Periodic Report Summary 1 - CONSERVEAS (Using evolution to uncover the importance of alternative pre mRNA splicing)
The project was designed to use evolution to uncover the function of alternative splicing. The idea was to use high throughput RT-PCR to find the most conserved tissue specific alternative splices. This screen was carried out with the grant and is detailed in the already published work and the 9 highly conserved splices are available for the community to research the function of as was specified for the later years of this grant. In any case these follow up studies will require a gamut of techniques that I was not set up to deliver. The idea of working in zebrafish as set out in the grant was abandoned when I realised that non-specific effects of injection of morpholino are so common as to make embarkation on that branch of the project unlikely to be fruitful. Therefore no zebrafish work was carried out with Marie Curie money. In summary then, in spite of the deviation of not performing any zebrafish work there was good research progress in the light of the objectives for the reporting period in terms of performance of PCR across vertebrates and reporting them in the first publication.
Within this broad remit work was undertaken to finish a recent publication with the help of an MSc student Alicia Madgwick. This work is now published in Plos ONE Neural differentiation modulates the vertebrate brain specific splicing program. Madgwick A, Fort P, Hanson PS, Thibault P, Gaudreau MC, Lutfalla G, Möröy T, Abou Elela S, Chaudhry B, Elliott DJ, Morris CM, Venables JP. PLoS One. 2015 May 19;10(5):e0125998. doi: 10.1371/journal.pone.0125998. eCollection 2015. In this work we studied brain specific splicing on a large scale using mouse tissues and the Canadian RT-PCR platform. Candidate brain specific splices were followed up in human tissues and the process was repeated in zebrafish. We therefore found 9 highly brain specific splices which form the basis of this publication to further and eclipse previous work by American groups published in Science at the end of 2013. Science. 2012 Dec 21;338(6114):1587-93. The evolutionary landscape of alternative splicing in vertebrate species and Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science. 2012 Dec 21;338(6114):1593-9. Our findings move beyond the state of the art in the field, because these prestigious authors failed to produce alternative splice events that shift completely form one isoform to the other in all vertebrates as we did. Therefore our results will form a valuable resource for the future study of the role of alternative splicing in development.
A further screen was initiated with all the simple splices in the Refseq database and this will have an impact on how we interpret alternative splicing results. These results are still being analysed.
These results with have a scientific impact in that they move the field forward with a technique (RT-PCR) that is not considered to be state of the art but will have to be considered more seriously, although the momentum of next generation sequencing will not be impeded by these findings as the potential of NGS is undeniable. There could be potential social impact of the nine alternative splice vents reported if they were developed as drug targets for curing brain diseases. I disseminated our results in lab meetings and institutional seminars. The lab of David Elliott is continuing the work and has all the necessary elements.
Our results are available on the Plos website and also the more detailed result also at the Canadian PCR public data portal as promised in the grant application http://rnomics.med.usherbrooke.ca/palace?purl=http://rnomics.med.usherbrooke.ca:3000/pcrreactiongroup/list/336#_48_INSTANCE_eQvuWKO5vCA0_%3Dhttp%253A%252F%252Frnomics.med.usherbrooke.ca%252Fc%252Fiframe%252Fproxy%253Fp_l_id%253D32920%2526p_p_id%253D48_INSTANCE_eQvuWKO5vCA0%2526
Within this broad remit work was undertaken to finish a recent publication with the help of an MSc student Alicia Madgwick. This work is now published in Plos ONE Neural differentiation modulates the vertebrate brain specific splicing program. Madgwick A, Fort P, Hanson PS, Thibault P, Gaudreau MC, Lutfalla G, Möröy T, Abou Elela S, Chaudhry B, Elliott DJ, Morris CM, Venables JP. PLoS One. 2015 May 19;10(5):e0125998. doi: 10.1371/journal.pone.0125998. eCollection 2015. In this work we studied brain specific splicing on a large scale using mouse tissues and the Canadian RT-PCR platform. Candidate brain specific splices were followed up in human tissues and the process was repeated in zebrafish. We therefore found 9 highly brain specific splices which form the basis of this publication to further and eclipse previous work by American groups published in Science at the end of 2013. Science. 2012 Dec 21;338(6114):1587-93. The evolutionary landscape of alternative splicing in vertebrate species and Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science. 2012 Dec 21;338(6114):1593-9. Our findings move beyond the state of the art in the field, because these prestigious authors failed to produce alternative splice events that shift completely form one isoform to the other in all vertebrates as we did. Therefore our results will form a valuable resource for the future study of the role of alternative splicing in development.
A further screen was initiated with all the simple splices in the Refseq database and this will have an impact on how we interpret alternative splicing results. These results are still being analysed.
These results with have a scientific impact in that they move the field forward with a technique (RT-PCR) that is not considered to be state of the art but will have to be considered more seriously, although the momentum of next generation sequencing will not be impeded by these findings as the potential of NGS is undeniable. There could be potential social impact of the nine alternative splice vents reported if they were developed as drug targets for curing brain diseases. I disseminated our results in lab meetings and institutional seminars. The lab of David Elliott is continuing the work and has all the necessary elements.
Our results are available on the Plos website and also the more detailed result also at the Canadian PCR public data portal as promised in the grant application http://rnomics.med.usherbrooke.ca/palace?purl=http://rnomics.med.usherbrooke.ca:3000/pcrreactiongroup/list/336#_48_INSTANCE_eQvuWKO5vCA0_%3Dhttp%253A%252F%252Frnomics.med.usherbrooke.ca%252Fc%252Fiframe%252Fproxy%253Fp_l_id%253D32920%2526p_p_id%253D48_INSTANCE_eQvuWKO5vCA0%2526