E-GEOD-38400
type: rnaseq mrna differential
RO_0002162: Arabidopsis thaliana
description: RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long non-coding RNAs (lncRNAs)1, which in Arabidopsis thaliana are produced by a specialized RNA Polymerase V (Pol V)2. lncRNAs guide Argonaute-siRNA complexes to specific genomic loci and mediate the establishment of DNA methylation3,4. The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF nucleosome remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding IDN2 protein5,6. RNA-mediated DNA methylation and transcriptional silencing was compromised in the swi3 mutant. Moreover, targets of SWI/SNF significantly overlapped with genes controlled by Pol V, which shows that the physical interaction reflects a functional relationship. We further found that non-coding transcription by Pol V affects nucleosome positioning on silenced regions. We propose that lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin remodeling complexes may be a more general function of lncRNAs. RNA-seq of 3 samples (Col-0, nrpe1 [a mutant defective in the largest subunit of Pol V and unable to produce lncRNA], swi3b, idn2) with 3 biological replicates.
uses data from: http://identifiers.org/pubmed/23246435

ATMRU1
type: EnsemblDatabaseReference

GRXS10
type: EnsemblDatabaseReference

AT1G56090
type: EnsemblDatabaseReference

(Assay) SRR504179
type: Assay

ANAC003 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.2
p value: 0.00339022346829812
refers to: ANAC003

AT2G07733
type: EnsemblDatabaseReference

(Sample) developmental stage/seedling
type: EFO_0001992
property type: developmental stage
property value: seedling

PSBE
type: EnsemblDatabaseReference

DML1
type: EnsemblDatabaseReference

(Sample) genotype/idn2-1
type: EFO_0000001
property type: genotype
property value: idn2-1

MYR1
type: EnsemblDatabaseReference

AT2G35382
type: EnsemblDatabaseReference

RSU1
type: EnsemblDatabaseReference

AT2G05200
type: EnsemblDatabaseReference

GRXS4
type: EnsemblDatabaseReference

AT1G49500 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.6
p value: 7.17655678333763E-4
refers to: AT1G49500

DML1 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -3.7
p value: 6.88632512858443E-6
refers to: DML1

AT5G35207
type: EnsemblDatabaseReference

AT2G07733 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.5
p value: 6.99717459078064E-4
refers to: AT2G07733

AT4G04223 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.3
p value: 1.97530124308827E-5
refers to: AT4G04223

AT1G56090 DOWN in 'nrpe1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.7
p value: 0.0442706899007526
refers to: AT1G56090

(Sample) age/2 to 3
type: EFO_0000001
property type: age
property value: 2 to 3

AT5G28300
type: EnsemblDatabaseReference

AT1G33840
type: EnsemblDatabaseReference

(Assay) SRR504185
type: Assay

AT3G54730
type: EnsemblDatabaseReference

AT5G27845
type: EnsemblDatabaseReference

ANAC003
type: EnsemblDatabaseReference

(Sample) genotype/nrpe1
type: EFO_0000001
property type: genotype
property value: nrpe1

AT5G27845 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 4.7
p value: 0.0154880897172585
refers to: AT5G27845

(Assay) SRR504181
type: Assay

ATMRU1
type: EnsemblDatabaseReference

GRXS5 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.8
p value: 1.10050513681397E-4
refers to: GRXS5

GRXS10
type: EnsemblDatabaseReference

GRXS4 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.0
p value: 1.20605183368379E-6
refers to: GRXS4

AT3G29644 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 3.3
p value: 2.42408020763614E-9
refers to: AT3G29644

(Sample) ecotype/Col-0
type: EFO_0005148
property type: ecotype
property value: Col-0

(Assay) SRR504187
type: Assay

Analysis of 'idn2-1' vs 'wild type genotype'
type: RNASeqDifferentialAnalysis

AT1G49500
type: EnsemblDatabaseReference

(Sample) genotype/swi3b +/-
type: EFO_0000001
property type: genotype
property value: swi3b +/-

PSBE
type: EnsemblDatabaseReference

(Assay) SRR504186
type: Assay

AT1G33840 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 5.6
p value: 5.18043230894706E-17
refers to: AT1G33840

MYR1
type: EnsemblDatabaseReference

AT4G04293
type: EnsemblDatabaseReference

AT2G35382
type: EnsemblDatabaseReference

(Assay) SRR576329
type: Assay

AT2G05200
type: EnsemblDatabaseReference

GRXS4
type: EnsemblDatabaseReference

SEN1 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.3
p value: 0.0148877764321061
refers to: SEN1

AT2G35382 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.3
p value: 0.0286564165493755
refers to: AT2G35382

GRXS3 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.5
p value: 0.0363069555959921
refers to: GRXS3

AT4G04293 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.7
p value: 0.00767817376681846
refers to: AT4G04293

AT3G54770
type: EnsemblDatabaseReference

AT2G06002 DOWN in 'nrpe1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -3.9
p value: 0.0453965669619086
refers to: AT2G06002

(Factor value) GENOTYPE/swi3b +/-
type: EFO_0000001
property type: GENOTYPE
property value: swi3b +/-

AT3G59765
type: EnsemblDatabaseReference

AT1G33850 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 5.9
p value: 2.79462327353078E-14
refers to: AT1G33850

AT3G54730
type: EnsemblDatabaseReference

AT5G27845
type: EnsemblDatabaseReference

ANAC003
type: EnsemblDatabaseReference

(Factor value) GENOTYPE/idn2-1
type: EFO_0000001
property type: GENOTYPE
property value: idn2-1

AT3G59765 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.6
p value: 4.97985108417941E-4
refers to: AT3G59765

PSBE DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.8
p value: 0.0148877764321061
refers to: PSBE

