Eligos2

Epitranscriptional/(Epigenomical) Landscape Inferring from Glitches of ONT Signals (version 2)

Oxford Nanopore Technology (ONT) offers the sequencing platform enables us to sequence DNA and RNA in native from without amplification. Therefore, any existed modifications on the native sequences are preserved, resulting in the recorded ionic signals. The alterations of the signal, which differ from canonical base calling model, lead to the missed interpretation of base caller as sequencing errors. We use the errors to identify the positions of modifications on the RNA transcripts or DNA sequences.

ELIGOS is developed to identify the position of modification on the native RNA sequences from the distinction of error at specific base (ESB) between the native RNA sequences with the reference. We employ the standard statistical analysis, Fisher's exact test to evaluate the distinction of error. The reference can be unmodified RNA sequences derived from in vitro transcription, cDNA sequences or our develop background error model (rBEM), which mimic the systematic errors of unmodified RNA sequences.

ELIGOS can be currently applied to perform :

1. Differential epitranscriptome analysis between two different conditions (DNA,RNA) (see example 1)

2. Epitranscriptome profiling (RNA) (see example 2)

3. Identification of DNA modifications such as DNA adduct (see example 3)

Please cite:

1. Piroon Jenjaroenpun, Thidathip Wongsurawat, Taylor D Wadley, Trudy M Wassenaar, Jun Liu, Qing Dai, Visanu Wanchai, Nisreen S Akel, Azemat Jamshidi-Parsian, Aime T Franco, Gunnar Boysen, Michael L Jennings, David W Ussery, Chuan He, Intawat Nookaew, Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Research, 2020, gkaa620, https://doi.org/10.1093/nar/gkaa620
2. Intawat Nookaew, Piroon Jenjaroenpun, Hua Du, Pengcheng Wang, Jun Wu, Thidathip Wonsurawat, Sun Hee Moon, En Huang, Yinsheng Wang, Gunnar Boysen, Detection and discrimination of DNA adducts differing in size, regiochemistry and functional group by nanopore sequencing., Chemical Research in Toxicology, 2020, https://doi.org/10.1021/acs.chemrestox.0c00202