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

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CpG islands’ clustering uncovers early development genes in the human genome. / Babenko, Vladimir N.; Bogomolov, Anton G.; Babenko, Roman O. et al.

In: Computer Science and Information Systems, Vol. 15, No. 2, 06.2018, p. 473-485.

Research output: Contribution to journal › Article › peer-review

Harvard

Babenko, VN, Bogomolov, AG, Babenko, RO, Galieva, ER & Orlov, YL 2018, 'CpG islands’ clustering uncovers early development genes in the human genome', Computer Science and Information Systems, vol. 15, no. 2, pp. 473-485. https://doi.org/10.2298/CSIS170523004B

APA

Babenko, V. N., Bogomolov, A. G., Babenko, R. O., Galieva, E. R., & Orlov, Y. L. (2018). CpG islands’ clustering uncovers early development genes in the human genome. Computer Science and Information Systems, 15(2), 473-485. https://doi.org/10.2298/CSIS170523004B

Vancouver

Babenko VN, Bogomolov AG, Babenko RO, Galieva ER, Orlov YL. CpG islands’ clustering uncovers early development genes in the human genome. Computer Science and Information Systems. 2018 Jun;15(2):473-485. doi: 10.2298/CSIS170523004B

Author

Babenko, Vladimir N. ; Bogomolov, Anton G. ; Babenko, Roman O. et al. / CpG islands’ clustering uncovers early development genes in the human genome. In: Computer Science and Information Systems. 2018 ; Vol. 15, No. 2. pp. 473-485.

BibTeX

@article{820f66981f0248dda8c970db1899a097,

title = "CpG islands{\textquoteright} clustering uncovers early development genes in the human genome",

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.",

keywords = "Bioinformatics, CpG islands, DNA methylation, Genome annotation, Genome repeats, Human genome, Macrosatellite, DNA METHYLATION, SEQUENCES, genome annotation, TRANSCRIPTION, CTCF, HOX, bioinformatics, REGIONS, human genome, macrosatellite, PROTEINS, genome repeats",

author = "Babenko, {Vladimir N.} and Bogomolov, {Anton G.} and Babenko, {Roman O.} and Galieva, {Elvira R.} and Orlov, {Yuriy L.}",

year = "2018",

month = jun,

doi = "10.2298/CSIS170523004B",

language = "English",

volume = "15",

pages = "473--485",

journal = "Computer Science and Information Systems",

issn = "1820-0214",

publisher = "ComSIS Consortium",

number = "2",

}

RIS

TY - JOUR

T1 - CpG islands’ clustering uncovers early development genes in the human genome

AU - Babenko, Vladimir N.

AU - Bogomolov, Anton G.

AU - Babenko, Roman O.

AU - Galieva, Elvira R.

AU - Orlov, Yuriy L.

PY - 2018/6

Y1 - 2018/6

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - CpG islands

KW - DNA methylation

KW - Genome annotation

KW - Genome repeats

KW - Human genome

KW - Macrosatellite

KW - DNA METHYLATION

KW - SEQUENCES

KW - genome annotation

KW - TRANSCRIPTION

KW - CTCF

KW - HOX

KW - bioinformatics

KW - REGIONS

KW - human genome

KW - macrosatellite

KW - PROTEINS

KW - genome repeats

UR - http://www.scopus.com/inward/record.url?scp=85049921542&partnerID=8YFLogxK

U2 - 10.2298/CSIS170523004B

DO - 10.2298/CSIS170523004B

M3 - Article

AN - SCOPUS:85049921542

VL - 15

SP - 473

EP - 485

JO - Computer Science and Information Systems

JF - Computer Science and Information Systems

SN - 1820-0214

IS - 2

ER -

ID: 14864316