Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [smallRNA-Seq]

ABSTRACT: In Schizosaccharomyces pombe, Abp1 is homologous to mammalian CENP-B. Abp1 has various seemingly independent functions in the yeast nucleus. It binds to pericentromeric repeats and contribute to heterochromatin formation (ref). Abp1 is involved in regulating the directionality of mating-type switching by regulating the transcription of a member of the recombination-promoting complex (refs). Abp1 also preserves genome integrity by silencing the Tf2 retrotransposons and protecting replication forks during pausing (ref). The profile of the RNA extracted from abp1Δ cells shows an accumulation of RNA in size ranging between 100 and 200 bp. Solexa sequencing of these “little RNA” (liRNA) and comparison of their levels with the WT showed an increase in liRNA coming from various classes of genomic features. The biggest fold changes are attributed to liRNA coming from LTR retrotransposons and the rDNA genes repeats. We show that these liRNAs are targeted for degradation by the exosome and are the products of pervasive RNA Polymerase II transcription. Finally, we describe the genetic interactions of various transcriptional gene silencing effectors with the abp1 deletion in the silencing of the liRNA.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE81280 | GEO | 2016/07/08

SECONDARY ACCESSION(S): PRJNA321172

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_CNAG]

Project description:In Schizosaccharomyces pombe, Abp1 is homologous to mammalian CENP-B. Abp1 has various seemingly independent functions in the yeast nucleus. It binds to pericentromeric repeats and contribute to heterochromatin formation (ref). Abp1 is involved in regulating the directionality of mating-type switching by regulating the transcription of a member of the recombination-promoting complex (refs). Abp1 also preserves genome integrity by silencing the Tf2 retrotransposons and protecting replication forks during pausing (ref). The profile of the RNA extracted from abp1Δ cells shows an accumulation of RNA in size ranging between 100 and 200 bp. Solexa sequencing of these “little RNA” (liRNA) and comparison of their levels with the WT showed an increase in liRNA coming from various classes of genomic features. The biggest fold changes are attributed to liRNA coming from LTR retrotransposons and the rDNA genes repeats. We show that these liRNAs are targeted for degradation by the exosome and are the products of pervasive RNA Polymerase II transcription. Finally, we describe the genetic interactions of various transcriptional gene silencing effectors with the abp1 deletion in the silencing of the liRNA.

2016-07-08 | GSE81324 | GEO

The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_BGI]

2016-07-08 | GSE81323 | GEO

ABP1-regulated gene expression in etiolated Arabidopsis seedlings

Project description:The AUXIN BINDING PROTEIN 1 (ABP1) is an essential plant protein involved in the control of growth and development all along the plant life. This protein was initially identified on its capacity to bind the phytohormone auxin. Binding of auxin to ABP1 was shown to enhance cell expansion of leaf cells. Conversely, the functional inactivation of ABP1 was demonstrated to severely impair cell expansion in shoot tissues. To date, the mechanism by which ABP1 controls cell expansion is still poorly understood. ABP1 was reported to affect expression of various auxin regulated genes but little is known on broader effects of ABP1 on gene expression. Here we have investigated the role of ABP1 in the control of cell expansion using dark grown hypocotyls by analyzing changes in gene expression resulting from ABP1 inactivation. Experiments were performed using the control transgenic line Alc-GUS and the SS12K9, which express GUS and ABP1, respectively, in response to ethanol treatment. Three biological repeats were prepared. RNA samples were labelled with Cy5 and Cy3 as indicated below. Samples from the SS12K9 line were compared to the corresponding control line.

