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

Vladimir N. Babenko^{1, 2, 3}, Anton G. Bogomolov^{1, 2}, Roman O. Babenko², Elvira R. Galieva² and Yuriy L. Orlov^{1, 2, 3}

Institute of Cytology and Genetics SB RAS
Lavrentyeva 10, 630090 Novosibirsk, Russia
bob@bionet.nsc.ru
Novosibirsk State University
Pirogova 2, 630090 Novosibirsk, Russia
The A.O. Kovalevsky Institute of Marine Biological Research of RAS
Nakhimov ave. 2, 299011 Sevastopol, Russia
{mantis_anton,galieva,orlov}@bionet.nsc.ru

Abstract

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.

Key words

CpG islands, bioinformatics, human genome, macrosatellite, genome annotation, genome repeats, DNA methylation

Digital Object Identifier (DOI)

https://doi.org/10.2298/CSIS170523004B

Publication information

Volume 15, Issue 2 (June 2018)
Year of Publication: 2018
ISSN: 2406-1018 (Online)
Publisher: ComSIS Consortium

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How to cite

Babenko, V. N., Bogomolov, A. G., Babenko, R. O., Galieva, E. R., Orlov, Y. L.: CpG islands’ clustering uncovers early development genes in the human genome. Computer Science and Information Systems, Vol. 15, No. 2. (2018), https://doi.org/10.2298/CSIS170523004B