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Seminars, events & talks

Thursday, 11th January, 2018, 12:00 - 13:00, Chair: Evan Floden

Evolutionary Genomics

The impact of ribosome profiling in the observed conservation patterns of lncRNAs

Several recent studies have noted that a large fraction of long non-coding RNAs (lncRNAs) associate with ribosomes. Deep sequencing of ribosome-protected fragments, or ribosome profiling, provides detailed information on the regions that are translated in a transcript and revealed that many lncRNAs contain translated open reading frames with 3-nucleotide periodicity. However, ribosomes are not specifically selected during the biochemical isolation procedure, and non-ribosomal ribonucleoprotein complexes are also present in these samples. These regions show no periodicity and are highly localized, so ribosome profiling can also identify different RNA-protein complexes with high resolution. In our study we examine the patterns of ribosome profiling in mouse hippocampus to find enrichment of translated open reading frames and ribonucleoprotein complexes in different categories of lncRNAs. We identify conserved regions at sequence level between mouse and human to find putative functional regions in lncRNAs. We examine how the overlap with protein-coding transcripts and promoter signals also affects the conservation of lncRNA sequences.

Speaker: Jorge Ruiz Orera, Evolutionary Genomics (GRIB-IMIM)

Room Aula room 473.10 (4th floor)

Thursday, 2nd February, 2017, 12:00

Evolutionary Genomics

"Comparative Transcriptomics and RiboSeq: Looking at De Novo Gene Emergence in Saccharomycotina"

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription of the segment, potentially leading to a new protein with a novel function. What makes de novo genes different from other genes? Due to their unique origins, young de novo genes have no homology with other genes and may not initially be under the same selective constraints. While dozens of de novo genes have been observed in many species, the mechanisms driving their appearance are not yet well understood. To study this phenomena, we have performed deep RNA-seq and ribosome profiling (RP) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (non-annotated), and many were identified as putative de novo genes; these can then be tested for signals of translation using our RP data. We show that putative de novo genes have different properties when compared to phylogenetically conserved genes. Understanding the mechanisms behind de novo gene emergence in a 'simple' eukaryote like S. cerevisiae may help to explain some of the unique adaptations seen in more complex organisms.

Speaker: Will Blevins (Evolutionary Genomics group of GRIB)

Room Aula room 473.10 (4th floor PRBB)

Thursday, 19th January, 2017, 12:00

Evolutionary Genomics

"Evolution by innovation: Is the de novo emergence of coding genes a myth or a mystery - or both?"

In this lecture I will review the basics behind what makes proteins the most basic elements on which selection acts, how they mediate evolvability of organisms and why it seems so unlikely that a protein emergence de novo, i.e. by creation of a new ORF from previously untranscribed DNA. Since such emergence has, however, been observed we -- and many other groups around the world -- are desperately trying to resolve this mysterious puzzle which puts two fundamental schools of thought -- biophysics and genetics -- at odds.

Speaker: Erich Bornberg-Bauer Molecular Evolution and Bioinformatics. Institute for Evolution and Biodiversity. Universität Münster. Germany.

Room Aula room 473.10 (4th floor)

Thursday, 10th March, 2016, 12:00

Evolutionary Genomics

"The evolution of antisense gene expression"

Abstract: The advent of high­throughput genomic technologies has revealed that the transcriptome is more complex than initially thought. There are thousands of loci that transcribe transcripts that lack long conserved ORFs. Antisense transcripts or natural antisense transcripts are an intringuing class of RNAs transcribed from the opposite strand of a known gene. While some of these genes are reported to be functional, most of them are likely to be byproducts of the high transcriptional activity of the genome. We use deep strand­specific RNA sequencing to quantify and characterize the presence of antisense genes in human, finding that antisense transcription is widespread and that a high proportion of protein­coding genes are associated to antisense transcripts. We classify the age of antisense genes using homology searches against the transcriptomes assembled in chimpanzee, macaque and mouse. Birth and turnover of antisense genes is common in the primate lineage, being most of those genes non­coding and non­functional. We further find evidences of new translated proteins in some of those antisense genes, indicating that, from an evolutionary perspective, these transcripts are not useless, as they provide the 'raw material' for the evolution of new molecular functions mapper"

Speaker: Jorge Ruiz Orera - Evolutionary Genomics group of GRIB (IMIM-UPF)

Room Aula room 473.10 (4th floor)

Friday, 20th November, 2015, 11.00-12.00

Evolutionary Genomics

Comparative genomics of bats: the secret of extended longevity?

Of all mammals, bat possess the most unique and peculiar adaptations that render them as excellent models to investigate the mechanisms of extended longevity and potentially halted senescence. Indeed, they are the longest-lived mammals relative to their body size, with the oldest bat caught being 41 years old, living approx. 9.8 times longer than expected. Bats defy the 'rate-of-living' theories that propose a positive correlation between body size and longevity as they use twice the energy as other species of considerable size, but live far longer. The mechanisms that bats use to avoid the negative physiological effects of their heightened metabolism and deal with an increased production of deleterious Reactive Oxygen Species (ROS) is not known, however it is suggested that they either prevent or repair ROS damage. Bats also appear to have resistance to many viral diseases such as rabies, SARS and Ebola and have been shown to be reservoir species for a huge diversity of newly discovered viruses. This suggests that their innate immunity is different to other mammals, perhaps playing a role in their unexpected longevity. Here the potential genomic basis for their rare immunity and exceptional longevity is explored across multiple bat genomes and divergent 'ageing' related markers. A novel blood based population-level transcriptomics approach is developed to explore the molecular changes that occur in an ageing wild population of bats to uncover how bats 'age' so slowly compared with other mammals. This can provide a deeper understanding of the causal mechanisms of ageing, potentially uncovering the key molecular pathways that can be modified to halt, alleviate and perhaps even reverse this process in man.

