Paper Info
Title
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/di-nucleotide/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., break-points 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.
Year
DOI
Venue
2020
10.1371/journal.pcbi.1007968
PLOS COMPUTATIONAL BIOLOGY
DocType
Volume
Issue
Journal
16
6
ISSN
Citations 
PageRank 
1553-734X
0
0.34
References 
Authors
0
9
Name
Order
Citations
PageRank
Hui Yu12314.31
Shilin Zhao272.50
Scott Ness301.69
Huining Kang401.35
Quanhu Sheng5225.61
David C. Samuels621.37
Olufunmilola Oyebamiji701.35
Ying-Yong Zhao800.68
Yan Guo912.71