NET-Seq

PSI-Seq

PSI-Seq identifies RNA sequences containing pseudouridine sites using high-throughput sequencing. PSI-Seq uses N-Cyclohexyl-N′-(2-morpholinoethyl)carbodiimide (CMC) to modify pseudouridines selectively, effectively halting reverse transcription. The cDNA libraries are prepared by the ARTseq method. Briefly, samples are poly(A)-selected, treated with DNase, and fragmented. CMC is added to modify existing pseudouridines, and the 3′ ends of the RNA are ligated to linker-adapters. Next, the RNA fragments are reverse-transcribed to cDNA; however, upon encountering CMC-modified pseudouridines, reverse transcription is halted. cDNA strands of 20–80 nt are isolated and processed into cDNA libraries using the Ribo-Seq/ARTseq method before high-throughput sequencing.

Similar methods: Pseudo-seq, Ψ-Seq, CeU-Seq.

Pros:

• Identifies pseudouridylation sites in ncRNAs
• Single-base resolution
• Uses a regression analysis to compare reads in a specific location between treated and mock-treated libraries¹

Cons:

• None reported yet

• PSI-Seq: Lovejoy A. F., Riordan D. P. and Brown P. O. Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae. PLoS One. 2014;9:e110799
• 1. Zaringhalam M. and Papavasiliou F. N. Pseudouridylation meets next-generation sequencing. Methods. 2016;107:63-72

1. Zaringhalam M. and Papavasiliou F. N. Pseudouridylation meets next-generation sequencing. Methods. 2016;107:63-72

1. Lovejoy A. F., Riordan D. P. and Brown P. O. Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae. PLoS One. 2014;9:e110799