CpG islands’ clustering uncovers early development genes in the human genome

Vladimir N. Babenko, Anton G. Bogomolov, Roman O. Babenko, Elvira R. Galieva, Yuriy L. Orlov

Research output: Contribution to journalArticlepeer-review


We address the problem of the annotation of CpG islands (CGIs) clusters in the human genome. Upon analyzing gene content within CGIs clusters, piRNA, tRNA, and miRNA-encoding genes were found as well as CpG-rich homeobox genes reported previously. Chromosome-wide CGI density is positively correlated with replication timing, confirming that CGIs may serve as open chromatin markers. Early embryonic stage expressed KRAB-ZNF genes abundant at chromosome 19 were found to be interlinked with CGI clusters. We detected that a number of long CGIs and CGI clusters are, in fact, tandem copies with multiple annotated macrosatellites and paralogous genes. This finding implies that tandem expansion of CGIs may serve as a substrate for non-homologous recombination events.

Original languageEnglish
Pages (from-to)473-485
Number of pages13
JournalComputer Science and Information Systems
Issue number2
Publication statusPublished - Jun 2018


  • Bioinformatics
  • CpG islands
  • DNA methylation
  • Genome annotation
  • Genome repeats
  • Human genome
  • Macrosatellite
  • genome annotation
  • CTCF
  • HOX
  • bioinformatics
  • human genome
  • macrosatellite
  • genome repeats

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