2015-04-07 | E-GEOD-46196 | biostudies-arrayexpress

ABP1-regulated gene expression in etiolated Arabidopsis seedlings

2015-04-07 | GSE46196 | GEO

ABP1-TMK auxin perception mediates rapid phosphorylation for regeneration and auxin canalization

Project description:The phytohormone auxin triggers transcriptional reprograming utilizing a well-characterized nuclear perception machinery. In contrast, mechanisms underlying other auxin effects, such as auxin feed-back on its transport, rapid regulation of ion fluxes or ultrafast global phospho-response, remain enigmatic. Auxin Binding Protein 1 (ABP1) has been contested as an auxin receptor candidate since decades. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at the acidic pH typical for the apoplast. ABP1 and its plasma membrane-localized partner, Transmembrane Kinase 1 (TMK1) are required for auxin-induced phosphorylation of about thousand proteins. Loss-of-function abp1 alleles but not complemented lines show defects in in vitro shoot regeneration and formation of auxin-transporting channels for vasculature formation and regeneration. These results support a role of ABP1-TMK1 in cell surface auxin perception mediating global auxin phospho-response and regenerative development.

2022-08-25 | PXD031063 | Pride

Bacillus subtilis strain:ABP1

Project description:Bacillus subtilis strain:ABP1 Genome sequencing and assembly

| PRJNA523170 | ENA

A Stem Cell-Like Chromatin Pattern May Predispose Tumor Suppressor Genes to DNA Hypermethylation

Project description:Many cancers may originate in stem or early progenitor cells 1-4 which depend on epigenetic modulation of gene expression for normal function (ref). We have studied whether epigenetic states in cancers, and particularly abnormal gene silencing associated with promoter DNA hypermethylation in CpG rich regions (refs), may represent links between cancer and stem cell epigenetic patterns. We studied embryonal carcinomas (EC) which are malignancies of embryonic stem (ES) cells, but retain high potential for multi-lineage differentiation 5-8. Surprisingly, genes DNA hypermethylated and silenced in adult cancers are unmethylated in ES and EC cells. Remarkably, the promoter chromatin of the genes in EC cells is virtually identical to the same genes in adult cancers when the latter are induced to de-methylate. This chromatin, as recently reported for CpG island promoters of low expression, developmentally related, genes in ES cells (refs), is “bivalent” and contains both active and repressive histone modifications. The latter includes trimethyl lysine 27 of histone H3 (H3K27me3), which may recruit DNA methylation (refs), and the promoter regions are enriched for polycomb group (PcG) proteins which place this H3K27me3 mark. Thus, many genes which undergo abnormal DNA methylation and permanent silencing in adult cancers may be programmed to do so by a pre-existent stem cell-like chromatin pattern inherent to the cells in which they arise. Keywords: Stem cell epigenetics expression microarray

2007-10-26 | GSE4809 | GEO

Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing

Project description:Expression profiling, ChiP-CHIP and phenotypic analysis were used to investigate the functional relationships of class III NAD+-dependent HDACs (Sirtuins) in fission yeast. We detected significant histone acetylation increases in Sirtuin mutants at their specific genomic binding targets and were thus able to identify an in vivo substrate preference for each Sirtuin. At heterochromatic loci, we demonstrate that although Hst2 is mainly cytoplasmic, a nuclear pool of Hst2 co-localises with the other Sirtuins at silent regions (cen, mat, tel, rDNA) and that like the other Sirtuins, Hst2 is required for rDNA and centromeric silencing. Interestingly we found specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation. Hst2 directly represses genes involved in transport and membrane function whereas Hst4 represses amino acid biosynthesis genes and Tf2 retrotransposons. A specific role for Hst4 in Tf2 5’ mRNA processing was revealed. Thus, Sirtuins share functions at many genomic targets, but Hst2 and Hst4 have also evolved unique functions in gene regulation. Keywords: chromatin; fission yeast; gene silencing; retrotransposon; Sirtuin; HDAC

2007-04-24 | GSE6114 | GEO

The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat

Project description:The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat

| PRJNA321294 | ENA

Transcriptional response of Acinetobacter baumannii AB1 to bacteriophage Abp1 infection

Project description:Transcriptional response of Acinetobacter baumannii AB1 to bacteriophage Abp1 infection

| PRJNA481979 | ENA