Argonaute-Crosslinking and Immunprecipitation Argonaute-crosslinking and immunoprecipitation (AGO-CLIP) is a protocol that maps miRNA binding to AGO sites in C. elegans (Grosswendt et al., 2014). In this method, the photoreactive nucleoside 4-SU is first incorporated into C. elegans RNA in vivo. The 4-SU_labeled RNA is crosslinked […]

All of the RNA:Protein interaction sequencing methods are collected together under this heading

Transcript Leader Sequencing TL-Seq targets and enriches for the sequence around the 5′-UTRs of 5′-capped mRNA molecules before sequencing (Arribere et al., 2013). Poly(A)+ RNA is fragmented and selected for 50_80 nt fragments. RNA fragments with phosphorylated 5′ ends are dephosphorylated, using calf intestinal phosphatase […]

Transcript Isoform Sequencing Transcript isoform sequencing (TIF-Seq) identifies transcript isoforms by selective sequencing of full-length mRNA molecules with 5’caps and poly(A) tails (Pelechano et al., 2013). Capped mRNA molecules are selected by substituting the 5’caps with oligonucleotides. To achieve this result, 5′-phosphate groups are removed […]

Translation-Associated Transcript Leader Sequencing TATL-Seq works in conjunction with TL-Seq to target the sequence around the 5′-UTRs of mRNA attached to polysomes (Arribere et a., 2013). RNA from polysome gradient fractions is extracted, poly(A)-selected, and fragmented. Next, the TL-Seq protocol is followed to isolate and […]

Poly(A) Tail Sequencing TAIL-Seq focuses on sequencing the very ends of mRNA molecules (3′-UTRs and poly(A) tail regions) to explore their role in mRNA half-life, stability, their impact on translational efficiency, and to discover other aspects surrounding 3′-terminome function (Chang et al., 2014). Ribosomal RNA […]

Simultaneous Mapping of RNA Ends with Sequencing SMORE-Seq is an RNA-Seq method to identify TSS and polyadenylation sites (PAS) by sequencing the 5′ and 3′ ends simultaneously (Park et al., 2014). Poly(A)+ RNA is first isolated from total RNA, and the 5′ caps are removed […]

RNA Sequencing RNA-Seq describes the abundance and sequence of RNA transcripts. The method, first published by several groups in 2008 (Wilhelm et al., 2008). (Sultan et al., 2008). (Marioni et al., 2008). (Mortazavi et al., 2008). (Nagalakshmi et al., 2008).has effectively displaced older methods such […]

RNA-Mediated Oligonucleotide Annealing, Selection, and Ligation with Next-Generation Sequencing RNA-mediated oligonucleotide annealing, selection, and ligation with next-generation sequencing (RASL-Seq) is a 2-dimensional RNA sequencing method to quantify expression profiles of several hundred genes, under thousands of different conditions (Li et al., 2012). Custom probe pairs […]

Restriction Site Associated RNA Sequencing RARseq is a cDNA-based, genotype-by-sequencing method for identifying RNA SNPs and polymorphic loci for population genomics (Alabady et al., 2015). This method performs read alignment using sequencing data from single and dual restriction enzyme digestion libraries and aligns them using […]