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

doi:10.2298/CSIS170523004B

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 journal › Article › peer-review

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.

Original language	English
Pages (from-to)	473-485
Number of pages	13
Journal	Computer Science and Information Systems
Volume	15
Issue number	2
DOIs	https://doi.org/10.2298/CSIS170523004B
Publication status	Published - Jun 2018

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

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10.2298/CSIS170523004B

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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",

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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

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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 -

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

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Keywords

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