et al.

NATURE (2018)

Article Plant Sciences

RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis

Jiafu Zhu et al.

NATURE PLANTS (2018)

Article Genetics & Heredity

Reevaluation of SNP heritability in complex human traits

Doug Speed et al.

NATURE GENETICS (2017)

Article Plant Sciences

Prospects for Genomic Selection in Cassava Breeding

Marnin D. Wolfe et al.

PLANT GENOME (2017)

Article Agriculture, Dairy & Animal Science

Accuracies of univariate and multivariate genomic prediction models in African cassava

Uche Godfrey Okeke et al.

GENETICS SELECTION EVOLUTION (2017)

Article Biotechnology & Applied Microbiology

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

Rurika Oka et al.

GENOME BIOLOGY (2017)

Review Biochemistry & Molecular Biology

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

Hannah K. Long et al.

Article Biochemical Research Methods

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

Dig Bijay Mahat et al.

NATURE PROTOCOLS (2016)

Article Multidisciplinary Sciences

Nascent RNA sequencing reveals distinct features in plant transcription

Jonathan Hetzel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

Open chromatin reveals the functional maize genome

Eli Rodgers-Melnick et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Plant Sciences

Plant Enhancers: A Call for Discovery

Blaise Weber et al.

TRENDS IN PLANT SCIENCE (2016)

Article Biochemistry & Molecular Biology

Enhancer Evolution across 20 Mammalian Species

Diego Villar et al.

Article Biochemistry & Molecular Biology

PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II

Fei Xavier Chen et al.

Review Biochemistry & Molecular Biology

Architectural and Functional Commonalities between Enhancers and Promoters

Tae-Kyung Kim et al.

Article Genetics & Heredity

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

Karl F. Erhard et al.

GENETICS (2015)

Article Biochemistry & Molecular Biology

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

Lucy H. Williams et al.

MOLECULAR CELL (2015)

Article Biochemical Research Methods

Identification of active transcriptional regulatory elements from GRO-seq data

Charles G. Danko et al.

NATURE METHODS (2015)

Article Multidisciplinary Sciences

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

Haifeng Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Transcription factor trapping by RNA in gene regulatory elements

Alla A. Sigova et al.

SCIENCE (2015)

Article Cell Biology

Enhancer RNAs: A Class of Long Noncoding RNAs Synthesized at Enhancers

Tae-Kyung Kim et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)

Article Genetics & Heredity

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

Karl F. Erhard et al.

GENETICS (2015)

Article Genetics & Heredity

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

Alexander Gusev et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2014)

Article Biochemical Research Methods

CrossMap: a versatile tool for coordinate conversion between genome assemblies

Hao Zhao et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

An atlas of active enhancers across human cell types and tissues

Robin Andersson et al.

NATURE (2014)

Article Multidisciplinary Sciences

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

Jeffrey C. Glaubitz et al.

PLOS ONE (2014)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

Alla A. Sigova et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

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

Hojoong Kwak et al.

SCIENCE (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

Karen Adelman et al.

NATURE REVIEWS GENETICS (2012)

Article Genetics & Heredity

Genome partitioning of genetic variation for complex traits using common SNPs

Jian Yang et al.

NATURE GENETICS (2011)

Article Multidisciplinary Sciences

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

Robert J. Elshire et al.

PLOS ONE (2011)

Article Genetics & Heredity

Genotype Imputation with Thousands of Genomes

Bryan Howie et al.

G3-GENES GENOMES GENETICS (2011)

Article Multidisciplinary Sciences

Widespread transcription at neuronal activity-regulated enhancers

Tae-Kyung Kim et al.

NATURE (2010)

Article Biochemical Research Methods

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP plus

Eugene V. Davydov et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Multidisciplinary Sciences

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

Leighton J. Core et al.

SCIENCE (2008)

Review Multidisciplinary Sciences

The plant immune system

Jonathan D. G. Jones et al.

NATURE (2006)

Article Biochemistry & Molecular Biology

Distribution and intensity of constraint in mammalian genomic sequence

GM Cooper et al.

GENOME RESEARCH (2005)