Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression at shoot apices between Wild Type and vip3-1-null allele

ABSTRACT: The aim of this study was to evaluate gene expression defects at the shoot apical meristem and young flower meristems of the vip3-1 null allele. VIP3 belongs to polymerase II-associated factor 1 complex (Paf1c), which is involved in several RNA polymerase II-dependent transcriptional processes. Arabidopsis vip3 mutants exhibit phylotactic defects and strong floral indeterminacy phenotypes.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE139201 | GEO | 2019/10/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Differential gene expression at shoot apices between Wild Type and vip3-1-null allele

Project description:Differential gene expression at shoot apices between Wild Type and vip3-1-null allele

| PRJNA578729 | ENA

Connective Auxin Transport in the Shoot Facilitates Communication between Shoot Apices.

Project description:The bulk polar movement of the plant signaling molecule auxin through the stem is a long-recognized but poorly understood phenomenon. Here we show that the highly polar, high conductance polar auxin transport stream (PATS) is only part of a multimodal auxin transport network in the stem. The dynamics of auxin movement through stems are inconsistent with a single polar transport regime and instead suggest widespread low conductance, less polar auxin transport in the stem, which we term connective auxin transport (CAT). The bidirectional movement of auxin between the PATS and the surrounding tissues, mediated by CAT, can explain the complex auxin transport kinetics we observe. We show that the auxin efflux carriers PIN3, PIN4, and PIN7 are major contributors to this auxin transport connectivity and that their activity is important for communication between shoot apices in the regulation of shoot branching. We propose that the PATS provides a long-range, consolidated stream of information throughout the plant, while CAT acts locally, allowing tissues to modulate and be modulated by information in the PATS.

| S-EPMC4847802 | biostudies-literature

The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide [ChIP-seq]

Project description:We have determined the distribution of two subunits of Paf1C, namely ELF7 and VIP3. We have investigated the contribution of the Paf1 complex to the monoubiquitination of H2B genome-wide by ChIP-seq. Finally, we have investigated the effect of defective Paf1C on the distribution of total RNAPII.

2024-03-07 | GSE244846 | GEO

Ubiquitin-dependent transfer of PAF1c from MYC onto RNA Polymerase controls double-strand break repair at active promoters

Project description:MYC family proteins are oncogenic transcription factors that can globally affect the function of RNA Polymerase II (RNAPII). The ability of MYC proteins to promote transcription elongation depends on their ubiquitination, but the underlying mechanism and its biological relevance are unknown. Here we show that MYC and the Polymerase II associated factor, PAF1c, interact directly and their function is mutually dependent, since the specific binding of MYC to active promoters depends on PAF1c and, conversely, PAF1c is required for MYC-dependent pause release. Upon binding, PAF1c is rapidly transferred from MYC onto RNAPII and this transfer is driven by the HUWE1 ubiquitin ligase. Both MYC and HUWE1 globally control histone H2B ubiquitylation, which promotes transcriptional elongation and alters chromatin structure for double-strand break repair. Consistently, MYC suppresses the accumulation of double-strand breaks at promoters in response to topoisomerase II inhibition. While depletion of PAF1c has only minor effects on MYC-dependent gene expression, MYC induces rampant transcription-dependent DNA damage in PAF1c-depleted cells. We propose that the HUWE1-dependent transfer of PAF1c from MYC onto RNAPII is critical for absorbing the topological stress accompanied with deregulated and oncogenic transcription.

2021-02-15 | PXD023242 | Pride

The PAF1 complex promotes 3‘ processing of pervasive transcripts

Project description:The PAF1 complex (PAF1C) functions in multiple transcriptional processes involving RNA Polymerase II (Pol II). eRNAs and PROMPTs are pervasive transcripts transcribed by Pol II and rapidly degraded by the nuclear exosome complex after 3’ endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C has an unexpected role in the termination of eRNAs and PROMPTs that are cleaved 1-3 kb downstream of the transcription start site. Mechanistically, PAF1C facilitates recruitment of Integrator to sites of pervasive transcript cleavage, promoting timely cleavage and transcription termination. We also show that PAF1C recruits Integrator to coding genes, where PAF1C then dissociates from Integrator upon entry into processive elongation. Our results demonstrate an unexpected function for PAF1C in limiting the length and accumulation of pervasive transcripts that result from nonproductive transcription

2022-03-03 | PXD031531 | Pride

The PAF1 complex promotes 3‘ processing of pervasive transcripts [3'-seq]

Project description:The PAF1 complex (PAF1C) functions in multiple transcriptional and co-transcriptional processes. Although many aspects of the requirement for PAF1 in coding gene transcription have been heavily studied, the function of PAF1C at sites of non-coding transcription is poorly understood. eRNAs and PROMPTs are pervasive transcripts transcribed by RNA Polymerase II and rapidly degraded after 3’ endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C depletion results in near universal 3’ end processing defects in pervasive transcripts, leading to transcription termination dysregulation. Mechanistically, PAF1C recruits Integrator to chromatin through direct interactions promoting timely cleavage and transcription termination of pervasive transcripts. We also show that PAF1C recruits Integrator to the promoters of coding genes, where PAF1C then dissociates from the Integrator complex upon entry into processive elongation. Our results demonstrate an unexpected function for PAF1C in limiting the length and accumulation of pervasive transcripts, while highlighting a general requirement for PAF1C in Integrator recruitment.

2022-03-15 | GSE196368 | GEO

The PAF1 complex promotes 3‘ processing of pervasive transcripts [RNA-seq]

2022-03-15 | GSE162829 | GEO

The PAF1 complex promotes 3‘ processing of pervasive transcripts [PRO-Seq]

2022-03-15 | GSE163501 | GEO

The PAF1 complex promotes 3‘ processing of pervasive transcripts [ChIP-seq]

2022-03-15 | GSE162842 | GEO

RNA sequencing of polymerase II-associated factor 1 complex (PAF1c) mutants at 10°C and 23°C under LD conditions

Project description:We sequenced mRNA of WT (Col-0) and PAF1c single mutants (php, elf7, vip3, vip4, vip5, and vip6) grown at 10°C and 23°C under LD conditions. RNA was extracted from seedlings of 1.02 developmental stage at both temperatures and proceeded for library preparation

2022-03-02 | GSE171778 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data