Nascent transcription affected by RNA polymerase IV in Zea mays (Q35342805)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25653306%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

title

Nascent transcription affected by RNA polymerase IV in Zea mays (English)

1 reference

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29 February 2020

1 reference

2

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29 February 2020

Natalie C Deans

3

1 reference

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29 February 2020

author name string

Karl F Erhard

1

1 reference

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29 February 2020

Allison E McClish

4

1 reference

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29 February 2020

Jay B Hollick

5

1 reference

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29 February 2020

language of work or name

English

0 references

publication date

4 February 2015

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29 February 2020

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29 February 2020

volume

199

1 reference

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29 February 2020

page(s)

1107-1125

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29 February 2020

issue

4

1 reference

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describes a project that uses

29 February 2020

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4391576/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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

27 July 2018

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

27 July 2018

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Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits

27 July 2018

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

27 July 2018

1 reference

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Pol IV-Dependent siRNA Production is Reduced in Brassica rapa

27 July 2018

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A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

27 July 2018

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Pol II docking and pausing at growth and stress genes in C. elegans

27 July 2018

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Maize RNA polymerase IV defines trans-generational epigenetic variation.

27 July 2018

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Dogma derailed: the many influences of RNA on the genome

27 July 2018

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Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

27 July 2018

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Spreading of heterochromatin is limited to specific families of maize retrotransposons

27 July 2018

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

27 July 2018

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In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing

27 July 2018

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Defining the status of RNA polymerase at promoters

27 July 2018

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Paramutation: a trans-homolog interaction affecting heritable gene regulation

27 July 2018

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

27 July 2018

1 reference

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piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Repeat associated small RNAs vary among parents and following hybridization in maize

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Trans chromosomal methylation in Arabidopsis hybrids

27 July 2018

1 reference

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Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications.

27 July 2018

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The genome of the mesopolyploid crop species Brassica rapa

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Genome-wide characterization of the HD-ZIP IV transcription factor family in maize: preferential expression in the epidermis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Paramutation of tobacco transgenes by small RNA-mediated transcriptional gene silencing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Differential expression analysis for sequence count data

27 July 2018

1 reference

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The B73 Maize Genome: Complexity, Diversity, and Dynamics

27 July 2018

1 reference

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Diversity of Pol IV function is defined by mutations at the maize rmr7 locus

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs

27 July 2018

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Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome

27 July 2018

1 reference

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Production and processing of siRNA precursor transcripts from the highly repetitive maize genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Divergent transcription: a new feature of active promoters

27 July 2018

1 reference

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

A paramutation phenomenon is involved in the genetics of maize low phytic acid1-241 (lpa1-241) trait

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

A novel Snf2 protein maintains trans-generational regulatory states established by paramutation in maize

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Epigenetic regulation of flowering

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Maize sex determination and abaxial leaf fates are canalized by a factor that maintains repressed epigenetic states

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Multiple trans-sensing interactions affect meiotically heritable epigenetic states at the maize pl1 locus

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Role of RNA polymerase IV in plant small RNA metabolism

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

A Test for Somatic Mutation in the Origination of Conversion-Type Inheritance at the B Locus in Maize

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

A Genetic Change Associated with the R Locus in Maize Which Is Directed and Potentially Reversible

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Rmr6 maintains meiotic inheritance of paramutant states in Zea mays

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

RNA polymerase IV directs silencing of endogenous DNA.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Chromatin conversations: mechanisms and implications of paramutation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Chromosome organization and genic expression

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Transgene-induced silencing identifies sequences involved in the establishment of paramutation of the maize p1 gene

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Paramutation of the r1 locus of maize is associated with increased cytosine methylation.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Allelic interactions heritably alter the activity of a metastable maize pl allele.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Genetic perturbation of the maize methylome.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Paramutation in Drosophila linked to emergence of a piRNA-producing locus.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

BEDTools: a flexible suite of utilities for comparing genomic features

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Tissue- and expression level-specific chromatin looping at maize b1 epialleles.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

RNA polymerase IV functions in paramutation in Zea mays.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Divergent transcription from active promoters

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Targets of RNA-directed DNA methylation

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

A multistep process gave rise to RNA polymerase IV of land plants.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

A poplar tree proteinase inhibitor-like gene promoter is responsive to wounding in transgenic tobacco.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391576

Paramutation at the R locus in maize

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25653306

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Paramutation at the sulfurea locus of Lycopersicon esculentum Mill. : VII. Determination of the time of occurrence of paramutation by the quantitative evaluation of the variegation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25653306

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1534/GENETICS.115.174714

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25653306%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25653306%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference