@article {Wang859488, author = {Jingwen Wang and Bingnan Li and Sueli Marques and Lars M. Steinmetz and Wu Wei and Vicent Pelechano}, title = {Improved transcriptome annotation and read-through transcript identification with TIF-Seq2}, elocation-id = {859488}, year = {2019}, doi = {10.1101/859488}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Eukaryotic transcriptomes are complex involving thousands of overlapping transcripts. The interleaved nature of the transcriptome complicates its annotation, limits our ability to identify regulatory regions and, in some cases, can lead to misinterpretation of gene expression. To improve the annotation of complex genomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5{\textquoteright} and 3{\textquoteright} end of individual mRNA molecules at single-nucleotide resolution. We investigate the transcriptome of a well characterized human cell line (K562) and identify thousands of new transcript isoforms. By focusing on RNAs challenging to investigate with RNA-seq, we accurately define boundaries of lowly expressed intergenic and read-through transcripts. We validate those novel features in cell lines and in Chronic Myeloid Leukaemia patients. Our results demonstrate that TIF-Seq2 improves the annotation of complex genomes facilitating the assignment of promoters to genes and the identification of transcriptionally fused proteins.}, URL = {https://www.biorxiv.org/content/early/2019/11/29/859488}, eprint = {https://www.biorxiv.org/content/early/2019/11/29/859488.full.pdf}, journal = {bioRxiv} }