RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome (Q36331974)

13 August 2017

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome (English)

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13 August 2017

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13

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13 August 2017

Cory D Hirsch

6

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author name string

Qing Li

1

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13 August 2017

Jonathan I Gent

2

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13 August 2017

Greg Zynda

3

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13 August 2017

Jawon Song

4

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13 August 2017

Irina Makarevitch

5

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13 August 2017

Candice N Hirsch

7

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13 August 2017

R Kelly Dawe

8

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13 August 2017

Thelma F Madzima

9

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13 August 2017

Karen M McGinnis

10

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13 August 2017

Damon Lisch

11

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13 August 2017

Robert J Schmitz

12

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13 August 2017

Nathan M Springer

14

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13 August 2017

language of work or name

English

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publication date

9 November 2015

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Proceedings of the National Academy of Sciences of the United States of America

13 August 2017

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13 August 2017

112

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13 August 2017

47

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13 August 2017

14728-14733

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Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

HTSeq--a Python framework to work with high-throughput sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Diverse gene-silencing mechanisms with distinct requirements for RNA polymerase subunits in Zea mays

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Genomic distribution of H3K9me2 and DNA methylation in a maize genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Spreading of heterochromatin is limited to specific families of maize retrotransposons

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Integrative genomics viewer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Differential expression analysis for sequence count data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Conservation and divergence of methylation patterning in plants and animals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Genome-wide evolutionary analysis of eukaryotic DNA methylation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

BEDTools: a flexible suite of utilities for comparing genomic features

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

The B73 Maize Genome: Complexity, Diversity, and Dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

BSMAP: whole genome bisulfite sequence MAPping program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

The Sequence Alignment/Map format and SAMtools

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Clustal W and Clustal X version 2.0

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

A faster circular binary segmentation algorithm for the analysis of array CGH data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

An RNA-dependent RNA polymerase is required for paramutation in maize

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Genetic perturbation of the maize methylome

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4664327

Cutadapt removes adapter sequences from high-throughput sequencing reads

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1514680112

Epigenetic and genetic influences on DNA methylation variation in maize populations

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1514680112

21 January 2018

Identifiers

DOI

10.1073/PNAS.1514680112

1 reference

13 August 2017

0 references

1 reference

13 August 2017

PubMed publication ID

26553984

1 reference