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TranscriptomicsTranscriptional gene silencing mediated by interplay of MOM1 and Pol V
In plants, multiple levels of epigenetic control suppress transposon movement and permit somatic as well as transgenerational transmission of gene expression patterns. A variety of factors are involved that establish and/or maintain epigenetic marks, such as covalent modification of DNA and histones...
ORGANISM(S): Arabidopsis thaliana 
2010-06-19 | E-GEOD-17940 | biostudies-arrayexpress
TranscriptomicsThe DDR complex facilitates the genome-wide association of RNA Polymerase V to promoters and evolutionarily young transposons
The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found tha...
ORGANISM(S): Arabidopsis thaliana 
2012-08-05 | E-GEOD-39247 | biostudies-arrayexpress
ProteomicsMethylated-antibody affinity purification to improve proteomic identification of plant RNA polymerase Pol V complex and the interacting proteins
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific bindin...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2017-02-28 | PXD005422 | Pride
On-bead digestion Pol v complex Chemical cross-link Reductive methylation Ap-ms 
ProteomicsAffinity purified epitope-taggedPol V LC-MSMS
The full mass spectrometry report of affinity purified epitope-tagged Pol V from A. thiniana T87 cells.
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-07-20 | PXD041996 | Pride
T87 Pol v 
TranscriptomicsProfiling of RNA Pol II occupancy in Drosophila neural stem cell populations using TaDa (Targeted DamID)
Cell-type specific transcriptional profiling is key to understanding cell fate specification and function. In order to achieve this it has been necessary, to date, to isolate specific cell types from complex tissues. We have developed 'TaDa', a technique that enables cell-specific profiling without ...
ORGANISM(S): Drosophila melanogaster 
2013-06-21 | E-GEOD-46803 | biostudies-arrayexpress
TranscriptomicsA SWI/SNF nucleosome remodeling complex acts in non-coding RNA-mediated transcriptional silencing
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-...
ORGANISM(S): Arabidopsis thaliana 
2012-12-01 | E-GEOD-38400 | biostudies-arrayexpress
TranscriptomicsChIP-chip by array of yeast to determine genome-wide occupancy profiles for RNA polymerase (Pol) II, its phosphorylated forms, and transcription factors
To investigate the chromatin transcription cycle, we determined genome-wide occupancy profiles for RNA polymerase (Pol) II, its phosphorylated forms, and transcription factors in growing yeast. ChIP-chip was performed to identify the genomic binding locations for Rpb3, TFIIB, Tfg1, Kin28, Cet1, Spt4...
ORGANISM(S): Saccharomyces cerevisiae 
2010-08-23 | E-TABM-1033 | biostudies-arrayexpress
TranscriptomicsThe RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation
Enhancers play a central role in precisely regulating the spatiotemporal expression of developmentally regulated genes. The molecular mechanisms and factors required for controlling the inactive or poised enhancers and their function in future gene activation remain elusive. Here, we have identified...
ORGANISM(S): Mus musculus 
2012-12-30 | E-GEOD-38148 | biostudies-arrayexpress
GenomicsThe SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [Yeast cells]
The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon ...
ORGANISM(S): Saccharomyces cerevisiae 
2014-08-29 | E-GEOD-52997 | biostudies-arrayexpress
ProteomicsCrosslinking mass spectrometry of yeast Pol I pre-initiation complex
In eukaryotic cells, ribosomal RNA is transcribed by RNA polymerase I (Pol I). To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC). In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3 and Core Factor (CF) composed of subunits Rrn...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-07-31 | PXD006510 | Pride
Pol i Transcription Core factor Pol i pre-initiation complex Crosslinking Ribosomal rna 
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