SEN1
type: EnsemblDatabaseReference

MYR1 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.4
p value: 0.0126020068215462
refers to: MYR1

NRPD1B
type: EnsemblDatabaseReference

ATPF
type: EnsemblDatabaseReference

AT4G04223
type: EnsemblDatabaseReference

GRXS13 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.5
p value: 0.0284994618544919
refers to: GRXS13

AT1G33850
type: EnsemblDatabaseReference

(Assay) SRR504184
type: Assay

GRXS13
type: EnsemblDatabaseReference

AT1G49500
type: EnsemblDatabaseReference

AT3G29644
type: EnsemblDatabaseReference

AT5G61190
type: EnsemblDatabaseReference

AT1G12730 DOWN in 'nrpe1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.7
p value: 0.0174256951296636
refers to: AT1G12730

AT4G04293
type: EnsemblDatabaseReference

Analysis of 'swi3b +/-' vs 'wild type genotype'
type: RNASeqDifferentialAnalysis

(Factor value) GENOTYPE/nrpe1
type: EFO_0000001
property type: GENOTYPE
property value: nrpe1

AT5G35207 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 5.4
p value: 1.20032402082522E-8
refers to: AT5G35207

AT1G11785 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.3
p value: 0.00774380617297478
refers to: AT1G11785

ATMRU1 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.3
p value: 0.0282286399047186
refers to: ATMRU1

AT1G62310
type: EnsemblDatabaseReference

RSU1 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 5.1
p value: 2.51468703027131E-6
refers to: RSU1

AT2G16310
type: EnsemblDatabaseReference

AT3G54770
type: EnsemblDatabaseReference

AT1G11785
type: EnsemblDatabaseReference

AT3G59765
type: EnsemblDatabaseReference

AT3G29644 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.6
p value: 0.00884928633561506
refers to: AT3G29644

AT5G28300 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.6
p value: 6.99717459078064E-4
refers to: AT5G28300

AT1G12730
type: EnsemblDatabaseReference

ATPF DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.6
p value: 4.86070152312244E-4
refers to: ATPF

GRXS5
type: EnsemblDatabaseReference

AT1G13650
type: EnsemblDatabaseReference

SEN1
type: EnsemblDatabaseReference

NRPD1B
type: EnsemblDatabaseReference

ATPF
type: EnsemblDatabaseReference

GRXS3
type: EnsemblDatabaseReference

AT3G48131
type: EnsemblDatabaseReference

AT4G04223
type: EnsemblDatabaseReference

AT5G61190 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.3
p value: 0.033180839478734
refers to: AT5G61190

(Assay) SRR504182
type: Assay

AT1G62310 DOWN in 'idn2-1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -1.4
p value: 0.00979902787311376
refers to: AT1G62310

AT1G33850
type: EnsemblDatabaseReference

AT2G06002
type: EnsemblDatabaseReference

GRXS13
type: EnsemblDatabaseReference

AT3G29644
type: EnsemblDatabaseReference

AT5G61190
type: EnsemblDatabaseReference

AT2G05200 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.5
p value: 5.96500647090866E-5
refers to: AT2G05200

Arabidopsis thaliana
type: OBI_0100026

NRPD1B DOWN in 'nrpe1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -2.3
p value: 4.57359775494582E-5
refers to: NRPD1B

AT1G13650 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.7
p value: 0.011324925624372
refers to: AT1G13650

AT3G54730 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 3.0
p value: 3.25286534322604E-4
refers to: AT3G54730

AT1G56090
type: EnsemblDatabaseReference

AT1G62310
type: EnsemblDatabaseReference

AT2G16310
type: EnsemblDatabaseReference

AT2G07733
type: EnsemblDatabaseReference

AT1G11785
type: EnsemblDatabaseReference

DML1
type: EnsemblDatabaseReference

(Assay) SRR576328
type: Assay

AT1G12730
type: EnsemblDatabaseReference

DML1 DOWN in 'nrpe1' vs 'wild type genotype'
type: DecreasedDifferentialExpressionRatio
fold change: -3.0
p value: 3.5923298026616E-4
refers to: DML1

(Sample) genotype/wild type genotype
type: EFO_0000001
property type: genotype
property value: wild type genotype

(Assay) SRR504183
type: Assay

RSU1
type: EnsemblDatabaseReference

GRXS10 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 1.7
p value: 0.00439302757923867
refers to: GRXS10

AT1G13650
type: EnsemblDatabaseReference

GRXS5
type: EnsemblDatabaseReference

(Sample) organism/Arabidopsis thaliana
type: Arabidopsis thaliana
property type: organism
property value: Arabidopsis thaliana

AT5G35207
type: EnsemblDatabaseReference

AT2G16310 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.9
p value: 0.00802341945588109
refers to: AT2G16310

AT3G48131
type: EnsemblDatabaseReference

Analysis of 'nrpe1' vs 'wild type genotype'
type: RNASeqDifferentialAnalysis

GRXS3
type: EnsemblDatabaseReference

AT2G06002
type: EnsemblDatabaseReference

AT3G48131 UP in 'nrpe1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 6.9
p value: 4.31601133283012E-5
refers to: AT3G48131

AT3G54770 UP in 'idn2-1' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 3.6
p value: 5.24875277874475E-13
refers to: AT3G54770

AT5G28300
type: EnsemblDatabaseReference

AT1G33840
type: EnsemblDatabaseReference

(Assay) SRR504180
type: Assay

AT3G29644 UP in 'swi3b +/-' vs 'wild type genotype'
type: IncreasedDifferentialExpressionRatio
fold change: 2.7
p value: 0.0299540156262984
refers to: AT3G29644

(Factor value) GENOTYPE/wild type genotype
type: EFO_0000001
property type: GENOTYPE
property value: wild type genotype

(Assay) SRR576327
type: Assay