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5CAPture-seq: a method for enriching full-length cDNA and identifying 5′ capped nucleotides

ABSTRACT: Current transcriptomic methods for mapping 5′-ends of eukaryotic RNA employ only 5′-end enriched samples. The absence of a matched unenriched control limits the ability to distinguish genuine 5′ ends from incomplete cDNAs. We developed a transcriptomic method based on sequencing of cDNA enriched for full-length fragments and an unenriched control. From the mapped sequence reads, enrichment scores are calculated for all transcribed nucleotides and a statistical model of the enrichment constructed. We tested the method in the human malaria parasite Plasmodium falciparum. Data were obtained from ring, trophozoite and schizont stages of the parasite intra-erythrocytic development cycle. Two groups of 5′ capped nucleotides were assigned by unsupervised clustering. The first group contains sites located mostly outside of annotated protein-coding exons in regions of high local nucleosomal occupancy, but low occupancies of ribosome and elongating RNA polymerase II. The majority of sites in the second group are intra-exonic and show different patterns, most notably a peak of ribosome occupancy centered on the 5′ end position and a biased representation among codons possibly prone to ribosome stalling. Our method can be used to annotate 5′ capped nucleotides, including intra-exonic nucleotides that can be distinguished from incomplete cDNA artifacts.

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE103036 | GEO | 2021/08/02

REPOSITORIES: GEO

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