NotI flanking sequences: a tool for gene discovery and verification of the human genome.
A set of 22 551 unique human NotI flanking sequences (16.2 Mb) was generated. More than 40% of the set had regions with significant similarity to known proteins and expressed sequences. The data demonstrate that regions flanking NotI sites are less likely to form nucleosomes efficiently and resemble promoter regions. The draft human genome sequence contained 55.7% of the NotI flanking sequences, Celera's database contained matches to 57.2% of the clones and all public databases (including non-human and previously sequenced NotI flanks) matched 89.2% of the NotI flanking sequences (identity > or =90% over at least 50 bp, data from December 2001). The data suggest that the shotgun sequencing approach used to generate the draft human genome sequence resulted in a bias against cloning and sequencing of NotI flanks. A rough estimation (based primarily on chromosomes 21 and 22) is that the human genome contains 15 000-20 000 NotI sites, of which 6000-9000 are unmethylated in any particular cell. The results of the study suggest that the existing tools for computational determination of CpG islands fail to identify a significant fraction of functional CpG islands, and unmethylated DNA stretches with a high frequency of CpG dinucleotides can be found even in regions with low CG content.
Kutsenko
Alexey S
AS
Center for Genomics and Bioinformatics, Karolinska Institute, 171 77 Stockholm, Sweden.
Gizatullin
Rinat Z
RZ
Al-Amin
Ali N
AN
Wang
Fuli
F
Kvasha
Sergei M
SM
Podowski
Raf M
RM
Matushkin
Yuri G
YG
Gyanchandani
Anita
A
Muravenko
Olga V
OV
Levitsky
Viktor G
VG
Kolchanov
Nikolay A
NA
Protopopov
Alexei I
AI
Kashuba
Vladimir I
VI
Kisselev
Lev L
LL
Wasserman
Wyeth
W
Wahlestedt
Claes
C
Zabarovsky
Eugene R
ER
D002461:Cell Line, Transformed; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*; D005796:Genes / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases