pENCODE: a plant encyclopedia of DNA elements

scientific article

pENCODE: a plant encyclopedia of DNA elements is …
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scholarly articleQ13442814

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P356DOI10.1146/ANNUREV-GENET-120213-092443
P3181OpenCitations bibliographic resource ID3328357
P932PMC publication ID4463858
P698PubMed publication ID25149370

P50authorRobert SchmitzQ61104607
Chad E NiederhuthQ85911335
Amanda Kelly LaneQ86874271
P2093author name stringLexiang Ji
P2860cites workGenome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thalianaQ35887070
MORC family ATPases required for heterochromatin condensation and gene silencing.Q36035505
Natural variation in Arabidopsis. How do we find the causal genes?Q36163079
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and functionQ36179867
The chromatin fingerprint of gene enhancer elementsQ36225648
'Leveling' the playing field for analyses of single-base resolution DNA methylomes.Q36470808
Gene body methylation is conserved between plant orthologs and is of evolutionary consequenceQ36583141
CHH islands: de novo DNA methylation in near-gene chromatin regulation in maizeQ36732449
The iPlant Collaborative: Cyberinfrastructure for Plant BiologyQ21129222
Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas systemQ21203587
The Amborella Genome and the Evolution of Flowering PlantsQ22065597
Mapping and quantifying mammalian transcriptomes by RNA-SeqQ22122035
An integrated encyclopedia of DNA elements in the human genomeQ22122150
Analysis of the genome sequence of the flowering plant Arabidopsis thalianaQ22122387
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)Q24540045
The accessible chromatin landscape of the human genomeQ24595581
An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactionsQ24614360
Integrative epigenomic mapping defines four main chromatin states in ArabidopsisQ24632836
Human DNA methylomes at base resolution show widespread epigenomic differencesQ24633677
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradomeQ24656974
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatinQ24673476
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maizeQ24675282
SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylationQ27681459
Minimum information about a microarray experiment (MIAME)-toward standards for microarray dataQ27860569
The Sequence Alignment/Map format and SAMtoolsQ27860966
Comprehensive mapping of long-range interactions reveals folding principles of the human genomeQ28131819
mRNA-Seq whole-transcriptome analysis of a single cellQ28240611
Topological domains in mammalian genomes identified by analysis of chromatin interactionsQ28264221
A first-generation haplotype map of maizeQ28266729
Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulationQ28274367
An expansive human regulatory lexicon encoded in transcription factor footprintsQ28274429
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectQ28301622
Whole-genome analysis of histone H3 lysine 27 trimethylation in ArabidopsisQ28469184
Deposition of histone variant H2A.Z within gene bodies regulates responsive genesQ28484353
Optical control of mammalian endogenous transcription and epigenetic statesQ28505596
Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environmentQ28728714
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genesQ28763700
An oestrogen-receptor-α-bound human chromatin interactomeQ29541719
Genome-wide mapping of in vivo protein-DNA interactionsQ29547162
Landscape of transcription in human cellsQ29547467
Systematic localization of common disease-associated variation in regulatory DNAQ29614895
Dynamic regulation of nucleosome positioning in the human genomeQ29615046
The long-range interaction landscape of gene promotersQ29615403
A map of the cis-regulatory sequences in the mouse genomeQ29615404
A general framework for estimating the relative pathogenicity of human genetic variantsQ29615730
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterningQ29615977
Highly integrated single-base resolution maps of the epigenome in ArabidopsisQ29616098
Architecture of the human regulatory network derived from ENCODE dataQ29617046
The developmental transcriptome of Drosophila melanogasterQ29617262
Genome-wide insertional mutagenesis of Arabidopsis thalianaQ29617345
Identification of functional elements and regulatory circuits by Drosophila modENCODEQ29617551
Global epigenomic reconfiguration during mammalian brain developmentQ29617800
The NIH Roadmap Epigenomics Mapping ConsortiumQ29619856
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.Q30448141
Spark: a navigational paradigm for genomic data explorationQ30563731
The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people questionQ30605046
High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.Q31095080
SMART--Sunflower Mutant population And Reverse genetic Tool for crop improvement.Q31112978
Epigenetic natural variation in Arabidopsis thalianaQ33288249
TILLING to detect induced mutations in soybean.Q33316413
Global identification of microRNA-target RNA pairs by parallel analysis of RNA endsQ33341604
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thalianaQ33367576
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marksQ33371693
Assessing the impact of transgenerational epigenetic variation on complex traitsQ33474817
A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheatQ33497643
A rich TILLING resource for studying gene function in Brassica rapaQ33551427
Genome-wide mapping of alternative splicing in Arabidopsis thalianaQ33560271
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergenceQ33777982
Conservation and divergence of methylation patterning in plants and animalsQ33928315
Genetic analysis of B-Peru, a regulatory gene in maizeQ33957439
Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory geneQ33961926
Sequences required for paramutation of the maize b gene map to a region containing the promoter and upstream sequencesQ33965581
Multiple reference genomes and transcriptomes for Arabidopsis thalianaQ36868961
Identification of a functional transposon insertion in the maize domestication gene tb1.Q36940067
Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes.Q37175967
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.Q37207914
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thalianaQ37282868
Enhanced Y1H assays for Arabidopsis.Q37289762
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).Q38355701
Maize HapMap2 identifies extant variation from a genome in flux.Q38943891
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selectionQ39817345
Sequencing of natural strains of Arabidopsis thaliana with short readsQ41346495
Patterns of population epigenomic diversity.Q41869587
Massive genomic variation and strong selection in Arabidopsis thaliana lines from SwedenQ41973736
Relationship between nucleosome positioning and DNA methylationQ42151152
Developmental control of the DNA replication and transcription programsQ42588657
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegansQ42588662
A spatial and temporal map of C. elegans gene expressionQ42588671
Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis.Q42657893
Efficient genome editing in plants using a CRISPR/Cas system.Q42957714
Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonucleaseQ43872258
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.Q45814242
Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly.Q46031902
Mapping the epigenetic basis of complex traits.Q46934949
Targeted genome modification of crop plants using a CRISPR-Cas system.Q47822803
Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maizeQ47985296
Genome-wide analysis of DNA methylation in soybean.Q50726588
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Q51525502
The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana.Q51551911
Tissue- and expression level-specific chromatin looping at maize b1 epialleles.Q51741969
Reverse genetics in Medicago truncatula using a TILLING mutant collection.Q51787548
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome.Q51848359
Whole-genome sequencing of multiple Arabidopsis thaliana populations.Q51856188
A link between RNA metabolism and silencing affecting Arabidopsis development.Q51956889
Deletion-based reverse genetics in Medicago truncatula.Q54465014
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression.Q54547285
Epigenetic and genetic influences on DNA methylation variation in maize populationsQ57539936
Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27Q57539937
A simple method for gene expression and chromatin profiling of individual cell types within a tissueQ34000729
Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant librariesQ34037510
Heritable epigenetic variation among maize inbredsQ34085631
Genome-wide evolutionary analysis of eukaryotic DNA methylation.Q34110385
Massively parallel functional dissection of mammalian enhancers in vivoQ34174436
Local DNA hypomethylation activates genes in rice endospermQ34276365
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome positionQ34375601
Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collectionQ34426724
A diploid wheat TILLING resource for wheat functional genomicsQ34470181
TILLING and ecotilling for riceQ34470722
Integrative annotation of chromatin elements from ENCODE dataQ34503932
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatinQ34548233
Chromatin signatures of the Drosophila replication programQ34548240
Genome-wide analysis of promoter architecture in Drosophila melanogaster.Q34548248
Broad chromosomal domains of histone modification patterns in C. elegansQ34548272
A global analysis of C. elegans trans-splicingQ34548280
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegansQ34548301
The transcriptional diversity of 25 Drosophila cell linesQ34548309
The emerging science of epigenomicsQ34566933
An RNA-dependent RNA polymerase is required for paramutation in maizeQ34569244
The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequencesQ34616116
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegansQ34625961
Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seqQ34632731
A TILLING Platform for Functional Genomics in Brachypodium distachyonQ34804504
Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathwaysQ35008864
Comprehensive analysis of the chromatin landscape in Drosophila melanogasterQ35030499
High-throughput approaches for plant epigenomic studiesQ35037464
Epigenetic diversity increases the productivity and stability of plant populationsQ35055855
Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in natureQ35221493
Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonalityQ35517391
Transgenerational epigenetic instability is a source of novel methylation variantsQ35533269
High-resolution mapping of open chromatin in the rice genomeQ35634495
Arabidopsis intragenomic conserved noncoding sequenceQ35652236
Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutationQ35780093
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectencyclopediaQ5292
P304page(s)49-70
P577publication date2014-08-15
P1433published inAnnual Review of GeneticsQ567358
P1476titlepENCODE: a plant encyclopedia of DNA elements
P478volume48

Reverse relations

cites work (P2860)
Q37435328Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes
Q58756700DNA methylation footprints during soybean domestication and improvement
Q38828884Genetic sources of population epigenomic variation
Q95933345Integrative analysis of reference epigenomes in 20 rice varieties
Q46282702PCSD: a plant chromatin state database
Q99240333Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future
Q97419158The regulatory landscape of early maize inflorescence development
Q37286128Widespread natural variation of DNA methylation within angiosperms

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