Transcriptome visualization and data availability at the Saccharomyces Genome Database

Ng, Patrick; Wong, Edith D.; MacPherson, Kevin; Aleksander, Suzi; Dunn, Barbara; Nash, Robert S.; Skrzypek, Marek S.; Gondwe, Felix; Jha, Sagar; Karra, Kalpana; Weng, Shuai; Miyasato, Stuart R.; Simison, Matt; Engel, Stacia R.; Cherry, J. Michael

doi:10.1093/nar/gkz892

Cited by 16 publications

(12 citation statements)

References 28 publications

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“…We separately considered the set of 784 S . cerevisiae genes marked as “dubious” in the Saccharomyces Genome Database [ 41 ]. Although they have been deemed unlikely to encode functional proteins, many of them are lineage-specific and so have been included in previous studies as potentially novel genes [ 11 ].…”

Section: Resultsmentioning

confidence: 99%

“… Top: Distributions of detectability prediction results for all S. cerevisiae lineage-specific genes annotated as of”dubious” coding status in the Saccharomyces Genome Database [ 41 ] in 3 yeast lineages (a, b, c). Bottom: Depiction of the lineage (yellow) and closest outgroup (blue) considered in the analyses in the corresponding column.…”

Section: Supporting Informationmentioning

confidence: 99%

“…We separately considered the set of 784 S. cerevisiae genes marked as "dubious" in the Saccharomyces Genome Database [41]. Although they have been deemed unlikely to encode functional proteins, many of them are lineage-specific and so have been included in previous At the evolutionary distance of the nearest outgroup S. castellii, the entire prediction interval lies below the detectability threshold, indicating an approximately 0% probability that an ortholog would be detected under the null model even if an S. castellii ortholog were present.…”

Section: Many Lineage-specific Genes Can Be Explained By Homology Detection Failurementioning

confidence: 99%

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Many, but not all, lineage-specific genes can be explained by homology detection failure

2020

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Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study.

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Section: Resultsmentioning

confidence: 99%

Section: Supporting Informationmentioning

confidence: 99%

Section: Many Lineage-specific Genes Can Be Explained By Homology Detection Failurementioning

confidence: 99%

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Many, but not all, lineage-specific genes can be explained by homology detection failure

2020

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“…Collapsed FASTA files were then aligned to the yeast genome using Novoalign 2.0 (Novocraft technologies). Reads were counted using multiBamCov from bedtools (Quinlan 2014), to transcript maps from Saccharomyces Genome Database (Ng et al 2020), using the “abundant transcript” data derived from (Pelechano, Wei, and Steinmetz 2013), adding default-length 25nt 5’UTRs and 125nt 3’UTRs for verified ORFs missing from that annotation. Bedgraph files were generated using genomeCoverageBed from bedtools (Quinlan 2014).…”

Section: Methodsmentioning

confidence: 99%

Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface

Bayne

Jayachandran

Kasprowicz

et al. 2020

Preprint

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The conserved fungal RNA binding protein Ssd1, is important in stress responses, cell division and virulence. Ssd1 is closely related to Dis3L2 of the RNase II family of nucleases, but lacks catalytic activity and may act by suppressing translation of associated mRNAs. Previous studies identified motifs that are enriched in Ssd1-associated transcripts, yet the sequence requirements for Ssd1 binding are not well understood. Here we present the crystal structure of Ssd1 at 1.9 Å resolution. Active RNase II enzymes have a characteristic, internal RNA binding path, but in Ssd1 this is blocked by remnants of regulatory sequences. Instead, RNA binding activity has likely been relocated to the outer surface of the protein. Using in vivo crosslinking and cDNA analysis (CRAC), we identify Ssd1-RNA binding sites. These are strongly enriched in 5′UTRs of a subset of mRNAs encoding cell wall proteins. Based on these and previous analyses, we identified a conserved bipartite motif that binds Ssd1 with high affinity in vitro. These studies provide a new framework for understanding the function of a pleiotropic post-transcriptional regulator of gene expression and give insights into the evolution of regulatory elements in the RNase II family.

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“…By definition, a TRM is a set of genes for which transcriptional activity is modulated by a specific transcription factor (TF) [ 6 ]. In the model yeast Saccharomyces cerevisiae , TRMs are well described [ 2 – 5 ] and public databases like YEASTRACT [ 7 ] or SGD [ 8 ], provide lists of target genes for any TF. All together TRMs were explored to better understand their individual organizations, but also their collective relationships [ 4 , 5 , 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Additional insights into the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome

et al. 2022

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Objectives Transcriptional regulatory modules are usually modelled via a network, in which nodes correspond to genes and edges correspond to regulatory associations between them. In the model yeast Saccharomyces cerevisiae, the topological properties of such a network are well-described (distribution of degrees, hierarchical levels, organization in network motifs, etc.). To go further on this, our aim was to search for additional information resulting from the new combination of classical representations of transcriptional regulatory networks with more realistic models of the spatial organization of S. cerevisiae genome in the nucleus. Results Taking advantage of independent studies with high-quality datasets, i.e. lists of target genes for specific transcription factors and chromosome positions in a three dimensional space representing the nucleus, particular spatial co-localizations of genes that shared common regulatory mechanisms were searched. All transcriptional modules of S. cerevisiae, as described in the latest release of the YEASTRACT database were analyzed and significant biases toward co-localization for a few sets of target genes were observed. To help other researchers to reproduce such analysis with any list of genes of their interest, an interactive web tool called 3D-Scere (https://3d-scere.ijm.fr/) is provided.

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Transcriptome visualization and data availability at the Saccharomyces Genome Database

Cited by 16 publications

References 28 publications

Many, but not all, lineage-specific genes can be explained by homology detection failure

Many, but not all, lineage-specific genes can be explained by homology detection failure

Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface

Additional insights into the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome

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