A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5 '-3 ' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe

Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes. In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex, the exosome. Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Rat1/Xrn2. Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus. Intriguingly, mutation in either of the two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not result in silencing defects at the main heterochromatic regions. We demonstrate that Dhp1 interacts with heterochromatic factors and is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome. Genomic and genetic analyses suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its RNA processing activity. The results describe the unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing and elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genom

The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome

Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome. However, the mechanism by which they are recognized and targeted to the exosome is not fully understood. Here we report that the MTREC complex, which has recently been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs, is also the major nuclear exosome targeting complex for CUTs and unspliced pre-mRNAs in Schizosaccharomyces pombe. The MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced pre-mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and RNA-processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of CUTs

Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis

Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The ‘U three protein’ (UTP) complexes and snoRNP particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5'-end of the pre-ribosomal RNA (5'-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2.15 Å resolution and analyze its function by UV RNA-crosslinking (CRAC) and in context of a recent cryo-EM structure of the 90S pre-ribosome. Utp4 consists of two orthogonal and highly basic β-propellers that perfectly fit the EM-data. The Utp4 structure highlights an unusual Velcro-closure of its C-terminal β-propeller as relevant for protein integrity and potentially Utp8 recognition in the context of the pre-ribosome. We provide a first model of the 5'-ETS RNA from the internally hidden 5'-end up to the region that hybridizes to the 3'-hinge sequence of U3 snoRNA and validate a specific Utp4/5'-ETS interaction by CRAC analysis.This work was supported by Deutsche Forschungsgemeinschaft (DFG) (SFB638, Z4 to I. S. and HU363/15-1 to E.H. and the Leibniz programme to I.S.); Cluster of Excellence CellNetworks (EcTOP1 to I.S. and E.H.); Funding for open access charge: DFG [Leibniz Programme]. M.K. was funded by a Kekule Fellowship (VCI)

Practical Approaches towards Complete Real-time Gaze Tracking

Visual context plays a key role in many computer vision tasks, and performance of eye/gaze-tracking methods also benefit from it. However, the size of contextual information (e.g. full face image) is very large w.r.t the primary input i.e. cropped image of the eye. This adds large computational costs to the algorithm and makes it inefficient, severely lim- iting its utility in real-time applications. In this paper, we perform a (computational) cost vs benefit analysis of var- ious input types that include context, leaning towards an efficient gaze-tracking system. We further study the effect of an alternate ranking loss based training strategy. Finally, we demonstrate some practical calibration techniques that can convert gaze-vectors into points-on-screen, an impor- tant application that is often overlooked in literature. We examine how data-efficient these techniques are in terms of how well they utilise expensive calibration data.Computer Science | Data Science and Technolog

Additional file 9: of Correction to: The coding and noncoding transcriptome of Neurospora crassa

Table S4. Light induced RNAs in Neurospora. (XLSX 118 kb

Additional file 6: of Correction to: The coding and noncoding transcriptome of Neurospora crassa

Figure S3. Examples of annotated protein-coding genes with no detectable sense mRNA but only antisense RNA. NCU05980, which encodes for carboxypeptidase S1, and NCU04233, which encodes for a hypothetical protein, are shown. ChIP-Seq of RNAPII Ser5-P and Ser2-P [28], pooled RNA-Seq and strand-specific RNA-Seq datasets are presented. (PDF 42 kb

Additional file 7: Table S5. of The coding and noncoding transcriptome of Neurospora crassa

Splicing analysis: detected annotated and novel splice sites, novel alternative splice sites, splice sites detected in lincRNAs and antisense transcripts (XLSX 974 kb

Additional file 5: Table S3. of The coding and noncoding transcriptome of Neurospora crassa

List of identified Neurospora antisense transcripts (XLSX 300 kb

Additional file 11: Figure S6. of The coding and noncoding transcriptome of Neurospora crassa

NEUTRA tool. (A) Selected statistics and expression profiles of the gene entry frequency (NCU02265) generated by “Search by Gene” tool. Circadian expression profile (left) and time resolved RNAPII Ser2-P ChIP-seq analysis (right) are depicted. (B) Snapshot of the genome browser. The gene model of vivid (NCU03967) and the selected datasets are shown. (PDF 76.8 kb

Additional file 2: Figure S2. of The coding and noncoding transcriptome of Neurospora crassa

Characterization of the 434 non-annotated intergenic transcripts, which were detected above threshold in the polysome fractionation dataset. (a) Size distribution of protein-coding genes (n = 9730, median length 1782 bp), lincRNA genes that were below the threshold in the polysome fractionation dataset (n = 1060, median length 551 bp), lincRNA genes that were above the threshold with no significant coding potential (n = 418, median length 451 bp) and novel possibly coding genes (n = 16, median length 725 bp). (b) RNAPII ChIP-Seq index analysis of the 434 intergenic transcripts, which were detected above threshold in the polysome fractionation dataset. The data was smoothened with a window size of 100 bp. (PDF 140 kb