Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats

Abstract

Very short tandem repeats bear substantial genetic, evolutional, and pathological significance in genome analyses. Here, we compiled a census of tandem mono-nucleotide/dinucleotide/tri-nucleotide repeats (MNRs/DNRs/TNRs) in GRCh38, which we term "polytracts" in general. Of the human genome, 144.4 million nucleotides (4.7%) are occupied by polytracts, and 0.47 million single nucleotides are identified as polytract hinges, i.e., breakpoints of tandem polytracts. Preliminary exploration of the census suggested polytract hinge sites and boundaries of AAC polytracts may bear a higher mapping error rate than other polytract regions. Further, we revealed landscapes of polytract enrichment with respect to nearly a hundred genomic features. We found MNRs, DNRs, and TNRs displayed noticeable difference in terms of locational enrichment for miscellaneous genomic features, especially RNA editing events. Non-canonical and C-to-U RNA-editing events are enriched inside and/or adjacent to MNRs, while all categories of RNA-editing events are under-represented in DNRs. A-to-I RNA-editing events are generally under-represented in polytracts. The selective enrichment of non-canonical RNA-editing events within MNR adjacency provides a negative evidence against their authenticity. To enable similar locational enrichment analyses in relation to polytracts, we developed a software Polytrap which can handle 11 reference genomes. Additionally, we compiled polytracts of four model organisms into a Track Hub which can be integrated into USCS Genome Browser as an official track for convenient visualization of polytracts.

Epitranscriptome Analysis of Oxidative Stressed Retinal Epithelial Cells Depicted a Possible RNA Editing Landscape of Retinal Degeneration

“…U-to-C was initially identified in the mRNA of Wilm’s tumor 1 (WT1) human transcript [ 13 ], while G-to-A was identified in the heterogeneous nuclear ribonucleoprotein K (hnRNP K) protein of colorectal cancer and surrounding tissues [ 14 ]. However, the exact mechanism of these RNA editing types is still under investigation, and there is also disagreement regarding the prevalence of such non-canonical RNA editing [ 15 ].…”

Genomic Variants Disrupt miRNA‐mRNA Regulation

“…RNA editing primarily takes the form of adenine-to-inosine (A-to-I) or cytosine-to-uracil (C-to-U) substitutions. [12] Studies have found that RNA editing can alter protein sequences, [13] affect drug sensitivity, [14] and cause poor cancer prognosis. [15] Because A-to-I subtitutions account for an overwhelming proportion of all RNA editing events (95 %), [16] we focused on A-to-I RNA editing in this study.…”

“…RNA editing is an enzymatic event that changes RNA molecules’ nucleotide sequence in relation to the corresponding DNA sequence. RNA editing primarily takes the form of adenine‐to‐inosine (A‐to‐I) or cytosine‐to‐uracil (C‐to‐U) substitutions [12] . Studies have found that RNA editing can alter protein sequences, [13] affect drug sensitivity, [14] and cause poor cancer prognosis [15] .…”

A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data

“…The [COORDINATE] parameter specifies a BED-formatted file for genomic locations of suspicious repeat regions. We have included the URLs to our published resource of very short tandem repeats23 in Supplementary Data 1. Users can download the human or yeast Mono-Nucleotide Repeats or Di-Nucleotide Repeats and subtract those regions.…”