0000000000517485
AUTHOR
David Rosenkranz
The FOXP2-Driven Network in Developmental Disorders and Neurodegeneration
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing either human FOXP2 cDNA or its orthologues from the common chimpanzee, Rhesus monkey, and marmoset, respectively. Subsequent RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation. Importantly, RT-qPCR and Western blotting indicated differential re…
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, …
easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
Video abstract A video abstract by the authors of this paper is available. video-abstract8870.mov
Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera
Abstract A monophyletic origin of endoparasitic thorny-headed worms (Acanthocephala) and wheel-animals (Rotifera) is widely accepted. However, the phylogeny inside the clade, be it called Syndermata or Rotifera, has lacked validation by mitochondrial (mt) data. Herein, we present the first mt genome of the key taxon Seison and report conflicting results of phylogenetic analyses: while mt sequence-based topologies showed monophyletic Lemniscea (Bdelloidea + Acanthocephala), gene order analyses supported monophyly of Pararotatoria (Seisonidea + Acanthocephala) and Hemirotifera (Bdelloidea + Pararotatoria). Sequence-based analyses obviously suffered from substitution saturation, compositional …
Piwi Proteins and piRNAs in Mammalian Oocytes and Early Embryos
SummaryGerm cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We present compelling evidence for strong Piwi and piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, whereas those in bovine ovary only express PIWIL1. In human, macaque, and bovine ovaries, we find piRNAs that resemble testis-borne pachytene piRNAs. Isolated bovine follicular oocytes were shown to contain abundant, relatively short piRNAs that preferentially target transposable elements. Using label-free quantitative pr…
5' tRNA halves are highly expressed in the primate hippocampus and might sequence-specifically regulate gene expression
Fragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA-derived small RNAs (tsRNAs) play prominent roles in diverse cellular processes across a wide spectrum of species. Contrasting the situation in other small RNA pathways the mechanisms behind these effects appear more diverse, more complex, and are generally less well understood. In addition, surprisingly little is known about the expression profiles of tsRNAs across different tissues and species. Here, we provide an initial overview of tsRNA expression in different species and tissues, revealing very high levels of 5′ tRNA halves (5′ tRHs) pa…
Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in acanthocephala via an epizoic stage
The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparas…
5’ tRNA halves are highly expressed in the primate hippocampus and sequence-specifically regulate gene expression
AbstractFragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA fragments (tRFs) play prominent roles in diverse cellular processes across a wide spectrum of species. Contrasting the situation in other small RNA pathways the mechanisms behind these effects appear more diverse, more complex and are generally less well understood. In addition, surprisingly little is known about the expression profiles of tRFs across different tissues and species. Here, we provide an initial overview of tRF expression in different species and tissues, revealing very high tRF-levels particularly in the primate hippoc…
Temperature-dependent small RNA expression in Drosophila melanogaster
Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures. In this commentary, we will dwell upon particular interesting aspects connected to our findings, hoping that our point of view may encourage other s…
Hybridization of mouse lemurs: different patterns under different ecological conditions
Abstract Background Several mechanistic models aim to explain the diversification of the multitude of endemic species on Madagascar. The island's biogeographic history probably offered numerous opportunities for secondary contact and subsequent hybridization. Existing diversification models do not consider a possible role of these processes. One key question for a better understanding of their potential importance is how they are influenced by different environmental settings. Here, we characterized a contact zone between two species of mouse lemurs, Microcebus griseorufus and M. murinus, in dry spiny bush and mesic gallery forest that border each other sharply without intermediate habitats…
Maternal overnutrition programs hedonic and metabolic phenotypes across generations through sperm tsRNAs
There is a growing body of evidence linking maternal overnutri-tion to obesity and psychopathology that can be conserved acrossmultiple generations. Recently, we demonstrated in a maternalhigh-fat diet (HFD; MHFD) mouse model that MHFD inducedenhanced hedonic behaviors and obesogenic phenotypes thatwere conserved across three generations via the paternal lineage,which was independent of sperm methylome changes. Here, weshow that sperm tRNA-derived small RNAs (tsRNAs) partly contrib-ute to the transmission of such phenotypes. We observe increasedexpression of sperm tsRNAs in the F1 male offspring born to HFD-exposed dams. Microinjection of sperm tsRNAs from the F1-HFDmale into normal zygotes…
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…
Co-chaperone Hsp70/Hsp90-organizing protein (Hop) is required for transposon silencing and Piwi-interacting RNA (piRNA) biogenesis
Piwi-interacting RNAs (piRNAs) are 26–30-nucleotide germ line-specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90-organizing protein homolog (Hop), a co-chaperone, interacts with piRNA-binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known whether Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons. Hop GLKD females can lay eggs at the same rate as wild-type counterparts, but the e…
Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence
AbstractThe role of the Piwi/piRNA pathway during mammalian oogenesis has remained enigmatic thus far, especially since experiments with Piwi knockout mice did not reveal any phenotypic defects in female individuals. This is in striking contrast with results obtained from other species including flies and zebrafish. In mouse oocytes, however, only low levels of piRNAs are found and they are not required for their function. We recently demonstrated dynamic expression of PIWIL1, PIWIL2, and PIWIL3 during mammalian oogenesis and early embryogenesis. In addition, small RNA analysis of human, crab-eating macaque and cattle revealed that piRNAs are also expressed in the female germline and closel…
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…
PIWIL3 Forms a Complex with TDRKH in Mammalian Oocytes.
P-element induced wimpy testis (PIWIs) are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 gene is absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression, distribution, and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrial-recruited three-membered complex…
Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals
Argonaute proteins comprising Piwi-like and Argonaute-like proteins and their guiding small RNAs combat mobile DNA on the transcriptional and post-transcriptional level. While Piwi-like proteins and associated piRNAs are generally restricted to the germline, Argonaute-like proteins and siRNAs have been linked with transposon control in the germline as well as in the soma. Intriguingly, evolution has realized distinct Argonaute subfunctionalization patterns in different species but our knowledge about mammalian RNA interference pathways relies mainly on findings from the mouse model. However, mice differ from other mammals by absence of functional Piwil3 and expression of an oocyte-specific …
piRNA cluster database: a web resource for piRNA producing loci
Piwi proteins and their guiding small RNAs, termed Piwi-interacting (pi-) RNAs, are essential for silencing of transposons in the germline of animals. A substantial fraction of piRNAs originates from genomic loci termed piRNA clusters and sequences encoded in these piRNA clusters determine putative targets for the Piwi/piRNA system. In the past decade, studies of piRNA transcriptomes in different species revealed additional roles for piRNAs beyond transposon silencing, reflecting the astonishing plasticity of the Piwi/piRNA system along different phylogenetic branches. Moreover, piRNA transcriptomes can change drastically during development and vary across different tissues. Since piRNA clu…
Mating systems and protein–protein interactions determine evolutionary rates of primate sperm proteins
To assess the relative impact of functional constraint and post-mating sexual selection on sequence evolution of reproductive proteins, we examined 169 primate sperm proteins. In order to recognize potential genome-wide trends, we additionally analysed a sample of altogether 318 non-reproductive (brain and postsynaptic) proteins. Based on cDNAs of eight primate species (Anthropoidea), we observed that pre-mating sperm proteins engaged in sperm composition and assembly show significantly lower incidence of site-specific positive selection and overall lower non-synonymous to synonymous substitution rates ( d N / d S ) across sites as compared with post-mating sperm proteins involved in capac…
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…
Bovine piRNA-like RNAs are associated with both transposable elements and mRNAs.
PIWI proteins and their associated piRNAs have been the focus of intensive research in the past decade; therefore, their participation in the maintenance of genomic integrity during spermatogenesis has been well established. Recent studies have suggested important roles for the PIWI/piRNA system outside of gametogenesis, based on the presence of piRNAs and PIWI proteins in several somatic tissues, cancers, and the early embryo. Here, we investigated the small RNA complement present in bovine gonads, gametes, and embryos through next-generation sequencing. A distinct piRNA population was present in the testis as expected. However, we also found a large population of slightly shorter, 24–27 n…
proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
Abstract Background Throughout the metazoan lineage, typically gonadal expressed Piwi proteins and their guiding piRNAs (~26-32nt in length) form a protective mechanism of RNA interference directed against the propagation of transposable elements (TEs). Most piRNAs are generated from genomic piRNA clusters. Annotation of experimentally obtained piRNAs from small RNA/cDNA-libraries and detection of genomic piRNA clusters are crucial for a thorough understanding of the still enigmatic piRNA pathway, especially in an evolutionary context. Currently, detection of piRNA clusters relies on bioinformatics rather than detection and sequencing of primary piRNA cluster transcripts and the stringency …
Profiling of RNA modifications by multiplexed stable isotope labelling
The combination of (15)N/(13)C stable isotope labelling (SIL) and LC-MS/MS revealed a total of 52 modifications in RNA from E. coli and yeast, including 10 previously undescribed modifications. Two modifications, N-ribosylnicotinamide and 2-methylthioadenosine, were newly detected in species hitherto thought not to contain these modifications.
Accelerated Evolution of Fetuin-A (FETUA, also AHSG) is Driven by Positive Darwinian Selection, not GC-Biased Gene Conversion
article i nfo Human Fetuin-A (FETUA, also termed AHSG) is a serum protein composed of two cystatin-like domains D1 and D2 of together 235 amino acids (aa) and an unrelated domain D3 of 114 aa. Though the protein plays a role in diverse physiological and pathological processes, comparably little is known about sequence evolution of FETUA. We therefore analyzed its molecular evolution on the basis of coding sequences of 16 primate species. Ratios of non-synonymous to synonymous substitution rates (dn/ds= ω) suggest that a previously reported acceleration of sequence evolution of exon 7, which encodes domain D3, is driven by positive selection instead of neutral evolution. Irrespective of the …
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