COLD SPRING HARBOR LABORATORY CONFERENCE EUKARYOTIC mRNA PROCESSING AUGUST 20 - 24, 2013 The proposed conference on 'Eukaryotic mRNA Processing' will convene scientists studying various aspects of mRNA processing, transport, RNA interference, informatics and turn-over. Major advances have recently been made in these areas, and the proposed conference will be a timely event for discussing the latest unpublished results and exchanging ideas, thereby fostering new developments in this rapidly moving field. The proposed 2013 conference will be held in August and is the ninth meeting of a conference that is held every other year at Cold Spring Harbor Laboratory. The most recent meeting was held in August 2011 and attracted 335 scientists internationally, who are actively investigating various aspects of messenger RNA maturation in eukaryotic cells, using genetic, biochemical, molecular, and cell biological approaches.

Intellectual Merit: As in the previous meetings, a major focus will be on nuclear events in mRNA maturation, including mRNA splicing and polyadenylation, as well as the relevance of mRNA maturation to the etiology of cancer, the connections between mRNA maturation steps, the emerging fields of RNA interference and microRNA function and the application of informatics and genome-wide approaches to the analysis of RNA processing. The meeting format will consist of eight plenary sessions and two poster sessions. Each plenary session will be subdivided into two parts (separated by a coffee break) that focus on related but separate topics. This subdivision, successfully piloted at the 2011 meeting, allows us to specifically seek out a broader representation of fields and to recruit a more diverse set of faculty as session chairs. As always, all speakers will be selected on the basis of the submitted abstracts, which will encourage active participation by junior scientists. We will particularly encourage presentation of unpublished work by the students and postdoctoral fellows who are leading these projects, as has traditionally been a hallmark and a unique strength of the Cold Spring Harbor meetings.

Broader Impacts: The broader impacts of the proposed activity are manifold. First, they include the scientific implications for other fields beyond eukaryotic mRNA processing of, as discoveries in this field will continue to foster a rapid pace of fundamental discoveries and insights in our efforts to more fully understand gene expression in higher organisms. Second, they also include elements of education, training, resource sharing, and opportunities for interaction and collaboration. In particular, the meeting will provide: (i) training opportunities for junior scientists that will promote the development of presentation skills as well as overall scientific quality and analytical rigor; (ii) an intimate setting that will foster meaningful scientific interactions among scientists at all career levels; (iii) the dissemination of knowledge among multiple strata of research and educational institutions; (iv) sharing of resources, both material and informational; and (v) opportunities for the initiation of collaborations, which can benefit scientists from smaller labs and/or from primarily undergraduate (teaching) institutions who may have fewer resources and more limited access to cutting-edge technologies than do scientists from major research institutions.

Project Report

Cold Spring Harbor Laboratory Eukaryotic mRNA Processing August 20-24, 2013 Organized by: Tom Blumenthal, University of Colorado Kristen Lynch, University of Pennsylvania Karla Neugebauer, Yale University 336 PARTICIPANTS The eighth Eukaryotic mRNA processing meeting was held this summer to present and discuss recent developments in mRNA metabolism. As in the past, the regulation of alternative pre-mRNA splicing was a focus, as was the mechanism of spliceosome assembly and catalysis. Additional areas included mRNA 3’ end formation, mRNA decay, mRNA trafficking, and the coupling of RNA processing to transcription and export. Structural, live cell imaging and genome-wide approaches were interwoven into the sessions, reflecting state-of-the-art techniques currently applied to understanding how mRNA is processed in vivo and in vitro. Following on our aim to include all aspects of RNA biology, reports on miRNA, RNAi and non-coding RNA were encouraged and well represented. In addition to our traditional splicing mechanisms session, this topic was additionally visited in our kick-off session on RNA-protein interactions as well as a session on RNP assembly and functions. One highlight among splicing mechanisms was the presentation of a high resolution structure of the yeast PRP24 protein bound to the U6 snRNA, revealing extensive interfaces of the protein chaperone with the RNA that promote RNA rearrangements en route to mature U6 snRNP formation. These phenomena contrasted with energy-dependent rearrangements carried out by e.g. Prp5 and Prp16 in the spliceosome, as well as a study on the role of U6 snRNA at the catalytic center. This year, an overwhelming number of abstracts on alternative splicing regulation were received, reflecting the development of approaches to studying transcript isoforms in model organisms and tissues. This also reflects the momentum the field has gained in identifying RNA-protein interactions, thanks largely to in vivo cross-linking approaches, such as CLIP. Therefore many abstracts on alternative splicing also appeared in the sessions on RNA-protein interactions and RNP assembly and functions, in addition to the session on RNA Processing and Disease and Global Analyses. These included the development of splicing targeted therapeutics. Several presentations on alternative 3´ end formation established that polyA site choice is highly regulated and a major source of transcript variability, linking polyadenylation, transcription and quality control. A major advance in the field – namely the discovery of triple helix formation at 3’ ends, providing resistance to mRNA decay mechanisms – was described in the last session. In the RNA decay session, the nonsense mediated decay (NMD) pathway was a particular focus, including work showing that NMD sculpts the cellular transcriptome, disconnecting transcript abundance from transcriptional output, by altering the stability of specific transcripts. Several studies honed in on the activity of Staufen, a double-stranded RNA binding protein implicated in Staufen-mediated decay (SMCD), in order to understand how target specificity is achieved. The RNA Cell Biology and Co-transcriptional RNA processing sessions focused on genome-wide approaches to RNA-protein interactions that influence RNA localization, live-cell imaging, NGS approaches to measuring the kinetics of transcription and splicing in living cells, and changes in processing due to cell signaling and progression through the cell cycle.

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