title: Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance.
abstract: Since oligonucleotide composition in the genome sequence varies significantly among species even among those possessing the same genome G + C%, the composition has been used to distinguish a wide range of genomes and called as "genome signature". Oligonucleotides often represent motif sequences responsible for sequence-specific protein binding (e.g., transcription-factor binding). Occurrences of such motif oligonucleotides in the genome should be biased compared to those observed in random sequences and may differ among genomes and genomic portions. Self-Organizing Map (SOM) is a powerful tool for clustering high-dimensional data such as oligonucleotide composition on one plane. We previously modified the conventional SOM for genome informatics to batch learning SOM or "BLSOM". When we constructed BLSOMs to analyze pentanucleotide composition in 20-, 50-, and 100-kb sequences derived from the human genome, BLSOMs did not classify human sequences according to chromosome but revealed several specific zones composed primarily of sequences derived from pericentric regions. Interestingly, various transcription-factor-binding motifs were characteristically overrepresented in pericentric regions but underrepresented in most genomic sequences. When we focused on much shorter sequences (e.g., 1 kb), the clustering of transcription-factor-binding motifs was evident in pericentric, subtelomeric and sex chromosome pseudoautosomal regions. The biological significance of the clustering in these regions was discussed in connection with cell-type and -stage-dependent chromocenter formation and nuclear organization.
authors.affiliation: Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken, 526-0829, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Iwasaki
authors.forename: Kennosuke
authors.initials: K
authors.lastname: Wada
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Wada
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence; D030541:Databases, Genetic; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D059372:Nucleotide Motifs; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors
references.citation: Genome Biol Evol. 2013;5(3):578-90
references.pmid: 23431001
references.citation: Mol Biol Evol. 1985 Jan;2(1):13-34
references.pmid: 3916708
references.citation: Genome Res. 2007 Aug;17(8):1146-60
references.pmid: 17623812
references.citation: Nat Rev Mol Cell Biol. 2009 Mar;10(3):192-206
references.pmid: 19234478
references.citation: Science. 1985 May 24;228(4702):953-8
references.pmid: 4001930
references.citation: Nat Rev Mol Cell Biol. 2004 Apr;5(4):296-304
references.pmid: 15071554
references.citation: J Mol Biol. 1988 Sep 5;203(1):1-13
references.pmid: 3054117
references.citation: Gene. 2001 Oct 3;276(1-2):89-99
references.pmid: 11591475
references.citation: DNA Res. 2005;12(5):281-90
references.pmid: 16769690
references.citation: PLoS Genet. 2010 Feb 05;6(2):e1000835
references.pmid: 20140237
references.citation: Nat Genet. 2011 Mar;43(3):220-7
references.pmid: 21317888
references.citation: Trends Genet. 2011 May;27(5):177-85
references.pmid: 21497937
references.citation: Development. 2002 Feb;129(4):945-55
references.pmid: 11861477
references.citation: Trends Genet. 2011 Apr;27(4):141-8
references.pmid: 21295369
references.citation: Nat Genet. 2002 Mar;30(3):329-34
references.pmid: 11850619
references.citation: Genome Res. 2001 Apr;11(4):540-6
references.pmid: 11282969
references.citation: Annu Rev Genet. 1998;32:185-225
references.pmid: 9928479
references.citation: Dev Cell. 2010 Oct 19;19(4):625-38
references.pmid: 20951352
references.citation: Gene. 2006 Jan 3;365:27-34
references.pmid: 16364569
references.citation: Genome Res. 2003 Apr;13(4):693-702
references.pmid: 12671005
references.citation: Nat Cell Biol. 2004 Aug;6(8):784-91
references.pmid: 15247924