Speaker: Emma Teeling, School of Biology and Environmental Science, University College Dublin, Ireland

Room Ramón y Cajal Room

Thursday, 12th November, 2015, 12:00

Evolutionary Genomics

"Linneage specific genes and evolutionary innovation in mammals"

The birth of new genes de novo from previously non-genic genomic regions is increasingly being recognized as an important mechanism of evolutionary innovation. However, these genes, which do not have homologues outside the species or taxon, remain poorly characterized. Here we used 68 complete genome sequences from different mammalian species to obtain the first global census of protein coding gene families likely to have originated in the past 200 Million years of mammalian evolution.

Speaker: JOSE LUIS VILLANUEVA - Evolutionary Genomics, GRIB

Room Aula room 473.10 (4th floor)

Thursday, 22th May, 2014, 11:00

Evolutionary Genomics

Exploring hibernation in mammals through transcriptomics: the case of the hibernating lemur

Hibernation is a complex physiological response some mammalian species employ to evade energetic demands. Hibernators conserve energy by essentially “shutting down” physiological processes; metabolic rate is severely depressed, body temperature plummets to ambient levels, and brain activity is greatly diminished (reviewed in Carey et al., 2003). In recent years the study of the molecular processes involved in mammalian hibernation has shifted from investigating a few carefully selected candidate genes to large-scale analysis of differential gene expression. The availability of high-throughput data provides an unprecedented opportunity to ask whether phylogenetically distant species show similar mechanisms of genetic control, and how these relate to particular genes and pathways involved in the hibernation phenotype.

In this talk, we are going to present our ongoing research in this field, comparing the genetic controls of hibernation in several mammalian species and presenting some results about the genetic regulation in the only primate known to naturally exhibit this behavior: the dwarf lemur (genus Cheirogaleus), endemic to Madagascar.

Carey, H. V, Andrews, M. T., & Martin, S. L. Mammalian hibernation: cellular and molecular responses to depressed metabolism and low temperature. Physiological reviews 2003; Vol: 83, 4 pages, doi:10.1152/physrev.00008.2003

Speaker: José Luis Villanueva - Evolutionary Genomics Group

Thursday, 27th February, 2014, 11:00

Evolutionary Genomics

Are long non-coding RNAs translated?: Ribosome profiling reveals the complexity of eukaryotic proteomes

We have compiled raw sequencing data from ribosome profiling experiments performed in different species (human, mouse, zebrafish, fruit fly, yeast) and used them to assemble transcripts, quantify transcript-ribosome associations, and investigate the coding potential and strength of purifying selection of the putatively translated open reading frames in some long non-coding RNAs. We detected extensive association of lincRNAs with ribosomes, not only observed in mammals but also in the other eukaryotic groups. Surprisingly, some of the lncRNAs show significant sequence similarity to proteins only annotated in Genbank, whereas others show not such similarity but still contain putative short open reading frames. The coding potential of ribosome-associated lncRNAs ORFs, measured using different codon frequency based sequence statistics, is intermediate between intronic ORFs and experimentally validated ORFs. These ORFs are subject to weaker selective constraints than most experimentally validated proteins as inferred from single nucleotide polymorphism densities. Our results suggest that many lncRNAs have coding properties and that this class of genes most likely includes protein-coding genes that are no longer functional as well as genes encoding new, poorly-conserved, peptides.

Speaker: Jorge Ruiz Orera - Evolutionary Genomics, GRIB (IMIM - UPF)

Room Aula-4th floor

Thursday, 26th September, 2013, 11:00

Evolutionary Genomics

Gut microbiotas in evolutionary studies: insights from cichlid fishes

With the advent of HT sequencing technologies we have just begun unveiling the genetic and functional diversity of gut microbial consortia, as well as their role in animal evolution. How does the gut microbiota evolve along the host lineages? Can the microbiota be considered as an inherited trait? And if so, is the microbiota a simple mirror or also a driver of the host evolution?

Both diet and host phylogeny are shown as crucial predictors of microbiota features, while the relative contribution of these two factors in recapitulating microbial communities relationships is currently under debate. Therefore closely related species that show a large differentiation of feeding habits represent an especially interesting system to investigate microbiota dynamics in response to concurrent host legacy constraints and selective pressures for rapid adaptation to different diet.

We are currently exploring specificity and dynamics of the gut microbiota in East African Cichlid fishes, which represent a large group of closely related species that underwent a spectacular dietary niche radiation. We recently profiled the gut microbiota of a young tribe of cichlids from lake Tanganyika that transitioned from a generalist feeding to a highly specialized diet primarily based on scales. How did the gut microbiota respond to such diet transition?

Speaker: Laura Baldo - Evolutionary Genomics. Biomedical Informatics, GRIB (IMIM - UPF)

Room Aula (473.10)

Thursday, 30th May, 2013, 11:00

Evolutionary Genomics

The isoform selection problem in genome-wide studies and its impact in alignment quality and positive selection

Speaker: Jose Luis Villanueva - Evolutionary Genomics (GRIB)

Room Aula (473.10)

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