TERA-Seq: True end-to-end sequencing of native RNA molecules for transcriptome characterization
Direct sequencing of single, native RNA molecules through nanopores has a strong potential to transform research in all aspects of RNA biology and clinical diagnostics. The existing platform from Oxford Nanopore Technologies is unable to sequence the very 5′ ends of RNAs and is limited to polyadenylated molecules. Here, we develop True End-to-end RNA Sequencing (TERA-Seq), a platform that addresses these limitations, permitting more thorough transcriptome characterization than ever before. TERA-Seq describes both poly- and non-polyadenylated RNA molecules and accurately identifies their native 5′ and 3′ ends by ligating uniquely designed adapters that are sequenced along with the transcript. TERA-Seq will prove useful in many applications where true end-to-end direct sequencing of single, native RNA molecules and their isoforms is desirable.

Source code and fast5 files for TERA-Seq publication have been deposited on GitHub.

By developing Akron-seq, a novel approach that captures the native 3′ and 5′ ends of capped and polyadenylated RNAs, respectively, we showed that canonical human mRNAs are subject to repeated cotranslational and ribosome-phased endonucleolytic cuts at the exit site of the mRNA ribosome channel, in a process that we termed ribothrypsis. Source code for ribothrypsis analysis has been deposited on GitHub.

CLIPSeqTools is a collection of command-line applications used for the analysis of CLIP-Seq datasets. CLIP-Seq stands for UV cross-linking and immunoprecipitation coupled with high-throughput sequencing. The source code has been deposited on GitHub and a webpage with documentation and usage examples has been created.

GenOO is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The source code has been deposited on GitHub.

Zissimos Mourelatos Research Lab website