TARDIS, a targeted RNA directional sequencing method for rare RNA discovery.

Abstract:

:High-throughput transcriptional analysis has unveiled a myriad of novel RNAs. However, technical constraints in RNA sequencing library preparation and platform performance hamper the identification of rare transcripts contained within the RNA repertoire. Herein we present targeted-RNA directional sequencing (TARDIS), a hybridization-based method that allows subsets of RNAs contained within the transcriptome to be interrogated independently of transcript length, function, the presence or absence of poly-A tracts, or the mechanism of biogenesis. TARDIS is a modular protocol that is subdivided into four main phases, including the generation of random DNA traps covering the region of interest, purification of input RNA material, DNA trap-based RNA capture, and finally RNA-sequencing library construction. Importantly, coupling RNA capture to strand-specific RNA sequencing enables robust identification and reconstruction of novel transcripts, the definition of sense and antisense RNA pairs and, by the concomitant analysis of long and natural small RNA pools, it allows the user to infer potential precursor-product relations. TARDIS takes ∼10 d to implement.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Portal MM,Pavet V,Erb C,Gronemeyer H

doi

10.1038/nprot.2015.120

subject

Has Abstract

pub_date

2015-12-01 00:00:00

pages

1915-38

issue

12

eissn

1754-2189

issn

1750-2799

pii

nprot.2015.120

journal_volume

10

pub_type

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