0000000001304607
AUTHOR
Daniel Gebert
unitas: the universal tool for annotation of small RNAs
AbstractBackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.ResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, …
RNA-based regulation of transposon expression
Throughout the domains of life, transposon activity represents a serious threat to genome integrity and evolution has realized different molecular mechanisms that aim to inhibit the transposition of mobile DNA. Small noncoding RNAs that function as guides for Argonaute effector proteins represent a key feature of so-called RNA interference (RNAi) pathways and specialized RNAi pathways exist to repress transposon activity on the transcriptional and posttranscriptional level. Transposon transcription can be diminished by targeted DNA methylation or chromatin remodeling via repressive Histone modifications. Posttranscriptional transposon silencing bases on degradation of transposon transcripts…
Supplementary Figures from Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
Figure S1. Pairwise comparison of DBF-scores based on different models. Each plot comprises DBF-scores of 27,628 Arabidopsis thaliana ORFs in a pairwise comparison of two different models.; Figure S2. Codon GC-content and ORF structuring. a) Mean GC content of codons for each amino acid divided into those that are found more frequently in highly structured oORFs (DBF high) and those that are found more frequently in lowly structured oORFs (DBF low) using exemplarily data from Mus musculus (see figure 3c). b) Mean GC content of codons for each amino acid sorted by DBF score (see figure 3d). c) Mean GC content of codons for amino acids of set 1 compared to set 2 (see figure 3d). ***: p<0.0…
Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures
The majority of Drosophila genes are expressed in a temperature-dependent manner, but the way in which small RNAs may contribute to this effect is completely unknown as we currently lack an idea of how small RNA transcriptomes change as a function of temperature. Applying high-throughput sequencing techniques complemented by quantitative real-time PCR experiments, we demonstrate that altered ambient temperature induces drastic but reversible changes in sequence composition and total abundance of both miRNA and piRNA populations. Further, mRNA sequencing reveals that the expression of miRNAs and their predicted target transcripts correlates inversely, suggesting that temperature-responsive m…
Conserved and ubiquitous expression of piRNAs and PIWI genes in mollusks antedates the origin of somatic PIWI/piRNA expression to the root of bilaterians
AbstractPIWI proteins and a specific class of small non-coding RNAs, termed Piwi interacting RNAs (piRNAs), suppress transposon activity in animals on the transcriptional and post-transcriptional level, thus protecting genomes from detrimental insertion mutagenesis. While in vertebrates the PIWI/piRNA system appears to be restricted to the germline, somatic expression of piRNAs directed against transposons is widespread in arthropods, likely representing the ancestral state for this phylum. Here, we show that somatic expression of PIWI genes and piRNAs directed against transposons is conserved in mollusks, suggesting that somatic PIWI/piRNA expression was already realized in an early bilate…
Widespread selection for high and low secondary structure in coding sequences across all domains of life
AbstractCodon composition, GC-content and local RNA secondary structures can have a profound effect on gene expression and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that in some cases selection favors more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and if this is a universal phenomenon in nature.We searched for signs of structural selection in a global manner, analyzing a set of one million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed s…
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database.
Abstract PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically…
Supplementary Table 2 from Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
Correlation of DBF-scores of homologous coding sequences across different species
Supplementary Table 3 from Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
(Absence of) Correlation between DBF-scores and gene expression
Supplementary Table 4 from Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
Estimates on the number of genes per species being subject to structural selection
Supplementary Table 1 from Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
Distribution of DBF-scores per species
Supplementary Table 5 from Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life
Enrichment of codons and amino acids in ORFs with high/low DBF-scores