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RNA polymerase mapping in plants identifies enhancers enriched in causal variants
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/0471250953.bi1112s47openalex-snapshot
BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
inferredcites →https://doi.org/10.1002/ajb2.1002openalex-snapshot
Adaptation in plant genomes: Bigger is different
inferredcites →https://doi.org/10.1002/bies.201200179openalex-snapshot
Pausing for thought: Disrupting the early transcription elongation checkpoint leads to developmental defects and tumourigenesis
inferredcites →https://doi.org/10.1002/j.1460-2075.1985.tb03995.xopenalex-snapshot
Light‐inducible and tissue‐specific expression of a chimaeric gene under control of the 5′‐flanking sequence of a pea chlorophyll a/b‐binding protein gene
inferredcites →https://doi.org/10.1016/j.ajhg.2014.10.004openalex-snapshot
Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
inferredcites →https://doi.org/10.1016/j.cell.2015.01.006openalex-snapshot
Enhancer Evolution across 20 Mammalian Species
inferredcites →https://doi.org/10.1016/j.cell.2015.07.042openalex-snapshot
PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II
inferredcites →https://doi.org/10.1016/j.cell.2015.08.008openalex-snapshot
Architectural and Functional Commonalities between Enhancers and Promoters
inferredcites →https://doi.org/10.1016/j.cell.2016.09.018openalex-snapshot
Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1016/j.tplants.2016.07.013openalex-snapshot
Plant Enhancers: A Call for Discovery
inferredcites →https://doi.org/10.1038/nature09033openalex-snapshot
Widespread transcription at neuronal activity-regulated enhancers
inferredcites →https://doi.org/10.1038/nature25966openalex-snapshot
Dysregulation of expression correlates with rare-allele burden and fitness loss in maize
inferredcites →https://doi.org/10.1038/ng.3142openalex-snapshot
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
inferredcites →https://doi.org/10.1038/ng.3845openalex-snapshot
Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation
inferredcites →https://doi.org/10.1038/ng.3865openalex-snapshot
Reevaluation of SNP heritability in complex human traits
inferredcites →https://doi.org/10.1038/ng.823openalex-snapshot
Genome partitioning of genetic variation for complex traits using common SNPs
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3329openalex-snapshot
Identification of active transcriptional regulatory elements from GRO-seq data
inferredcites →https://doi.org/10.1038/nprot.2016.086openalex-snapshot
Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)
inferredcites →https://doi.org/10.1038/nrg2719openalex-snapshot
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
inferredcites →https://doi.org/10.1038/nrg3293openalex-snapshot
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
inferredcites →https://doi.org/10.1038/s41467-018-03006-4openalex-snapshot
Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast
inferredcites →https://doi.org/10.1073/pnas.1221904110openalex-snapshot
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
inferredcites →https://doi.org/10.1073/pnas.1519067112openalex-snapshot
CG gene body DNA methylation changes and evolution of duplicated genes in cassava
inferredcites →https://doi.org/10.1073/pnas.1603217113openalex-snapshot
Nascent RNA sequencing reveals distinct features in plant transcription
inferredcites →https://doi.org/10.1073/pnas.89.23.11219openalex-snapshot
Transcription of the hypersensitive site HS2 enhancer in erythroid cells.
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/nar/gky244openalex-snapshot
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities
inferredcites →https://doi.org/10.1101/108662openalex-snapshot
Prospects for genomic selection in cassava breeding
inferredcites →https://doi.org/10.1101/208181openalex-snapshot
Leveraging Transcriptomics Data for Genomic Prediction Models in Cassava
inferredcites →https://doi.org/10.1101/cshperspect.a018622openalex-snapshot
Enhancer RNAs: A Class of Long Noncoding RNAs Synthesized at Enhancers: Figure 1.
inferredcites →https://doi.org/10.1101/gr.3577405openalex-snapshot
Distribution and intensity of constraint in mammalian genomic sequence
inferredcites →https://doi.org/10.1105/tpc.15.00537openalex-snapshot
Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures
inferredcites →https://doi.org/10.1105/tpc.3.9.877openalex-snapshot
A Mutation in the Arabidopsis TFL1 Gene Affects Inflorescence Meristem Development
inferredcites →https://doi.org/10.1126/science.1162228openalex-snapshot
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
inferredcites →https://doi.org/10.1126/science.1229386openalex-snapshot
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
inferredcites →https://doi.org/10.1128/mcb.23.6.1863-1873.2003openalex-snapshot
Human Transcription Elongation Factor NELF: Identification of Novel Subunits and Reconstitution of the Functionally Active Complex
inferredcites →https://doi.org/10.1186/s12711-017-0361-yopenalex-snapshot
Accuracies of univariate and multivariate genomic prediction models in African cassava
inferredcites →https://doi.org/10.1186/s13059-017-1273-4openalex-snapshot
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pcbi.1001025openalex-snapshot
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0090346openalex-snapshot
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
inferredcites →https://doi.org/10.1534/g3.111.001198openalex-snapshot
Genotype Imputation with Thousands of Genomes
inferredcites →https://doi.org/10.1534/g3.116.033332openalex-snapshot
Marker-Based Estimates Reveal Significant Nonadditive Effects in Clonally Propagated Cassava ( Manihot esculenta ): Implications for the Prediction of Total Genetic Value and the Selection of Varieties
inferredcites →https://doi.org/10.1534/genetics.115.174714openalex-snapshot
Nascent Transcription Affected by RNA Polymerase IV inZea mays
inferredcites →https://doi.org/10.3835/plantgenome2015.11.0118openalex-snapshot
Genome‐Wide Association and Prediction Reveals Genetic Architecture of Cassava Mosaic Disease Resistance and Prospects for Rapid Genetic Improvement
inferredcites →https://doi.org/10.3835/plantgenome2017.03.0015openalex-snapshot
Prospects for Genomic Selection in Cassava Breeding
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41477-019-0589-3openalex-snapshot
An inferred fitness consequence map of the rice genome
inferred← citeshttps://doi.org/10.1038/s41598-021-02794-yopenalex-snapshot
A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)
inferred← citeshttps://doi.org/10.1093/nar/gkaa370openalex-snapshot
Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes
inferred← citeshttps://doi.org/10.1093/plcell/koac108openalex-snapshot
PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave
inferred← citeshttps://doi.org/10.1101/2021.09.23.461500openalex-snapshot
A population based expression atlas provides insights into disease resistance and other physiological traits in cassava ( Manihot esculenta Crantz)
inferred← citeshttps://doi.org/10.1105/tpc.19.00815openalex-snapshot
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways
inferred← citeshttps://doi.org/10.1111/ppl.13421openalex-snapshot
Enhancers as potential targets for engineering salinity stress tolerance in crop plants
inferred← citeshttps://doi.org/10.1186/s13059-021-02543-4openalex-snapshot
Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
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