title: NotI clones in the analysis of the human genome.
abstract: Not I linking clones contain sequences flanking Not I recognition sites and were previously shown to be tightly associated with CpG islands and genes. To directly assess the value of Not I clones in genome research, high density grids with 50 000 Not I linking clones originating from six representative Not I linking libraries were constructed. Altogether, these libraries contained nearly 100 times the total number of Not I sites in the human genome. A total of 3437 sequences flanking Not I sites were generated. Analysis of 3265 unique sequences demonstrated that 51% of the clones displayed significant protein similarity to SWISSPROT and TREMBL database proteins based on MSPcrunch filtering with stringent parameters. Of the 3265 sequences, 1868 (57.2%) were new sequences, not present in the EMBL and EST databases (similarity < or =90%). Among these new sequences, 795 (24.3%) showed similarity to known proteins and 712 (21.8%) displayed an identity of >75% at the nucleotide level to sequences from EMBL or EST databases. The remaining 361 (11.1%) sequences were completely new, i.e. <75% identical. The work also showed tight, specific association of Not I sites with the first exon and suggest that the so-called 3' ESTs can actually be generated from 5'-ends of genes that contain Not I sites in their first exon.
authors.affiliation: Center for Genomics Research, Karolinska Institute, Stockholm, Sweden. eugzab@ki.se
authors.forename: E R
authors.initials: ER
authors.lastname: Zabarovsky
authors.forename: R
authors.initials: R
authors.lastname: Gizatullin
authors.forename: R M
authors.initials: RM
authors.lastname: Podowski
authors.forename: V V
authors.initials: VV
authors.lastname: Zabarovska
authors.forename: L
authors.initials: L
authors.lastname: Xie
authors.forename: O V
authors.initials: OV
authors.lastname: Muravenko
authors.forename: S
authors.initials: S
authors.lastname: Kozyrev
authors.forename: L
authors.initials: L
authors.lastname: Petrenko
authors.forename: N
authors.initials: N
authors.lastname: Skobeleva
authors.forename: J
authors.initials: J
authors.lastname: Li
authors.forename: A
authors.initials: A
authors.lastname: Protopopov
authors.forename: V
authors.initials: V
authors.lastname: Kashuba
authors.forename: I
authors.initials: I
authors.lastname: Ernberg
authors.forename: G
authors.initials: G
authors.lastname: Winberg
authors.forename: C
authors.initials: C
authors.lastname: Wahlestedt
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D018899:CpG Islands; D017931:DNA Primers / Q000235:genetics; D016208:Databases, Factual; D015252:Deoxyribonucleases, Type II Site-Specific; D020224:Expressed Sequence Tags; D015723:Gene Library; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000235:genetics; D015183:Restriction Mapping
chemical_list: D017931:DNA Primers; D012333:RNA, Messenger; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases