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Series GSE87672 Query DataSets for GSE87672
Status Public on Feb 13, 2017
Title The RNA-induced transcriptional silencing complex is targeted to chromatin exclusively via base-pairing interactions with nascent transcripts
Organism Schizosaccharomyces pombe
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNAs are implicated in chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although well understood, fundamental mechanistic aspects of RNA-mediated chromatin regulation have remained obscure. It has not been possible to unambiguously distinguish whether small RNA loaded Argonaute proteins target the nascent transcript or the underlying DNA sequence. Here, we demonstrate that transcription of the target locus is indispensable for the formation of heterochromatin in fission yeast. Yet, high transcriptional activity opposes RNA-directed chromatin silencing. We further find that pre-mRNA splicing is compatible with RNA-directed heterochromatin formation. Small RNAs complementary to promoter distal introns trigger the formation of stable heterochromatin irrespective of pre-mRNA splicing. However, targeting a functional intron close to the 5’ end of a transcript results in a bistable chromatin state. Together, our results disprove siRNA-DNA base-pairing and provide mechanistic insights that will inform the experimental design of small RNA-directed chromatin silencing studies in multicellular organisms.
 
Overall design The study comprises of 8 small RNAs sequencing data sets from cells expressing a ura4-cox4 hairpin construct that gives rise to siRNAs against 4 engeneered target genes. Experiments were performed in wt and leo1 mutant cells.
 
Contributor(s) Shimada Y, Mohn F, Bühler M
Citation(s) 27941123
Submission date Oct 05, 2016
Last update date May 15, 2019
Contact name Fabio Mohn
E-mail(s) fabio.mohn@fmi.ch
Organization name Friedrich Miescher Institute for Biomedical Research
Lab Buehler Lab
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (1)
GPL17225 Illumina HiSeq 2500 (Schizosaccharomyces pombe)
Samples (8)
GSM2338066 small RNA-seq_ade6-INT leo1D
GSM2338067 small RNA-seq_ade6-INT wt
GSM2338068 small RNA-seq_ade6-TNI leo1D
Relations
BioProject PRJNA345512
SRA SRP090906

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE87672_RAW.tar 56.1 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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