An improved iCLIP protocol

Crosslinking and Immunoprecipitation (CLIP) is a powerful technique to obtain transcriptome-wide maps of in vivo protein-RNA interactions, which are important to understand the post-transcriptional mechanisms mediated by RNA binding proteins (RBPs). Many variant CLIP protocols have been developed to improve the efficiency and convenience of cDNA library preparation. Here we describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions, and with public eCLIP and iCLIP PTBP1 data. We visualised enriched motifs surrounding the identified crosslink positions and RNA maps of these crosslinks around the alternative exons regulated by PTBP1. Notably, motif enrichment was higher in iiCLIP and iCLIP2 in comparison to public eCLIP and iCLIP, and we show how this impacts the specificity of RNA maps. In conclusion, iiCLIP is technically convenient and efficient, and enables production of highly specific datasets for identifying RBP binding sites.

JAFFAL: Detecting fusion genes with long read transcriptome sequencing

Massively parallel short read transcriptome sequencing has greatly expanded our knowledge of fusion genes which are drivers of tumor initiation and progression. In cancer, many fusions are also important diagnostic markers and targets for therapy. Long read transcriptome sequencing allows the full length of fusion transcripts to be discovered, however, this data has a high rate of errors and fusion finding algorithms designed for short reads do not work. While numerous fusion finding algorithms now exist for short read RNA sequencing data, methods to detect fusions using third generation or long read sequencing data are lacking. Here we present JAFFAL a method to identify fusions from long-read transcriptome sequencing. We validated JAFFAL using simulation, cell line and patient data from Nanopore and PacBio. We show that fusions can be accurately detected in long read data with JAFFAL, providing better accuracy than other long read fusion finders and within the range of a state-of-the-art method applied to short read data. By comparing Nanopore transcriptome sequencing protocols we find that numerous chimeric molecules are generated during cDNA library preparation that are absent when RNA is sequenced directly. Finally, we demonstrate that JAFFAL enables fusions to be detected at the level of individual cells, when applied to long read single cell sequencing. JAFFAL is open source and available as part of the JAFFA package at https://github.com/Oshlack/JAFFA/wiki.

Nanopore native RNA sequencing of a human poly(A) transcriptome: RNA extraction, cDNA conversion and direct RNA and cDNA library preparation for Oxford Nanopore

High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not carried forward in cDNA. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads. These native RNA reads had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. We describe methods for extracting intact RNA, poly-A selection, cDNA conversion for a portion of sample, and library preparation for both direct RNA and cDNA libraries.

GENE EXPRESSION AND SEQUENCING TECHNIQUES OF TRANSCRIPTOME TO ELUCIDATE NOVEL FUNCTION FOR PHOSPHOLIPASE (S) ENZYME

Sequencing of RNA, or RNA-Seq, is now a common method to analyze gene expression and to uncover novel RNA species. Aspects of RNA biogenesis and metabolism can be evaluated with specialized methods for cDNA library preparation. In this study, the review examines current RNA-Seq methods for general analysis of gene expression and several specific applications, including isoform and gene fusion detection, targeted sequencing and single-cell analysis.Elucidating the transcriptome may help in better understanding of phospholipase function and novel application in diagnostics and clinical therapeutics. Therefore this review article focusses on the transcriptome analysis of the phospholipase enzymes i.e phospholipase A2, D and C isozymes and characterizing their functional roles in specialized disorders or for therapy. Key words: RNA, sequencing, transcriptome, phospholipase D, gene, expression