TIGER · Transposable element Impacts on Gene Expression and Regulation

Transposable element Impacts on Gene Expression and Regulation

Transposable elements (TEs) are DNA sequences that are able to spread within and between genomes. TEs have been described in most species analyzed to date, constituting up to 90% of a host genome. While transposition may lead to evident harmful effects, TEs can also positively impact the host genome by, for instance, donating intrinsic regulatory elements such as promoters. Hence, TEs are responsible for formation and rewiring of gene regulatory networks and therefore may play a role in species diversity. The main goal of this research project is to understand the regulatory changes that TEs engage within host genomes. Some host species show higher rates of TE activity than others as observed in Drosophila, where TEs are thought to be responsible for 80% of the visible spontaneous mutations in contrast with 0.1% in humans. While many examples of TEs acting as regulatory sequences have been described in mammals and plants, very few cases were observed in Drosophila, mainly due to strains studied and methods used.The overall objective of this research project is to understand the extent of TE-derived regulatory sequences in different Drosophila species and strains and their impact in host gene expression and regulation. I planned to uncover gene expression differences between D. melanogaster strains due to TE-derived transcription start sites, and to study the epigenetic regulation of such promoters. In addition, I also included a new in silico research on the presence of TE sequences within transcripts obtained from RNA sequencing paired end data sets from both D. melanogaster and D. simulans wild-derived populations. The usage of wild-derived strains in genome-wide studies is completely novel. While most researchers to date have based their analysis on TE copies present in D. melanogaster sequenced strain, or have simply analyzed single TE copies, this proposal combines different approaches in order to completely grasp the impact of TEs on transcriptome diversity: 1) the usage of insertionally polymorphic copies (copies present in one strain and absent from another) and 2) genome-wide datasets. This project emerges from a very dynamic field of research, where only very recently TEs were shown to act as promoters in Drosophila. The findings of this project should be broadly significant for the fields of Drosophila genetics, transposable element biology, host defence and evolution.

Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз