Final answer:
Yes, changes of transposable elements in Drosophila can be detected using RNA-Seq as it sequences all expressed genes and captures post-transcriptional modifications. TE movements affecting gene expression can be inferred, though additional methods may be necessary to specifically correlate changes to TEs.
Step-by-step explanation:
Can Transposable Elements in Drosophila be Detected Using RNA-Seq?
RNA-Seq, a method used for gene expression analysis, has the potential to detect changes in transposable elements (TEs) within the Drosophila genome. Transposable elements, which are DNA sequences capable of changing position within a genome, can influence gene expression and genomic stability. The RNA-Seq technology is tailored to sequence all of the transcriptomes, which represents all expressed genes, including RNA interference (RNAi) related sequences that might be affected by the activity of TEs.
Understanding the post-transcriptional modifications of RNA molecules is crucial when investigating TEs since their movement can result in alternative splicing, gene silencing, or even gene activation. These events can be captured by RNA-Seq, allowing researchers to infer the presence and effect of transposable element movements. However, tracing the origin of such modifications specifically to TEs might require supplementary methods, like whole-genome sequencing and further bioinformatics analyses, to correlate RNA-Seq data with specific transposable element changes.
For research utilizing RNAi, such as the high-throughput screening that allows for the functional analysis of genes by silencing them, RNA-Seq can be useful in confirming the efficiency and specificity of the RNAi effect. In the example of the dung beetle experiment mentioned, RNAi blocked the orthodenticle gene, resulting in an unexpected 'third eye.' In Drosophila, such drastic changes due to TEs could be detected using RNA-Seq by observing changes in gene expression patterns related to the affected genes.