Project #13043
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#13043 : Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing
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Name of Applicant : allemand eric
Date of application : 07-03-2019
Unit : Epigenetic Regulation
Location : Monod - 4 floor - 08
Phone : 0145688880
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Project context and summary :

Disruption of GABAergic inhibitory circuits is one of the common alteration responsible for several psychiatric developmental disorders. Gephyrin (GPHN) is the common and main molecular organizer of inhibitory synapses. It acts as a hub under the postsynaptic membrane for the multiple protein-protein interactions. Intriguingly, inhibitory synapses are highly heterogeneous, bearing various inhibitory postsynaptic potential (IPSP) properties and also specific subcellular localization on their target neuron. The molecular mechanism responsible of this diversity is still unknown although it could result, in part, of alternative splicing regulation that will produce specific GPHN isoforms carrying versatile properties. Interestingly, exons alternatively included in Gphn transcripts are proposed to change the binding of GPHN protein with inhibitory receptor as well as its oligomerization. Thus, alternative splicing regulation of Gphn expression intuitively provides a potential molecular mechanism to finely regulate several aspect of inhibitory synapse development, however this regulation step is still largely unexplored. In collaboration with Fabrice Ango (IGF-Montpellier), we have designed an experimental approach to sequence GPHN transcripts using the technologies from Pacific Bioscience and Oxford Nanopore. It was applied to samples prepared from mouse and human tissues. To date, we got sequences from Pacific Bioscience sequencing and our interaction with E. Kornobis allow us to get preliminary data that have revealed a high level of complexity in alternative transcripts expressed by GPHN in Mouse brain samples. However, we are fighting to cluster these sequences and pulling together alternative GPHN transcripts with a bioinformatic pipeline able to decipher properly between light variation of sequences and sequencing errors associated to long read sequencing. Results obtained from currently available solutions, such as PacBio IsoSeq3 analysis pipeline, led us to believe that a more suitable software solution is needed, especially to properly characterize Gephyrin splicing diversity. We propose to build a new bioinformatic pipeline to analyze our data and usable to long read sequencing obtained with Pacific Bioscience and Oxford Nanopore technologies.

Related team publications :
Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Treutlein B, Gokce O, Quake SR, S├╝dhof TC. Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):E1291-9. doi: 10.1073/pnas.1403244111. Epub 2014 Mar 17. PMID: 24639501
Gephyrin and the regulation of synaptic strength and dynamics at glycinergic inhibitory synapses. Alvarez FJ. Brain Res Bull. 2017 Mar;129:50-65. doi: 10.1016/j.brainresbull.2016.09.003. Epub 2016 Sep 6. Review. PMID: 27612963
A Broad Set of Chromatin Factors Influences Splicing. Allemand E, Myers MP, Garcia-Bernardo J, Harel-Bellan A, Krainer AR, Muchardt C. PLoS Genet. 2016 Sep 23;12(9):e1006318. doi: 10.1371/journal.pgen.1006318. eCollection 2016 Sep. PMID: 27662573
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Project Type : Long
Status : Closed

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