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Series GSE81280 Query DataSets for GSE81280
Status Public on Jul 08, 2016
Title The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [smallRNA-Seq]
Organism Schizosaccharomyces pombe
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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.
Overall design Strand-specific small RNA-Seq of wild type and ABP1d Spombe cells
Contributor(s) Daulny A, Azorin F
Citation(s) 27345571
Submission date May 10, 2016
Last update date May 15, 2019
Contact name Oscar Reina Garcia
Organization name IRB Barcelona
Department Biostatistics and Bioinformatics
Street address C/Baldiri Reixac 10
City Barcelona
State/province Barcelona
ZIP/Postal code 08028
Country Spain
Platforms (1)
GPL9453 Illumina Genome Analyzer II (Schizosaccharomyces pombe)
Samples (4)
GSM2149075 RNASeq ABP1d 1
GSM2149076 RNASeq WT 1
GSM2149077 RNASeq ABP1d 2
This SubSeries is part of SuperSeries:
GSE81326 The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat
BioProject PRJNA321172
SRA SRP074758

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Supplementary file Size Download File type/resource
GSE81280_smallRNAs_ABP1d_regions_geo.bed.gz 5.2 Kb (ftp)(http) BED
GSE81280_smallRNAs_ABP1d_vs_WT_regions_geo.bed.gz 69.0 Kb (ftp)(http) BED
GSE81280_smallRNAs_WT_regions_geo.bed.gz 3.3 Kb (ftp)(http) BED
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Processed data are available on Series record

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