NDLI: Inversion symmetry of DNA k-mer counts: validity and deviations

Content Provider	Springer Nature : BioMed Central
Author	Shporer, Sagi Chor, Benny Rosset, Saharon Horn, David
Abstract	Background The generalization of the second Chargaff rule states that counts of any string of nucleotides of length k on a single chromosomal strand equal the counts of its inverse (reverse-complement) k-mer. This Inversion Symmetry (IS) holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. The existence of IS has been demonstrated in the literature, and other pair-wise candidate symmetries (e.g. reverse or complement) have been ruled out. Results Studying IS in the human genome, we find that IS holds up to k = 10. It holds for complete chromosomes, also after applying the low complexity mask. We introduce a numerical IS criterion, and define the k-limit, KL, as the highest k for which this criterion is valid. We demonstrate that chromosomes of different species, as well as different human chromosomal sections, follow a universal logarithmic dependence of KL ~ 0.7 ln(L), where L is the length of the chromosome. We introduce a statistical IS-Poisson model that allows us to apply confidence measures to our numerical findings. We find good agreement for large k, where the variance of the Poisson distribution determines the outcome of the analysis. This model predicts the observed logarithmic increase of KL with length. The model allows us to conclude that for low k, e.g. k = 1 where IS becomes the 2nd Chargaff rule, IS violation, although extremely small, is significant. Studying this violation we come up with an unexpected observation for human chromosomes, finding a meaningful correlation with the excess of genes on particular strands. Conclusions Our IS-Poisson model agrees well with genomic data, and accounts for the universal behavior of k-limits. For low k we point out minute, yet significant, deviations from the model, including excess of counts of nucleotides T vs A and G vs C on positive strands of human chromosomes. Interestingly, this correlates with a significant (but small) excess of genes on the same positive strands.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-016-3012-8.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-016-3012-8
Journal	BMC Genomics
Issue Number	1
Volume Number	17
Language	English
Publisher	BioMed Central
Publisher Date	2016-08-31
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Generalized Chargaff rules Chromosome k-mer distributions Inversion symmetry
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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