Periodic Reporting for period 1 - TIGER (Transposable element Impacts on Gene Expression and Regulation)
Reporting period: 2015-10-19 to 2017-10-18
During the troubleshooting period of the ChIP and the delays imposed by technical problems, I have developed two in silico projects: the first one aims at deciphering the role of TE sequences in differential expression of genes between Drosophila strains but as opposed to the previous proposal, this project will detect TSSs, exonizations and truncations. The second project aims at uncovering gene expression differences between strains of Drosophila simulans that are due to differential piRNA production. PiRNAs are well known regulators of TEs. Both projects are novel and took advantage of genome-wide data produced in the host laboratory allowing immediate use. We found that less than 2% of genes contain a TE sequence within its transcripts. Interestingly, ""chimeric genes"" present higher expression than genes lacking any TE sequences and in addition an over representation of chimeric genes is found in upregulated compared to stable or downregulated genes between drosophila strains. We are currently confirming such results in candidate genes that are upregulated and harbor TE sequences within their transcripts. In sum, this first in silico project suggests that in Drosophila, TEs could potentially increase the expression of host genes. Concerning the second in silico project, we have shown that small RNAs of 23-29bp with a ping pong signature are potentially able of targeting host genes. Interestingly, these piRNAs do not necessarily map to a TE sequence, suggesting either that the TE sequences are too degraded or that genes are able to produce their own piRNAs. But the most curious finding is that most genes are targeted by such piRNAs, with or without TE similarities. These piRNAs target coding domain sequences and are depleted from 5' untranslated regions, where most regulatory sequences are found. We are currently mining for gene expression between populations differences due to these piRNAs."
The two in silico projects will have published public pipelines that can be used by other researchers working on drosophila or other model species. In addition, while this project focuses on identifying TE derived TSSs, the data generated has many applications. There are several ways changes in gene expression can occur. By mapping all promoters, characterizing all the transcripts we will acquire extensive information on any promoter responsible for gene expression differences that may exist in D. melanogaster strains. These data can also be used to quantify TE expression differences between strains along with epigenetic regulation of such TEs. In conclusion, the data generated by this project should be of significant value for many researchers and will be the first genome-wide promoter and chromatin mapping survey in different wild-derived strains of D. melanogaster. In sum, the objectives proposed by this project are only the beginning of the exploitation of the data produced.