Comparative analysis of structured RNAs in S. cerevisiaeindicates a multitude of different functions

Steigele, Stephan; Huber, Wolfgang; Stocsits, Claudia; Stadler, Peter F.; Nieselt, Kay

doi:10.1186/1741-7007-5-25

Cited by 33 publications

(29 citation statements)

References 67 publications

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“…This genome-wide observation is consistent with a previous biophysical analysis, showing that RBP binding to RNAs is preferentially to unpaired nucleotides [10]. We also examined the distribution of binding affinities for the conserved secondary structures among seven yeast species [34], and found that the RBP binding affinities for conserved, structured regions are higher for CDSs, 5′ UTRs, 3′ UTRs, tRNAs, snoRNAs and snRNAs ( Figure 2D). This preference might be caused by positive structural selection in RBP binding sites.…”

Section: Rbps Bind Preferentially To Single-stranded Loops and Consersupporting

confidence: 76%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical non-coding RNAs (ncRNAs) and ~11% of long ncRNAs (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responses. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. . Many mRNAs are regulated by one or more RBPs as co-regulators. In Saccharomyces cerevisiae, there are approximately 600 annotated and predicted RBPs, but relatively few of them have been systematically studied to determine their regulatory targets [5]. In addition to mRNAs, numerous non-coding RNAs (ncRNAs) are targets of RBPs [6,7]. Previous studies revealed that RNAs were regulated by many RBPs post-transcriptionally [8]. It is widely accepted that altering the expression of RBPs will change cellular physiology profoundly. Studies using animal models have revealed that RBPs are involved in many human diseases, such as neurologic disorders and cancers [9]. Although the mechanisms that confer the specificity of RBP-RNA interaction are poorly understood, it is clear that this specificity is determined by both the primary sequence and secondary structure of the target RNA [10,11]. The secondary structures recognized by some RBPs are known. For example, the SAM domain of the yeast post-transcriptional regulator Vts1p recognizes the shape of the SRE of the RNA ligand [12].Currently, the most direct and powerful approach to profiling RBP-RNA interactions is UV crosslinking and immunoprecipitation (CLIP) of RNA-protein complexes,

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Section: Rbps Bind Preferentially To Single-stranded Loops and Consersupporting

confidence: 76%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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“…Recently, genome-wide approaches to monitor transcription have revealed several surprising features of the eukaryotic transcriptome, including extensive intergenic transcription, antisense transcription and a notable number of noncoding RNAs (ncRNA)1-6. Furthermore, it has been found that, in some cases, it is the act of transcription (or the attendant chromatin modifications) that is important, rather than the ncRNA produced7.…”

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confidence: 99%

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping

et al. 2008

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We have determined the high-resolution strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA-DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA-DNA hybrid to detect RNA molecules hybridized to a high-density DNA oligonucleotide tiling microarray. HybMap showed exceptional dynamic range and reproducibility, and allowed us to identify strand-specific coding, noncoding and structural RNAs, as well as previously unknown RNAs conserved in distant yeast species. Notably, we found that virtually the entire euchromatic genome (including intergenics) is transcribed, with heterochromatin dampening intergenic transcription. We identified features including large numbers of condition-specific noncoding RNAs, extensive antisense transcription, new properties of antisense transcripts and induced divergent transcription. Furthermore, our HybMap data informed the efficiency and locations of RNA splicing genome-wide. Finally, we observed strand-specific transcription islands around tRNAs at heterochromatin boundaries inside centromeres. Here, we discuss these new features in terms of organism fitness and transcriptome evolution.

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“…On the other hand, there is no reliable signal for secondary structure conservation in too short alignments. Previous RNAz-based studies discuss these issues in more detail 8,15,16 . A brief overview of our computational procedure is presented in Fig.…”

Section: Rnaz Screen: Unbiased Prediction Of Structured Rnasmentioning

confidence: 99%

“…First we report an RNAzbased survey of teleost fish genomes. We demonstrate that like many other groups of organisms (mammals 8,9 , urochordates 13 , nematodes 14 , insects 15 , and yeasts 16 ) teleost genomes contain a large number of previously undescribed, clade-specific, non-coding RNAs. Secondly, we investigate from a global perspective the fate of ncRNAs in the wake of a genome duplication.…”

Section: Introductionmentioning

confidence: 99%

Duplicated Rna Genes in Teleost Fish Genomes

Rose

Jöris

Hackermüller

et al. 2008

J. Bioinform. Comput. Biol.

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Teleost fishes share a duplication of their entire genomes. We report here on a computational survey of structured non-coding RNAs in teleost genomes, focussing on the fate of fish-specific duplicates. As in other metazoan groups we find evidence for a large number (11 543) of structured RNAs, most of which (∼ 86%) are clade-specific or evolve so fast that their tetrapod homologs cannot be detected. In surprising contrast to protein-coding genes, the fish-specific genome duplication did not lead to a large number of paralogous ncRNAs: only 188 candidates, mostly microRNAs, appear in a larger copy number in teleosts than in tetrapods suggesting that large-scale gene duplications do not play a major role in the expansion of the vertebrate ncRNA inventory.

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Comparative analysis of structured RNAs in S. cerevisiaeindicates a multitude of different functions

Cited by 33 publications

References 67 publications

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping

Duplicated Rna Genes in Teleost Fish Genomes

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