@article{fdi:010091775,
  title = {{I}dentification and quantification of transposable element transcripts using {L}ong-{R}ead {RNA}-seq in {D}rosophila germline tissues},
  author = {{R}ebollo, {R}. and {G}erenton, {P}. and {C}umunel, {E}. and {M}ary, {A}. and {S}abot, {F}ran{\c{c}}ois and {B}urlet, {N}. and {G}illet, {B}. and {H}ughes, {S}. and {S}. {O}liveira, {D}. and {G}oubert, {C}. and {F}ablet, {M}. and {V}ieira, {C}. and {L}acroix, {V}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ransposable elements ({TE}s) are repeated {DNA} sequences potentially able to move throughout the genome. {I}n addition to their inherent mutagenic effects, {TE}s can disrupt nearby genes by donating their intrinsic regulatory sequences, for instance, promoting the ectopic expression of a cellular gene. {TE} transcription is therefore not only necessary for {TE} transposition per se but can also be associated with {TE}-gene fusion transcripts, and in some cases, be the product of pervasive transcription. {H}ence, correctly determining the transcription state of a {TE} copy is essential to apprehend the impact of the {TE} in the host genome. {M}ethods to identify and quantify {TE} transcription have mostly relied on short {RNA}-seq reads to estimate {TE} expression at the family level while using specific algorithms to discriminate copy-specific transcription. {H}owever, assigning short reads to their correct genomic location, and genomic feature is not trivial. {H}ere we retrieved full-length c{DNA}  ({T}elo{P}rime, {L}exogen) of {D}rosophila melanogaster gonads and sequenced them using {O}xford {N}anopore {T}echnologies. {W}e show that long-read {RNA}-seq can be used to identify and quantify transcribed {TE}s at the copy level. {I}n particular, {TE} insertions overlapping annotated genes are better estimated using long reads than short reads. {N}evertheless, long {TE} transcripts (> 4.5 kb)  are not well captured. {M}ost expressed {TE} insertions correspond to copies that have lost their ability to transpose, and within a family, only a few copies are indeed expressed. {L}ong-read sequencing also allowed the identification of spliced transcripts for around 107 {TE} copies. {O}verall, this first comparison of {TE}s between testes and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level.},
  keywords = {},
  booktitle = {},
  journal = {{P}eer {C}ommunity {J}ournal},
  volume = {4},
  numero = {},
  pages = {e89 [23 ]},
  ISSN = {2804-3871},
  year = {2024},
  DOI = {10.24072/pcjournal.457},
  URL = {https://www.documentation.ird.fr/hor/fdi:010091775},
}