Project description:To obtain a comprehensive survey of the structure and expression level of transcripts across the yeast genome, we used tiling arrays to profile wild-type transcriptomes in ethanol (YPE), glucose (YPD, SDC), and galactose (YPGal), which together encompass the main laboratory growth conditions of yeast. Transcript start and end positions were mapped to the genome by a segmentation algorithm and subsequent manual curation. To identify Cryptic Unstable Transcripts (CUTs), profiles were also measured for a deletion mutant of Rrp6, an important component of the nuclear exosome, which is involved in the degradation of CUTs. Expression profiles are provided in a searchable web-database (http://steinmetzlab.embl.de/NFRsharing).
Project description:Widely transcribed and compact genomes face the major challenge of coping with frequent overlapping or concurrent transcription events. Efficient and timely transcription termination is crucial to control pervasive transcription. In yeast, RNA polymerase II (RNAPII) termination mainly occurs via two pathways, one generating mRNAs and one dedicated to non-coding RNAs, and is triggered by signals that are recognized on the nascent RNA by a specific complex. We describe here a novel pathway of RNAPII transcription termination that is triggered by the binding to the DNA of the transcriptional activator Reb1p. We show that termination follows road-block induced pausing of RNAPII and requires ubiquitylation of RNAPII. The released RNAs are rapidly degraded, which defines a new class of cryptic unstable transcripts. We show that Reb1p-dependent termination can prevent transcriptional interference. This work reveals a novel role for Reb1p and a new paradigm for preserving the functional integrity of nucleosome free regions.
Project description:Transcription profile in YPD media of 48 segregants spores obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Two CEL files were mislabelled: eQTL_080822_spore_38B.CEL and eQTL_080826_spore_21C.CEL, actually spores 24A and 8D respectively. The correct spore IDs are in the sample annotation (under StrainOrLine).
Project description:Transcription profiling was performed on 2 biological replicates of rrp6 deletion strains which were cultivated at 30C in YPAD medium and harvested at OD595~1
Project description:To profile genome-wide allele-specific expression in an unbiased manner we designed a high-resolution yeast tiling microarray that covers the genomes of both the laboratory strain S288c and the recently sequenced clinical isolate YJM789. This array design allows simultaneous expression profiling of allelic variants in a heterozygous hybrid strain. We hybridized cDNA from the heterozygous Y/S and from the homozygous S and Y strains grown in rich medium (YPD). Strand specificity during sample preparation was maintained by inclusion of actinomycin D during reverse transcription to prevent spurious synthesis of second strand cDNA.
Project description:Temporal expression profiling during sporulation for TAO3(4477C) allele replacement strains in S288c. Raw gene expression data CEL files for control TAO3(4477G) allele strain are given in E-MTAB-3454 (see 9 array files from \S_Spo0h0m_Scerevisiae_tlg.CEL\ to \S_Spo8h30m_Scerevisiae_tlg.CEL\).
Project description:RNAPII is responsible for transcription of protein-coding genes and short, regulatory RNAs. In Saccharomyces cerevisiae, termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex (comprised of Nrd1, Nab3, and Sen1) processing by the exosome, and the nuclear specific catalytic subunit, Rrp6. It has been shown that Rrp6 interacts directly with Nrd1, but whether or not Rrp6 is required for NNS-dependent termination is unclear. Loss of Rrp6 function may result in extension (or inhibition of termination) of NNS-dependent transcripts, or Rrp6 may only function after the fact to carry out RNA 3’ end processing. Here, we performed in-depth differential expression analyses and compare RNA-sequencing data of transcript length and abundance in cells lacking RRP6 to previously published sequencing data measuring the length of RNAs in Nrd1-depleted cells. We find many transcripts that were defined as unterminated upon loss of Nrd1 activity are of similar length in rrp6Δ, and expression levels of downstream genes are significantly decreased. This suggests a similar transcription interference mechanism occurs in cells lacking either Nrd1 or Rrp6, supporting the hypothesis that Rrp6 activity is required for proper NNS termination in vivo. Four biological replicates each for deletion mutant (RRP6) and reference cells (WT)