cphRNA 2014 - Symposium "non-coding RNAs: from Discovery to Function"

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cphRNA 2014 - Symposium "non-coding RNAs: from Discovery to Function"

2014-06-27: cphRNA 2014 - Symposium "non-coding RNAs: from Discovery to Function" (free), 09.15-17.05 at festauditoriet, A1-01.01, Frederiksberg Campus, Bulowsvej 17, 1870 Frederiksberg C, Denmark. Organised by RTH and COAT.

Speakers: Roderic Guigó, CRG, Barcelona; Jørgen Kjems, Aarhus University, Quaid Morris, The Donnely Center, Canada; Nikolaus Rajewsky, MDC, Berlin; Albin Sandelin, The Bioinformatics Centre, Copenhagen University and Renée Schroeder, MF. Perutz Lab, Uni Vienna

Registration is free but required if you would like to join the lunch. We kindly ask you to send one email; per person with your full name and affiliation to at the latest June 20th at noon.



8:30-9.10 Registration open
9:15 - 9:20 Welcome
Anders Krogh / Jan Gorodkin
9:20 - 10:05 RNA Heterogeneity in the Eukaryotic Cell
Roderic Guigo
10:05 - 10:50 Regulatory RNAs
Nikolaus Rajewsky
10:50 - 11:15 Coffee Break
11:15 - 12:00 (nc)RNAs from active enhancers and promoters enable a body-wide regulatory atlas
Albin Sandelin
12:00 - 14:00 Lunch and poster session in room A1.01.02
14:00 - 14:45 Circular RNA - function and biogenesis
Jørgen Kjems
14:45 - 15:10 Coffee Break
15:10 - 15:55 Predicting RNA-protein interactions: motifs and binding sites
Quaid Morris
15:55 - 16:40 Revisiting the coding potential of the E. coli genome
Renee Schroeder
16:40 - 17:00 Poster Award and closing remarks
Anders Krogh / Jan Gorodkin


RNA Heterogeneity in the Eukaryotic Cell
Roderic Guigo, Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona
The unfolding of the instructions encoded in the genome is triggered by the transcription of DNA into RNA, and the subsequent processing of the resulting primary RNA transcripts into functional mature RNAs. RNA is thus the first phenotype of the genome, mediating all other phenotypic changes at the organism level caused by changes in the DNA sequence. While current technology is too primitive to provide accurate measurements of the RNA content of the cell, the recent development of Massively Parallel Sequencing Instruments has dramatically increased the resolution with which we can monitor cellular RNA. Using these instruments, the ENCODE project has surveyed the RNA content of multiple cell lines and subcellular compartments. The results of these surveys underscore pervasive transcription, as well as great RNA heterogeneity between and within cells. Comparison of RNA surveys with other genome wide epigenetic surveys—such as those of binding sites for Transcription Factors, or of Histone modifications—reveals a very tightly coupling between the different pathways involved in RNA processing, transcription and splicing in particular.

Regulatory RNAs
Nikolaus Rajewsky, Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine
The talk will have three parts. In the first one Nikolaus will talk about their recents results (Grosswendt et al., Mol. Cell 2014) on identifying targets of miRNAs by various ligation reactions. These approaches allowed them to identify thousands of miRNA:target interactionsin vivo and to understand more about miRNA target recognition specificity. In the second part, he will focus on the transition from the unfertilized oocyte to the totipotent zygote. This important transition in life is marked by rapid post-transcriptional re-organization in the cytoplasm. The molecular mechanisms of this re-organization from a highly differentiated to a totipotent cell are largely unknown. They discovered that shortly after fertilization, thousands of mRNAs are specifically degraded in the zygote. They found a 3' UTR polyC motif that marks these mRNAs for destruction (Stoeckius et al., in press). Finally, he will talk about circular RNAs and their recent attempts to understand more about their biogenesis and expression (unpublished)."

(nc)RNAs from active enhancers and promoters enable a body-wide regulatory atlas
Albin Sandelin, The Bioinformatics Centre, Copenhagen University
Enhancers are one of the most essential regulatory features in the human genome, controlling development, homeostasis and differentiation. Therefore, localization and characterization of enhancers, their activity and how they interact with promoters is a central task in biology. Active enhancers can be detected by balanced transcription initiation and production of capped enhancer RNAs (eRNAs). Using massive validation assays, we show that this approach is be more than two times as accurate as enhancer detection with chromatin marks and hypersensitive DNA, and can be applied to much smaller cell samples like biopsies. We show that eRNAs are generated using the same mechanisms as mRNAs, but have different fates: their transcription terminates fast, they are unspliced and targeted by the exosome, much like exosome-sensitive RNAs located antisense and upstream of promoters (PROMPTS). Many of these properties can be explained by DNA sequence motifs found downstream of the site of initiation. We used the FANTOM5 panel of samples covering the majority of human cell types to produce an atlas of active, in vivo transcribed enhancers. The atlas was used to compare regulatory programs between different cells at unprecedented depth, identify disease-associated regulatory single nucleotide polymorphisms, and classify cell type-specific and ubiquitous enhancers. The oFANTOM5 enhancer atlas represents a unique resource for studies on cell type-specific enhancers and gene regulation.

Circular RNA - function and biogenesis
Jørgen Kjems, Interdisciplinary Nanoscience Center, Aarhus University
Circular RNA (circ-RNA) has emerged as a new group of regulatory RNAs.
They are synthesized by a "back splicing" event that appears to frequent in neuronal tissue, providing a whole new layer of gene complexity. Some of them regulate the activity of other non-coding RNAs and comprehensive profiling of circ-RNA in fetal porcine brain suggest a role in neuronal development.

Predicting RNA-protein interactions: motifs and binding sites
Quaid Morris, The Donnelly Centre, University of Toronto
How do RNA-binding proteins (RBPs) recognize their target sequences? In collaboration with Tim Hughes, we have directly measured primary RNA sequence motifs for more than 200 RBPs and inferred motifs for nearly 5,000 more RBPs by homology. This effort is continuing with the goal of defining sequence binding preferences for all metazoan RBPs with conserved RNA-binding domains.In almost all cases, RBP primary sequence specificity is not sufficient to uniquely select binding sites; I will also briefly touch on other features of RBP binding sites.Revisiting the coding potential of the E. coli genome

Renée Schroeder
Depart of Biochemistry & Cellbiology, University of Vienna
While it has become easy to define transcriptomes, it is still a challenge to assign function to newly discovered RNAs. We are using a combination of genomic SELEX and RNA seq with sppecialized libraries to address the role of non-codig RNAs. I will present this approach using the global regulator protein Hfq as lead molecule

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