Shape-based alignment of genomic landscapes in multi-scale resolution

Hiroki Ashida, Kiyoshi Asai, Michiaki Hamada

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Due to dramatic advances in DNA technology, quantitative measures of annotation data can now be obtained in continuous coordinates across the entire genome, allowing various heterogeneous 'genomic landscapes' to emerge. Although much effort has been devoted to comparing DNA sequences, not much attention has been given to comparing these large quantities of data comprehensively. In this article, we introduce a method for rapidly detecting local regions that show high correlations between genomic landscapes. We overcame the size problem for genome-wide data by converting the data into series of symbols and then carrying out sequence alignment. We also decomposed the oscillation of the landscape data into different frequency bands before analysis, since the real genomic landscape is a mixture of embedded and confounded biological processes working at different scales in the cell nucleus. To verify the usefulness and generality of our method, we applied our approach to well investigated landscapes from the human genome, including several histone modifications. Furthermore, by applying our method to over 20 genomic landscapes in human and 12 in mouse, we found that DNA replication timing and the density of Alu insertions are highly correlated genome-wide in both species, even though the Alu elements have amplified independently in the two genomes. To our knowledge, this is the first method to align genomic landscapes at multiple scales according to their shape.

Original languageEnglish
Pages (from-to)6435-6448
Number of pages14
JournalNucleic Acids Research
Volume40
Issue number14
DOIs
Publication statusPublished - 2012 Aug
Externally publishedYes

Fingerprint

Genome
DNA Replication Timing
Histone Code
Alu Elements
Biological Phenomena
Genome Size
Sequence Alignment
Human Genome
Cell Nucleus
Technology
DNA
Data Curation

ASJC Scopus subject areas

  • Genetics

Cite this

Shape-based alignment of genomic landscapes in multi-scale resolution. / Ashida, Hiroki; Asai, Kiyoshi; Hamada, Michiaki.

In: Nucleic Acids Research, Vol. 40, No. 14, 08.2012, p. 6435-6448.

Research output: Contribution to journalArticle

Ashida, Hiroki ; Asai, Kiyoshi ; Hamada, Michiaki. / Shape-based alignment of genomic landscapes in multi-scale resolution. In: Nucleic Acids Research. 2012 ; Vol. 40, No. 14. pp. 6435-6448.
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