A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes

Ganapathiraju MK, Subramanian S, Chaparala S, Karundkaran KB. A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. Human Genome Variation 2020 Nov 20;7(1):40. doi:10.1038/s41439-020-00127-5. PMID: 33298903 PMCID: PMC7680136

A palindrome in DNA is like a palindrome in language, but when read backwards, it is a complement of the forward sequence; effectively, the two halves of a sequence complement each other from its midpoint like in a double strand of DNA. Palindromes are distributed throughout the human genome and play significant roles in gene expression and regulation. Palindromic mutations are linked to many human diseases, such as neuronal disorders, mental retardation, and various cancers. In this work, we computed and analyzed the palindromic sequences in the human genome and studied their conservation in personal genomes using 1000 Genomes data. We found that ~30% of the palindromes exhibit variation, some of which are caused by rare variants. The analysis of disease/trait-associated single-nucleotide polymorphisms in palindromic regions showed that disease-associated risk variants are 14 times more likely to be present in palindromic regions than in other regions. The catalog of palindromes in the reference genome and 1000 Genomes is being made available here with details on their variations in each individual genome to serve as a resource for future and retrospective whole-genome studies identifying statistically significant palindrome variations associated with diseases or traits and their roles in disease mechanisms.

Publication Year: 
2020
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Ganapathiraju MK, Subramanian S, Chaparala S, Karundkaran KB.
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