Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis

被引：47

作者：

Levitsky, VG ^{[1
]}

Podkolodnaya, OA ^{[1
]}

Kolchanov, NA ^{[1
]}

Podkolodny, NL ^{[1
]}

机构：

[1] Inst Cytol & Genet, Lab Theoret Genet, Novosibirsk 630090, Russia

来源：

BIOINFORMATICS | 2001年 / 17卷 / 11期

基金：

俄罗斯基础研究基金会;

关键词：

D O I：

10.1093/bioinformatics/17.11.998

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: A rapid growth in the number of genes with known sequences calls for developing automated tools for their classification and analysis. It became clear that nucleosome packaging of eukaryotic DNA is very important for gene functioning. Automated computer tools for characterization of nucleosome packaging density could be useful for studying of gene regulation and genome annotation. Results: A program for constructing nucleosome formation potential profiles of eukaryotic DNA sequences was developed. Nucleosome packaging density was analyzed for different functional types of human promoters. It was found that in promoters of tissue-specific genes, the nucleosome formation potential was essentially higher than in genes expressed in many tissues, or housekeeping genes. Hence, capability of nucleosome positioning in the promoter region may serve as a factor regulating gene expression.

引用

页码：998 / 1010

页数：13

共 48 条

[1] NUCLEOSOME DISPLACEMENT IN TRANSCRIPTION [J].

ADAMS, CC ;

WORKMAN, JL .

CELL, 1993, 72 (03) :305-308

[2] Naturally occurring nucleosome positioning signals in human exons and introns [J].

Baldi, P ;

Brunak, S ;

Chauvin, Y ;

Krogh, A .

JOURNAL OF MOLECULAR BIOLOGY, 1996, 263 (04) :503-510

[3] MULTIPLE NUCLEOSOME POSITIONING WITH UNIQUE ROTATIONAL SETTING FOR THE SACCHAROMYCES-CEREVISIAE 5S RIBOSOMAL-RNA GENE IN-VITRO AND IN-VIVO [J].

BUTTINELLI, M ;

DIMAURO, E ;

NEGRI, R .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993, 90 (20) :9315-9319

[4] PRINCIPLES OF SEQUENCE-DEPENDENT FLEXURE OF DNA [J].

CALLADINE, CR ;

DREW, HR .

JOURNAL OF MOLECULAR BIOLOGY, 1986, 192 (04) :907-918

[5] TGGA repeats impair nucleosome formation [J].

Cao, H ;

Widlund, HR ;

Simonsson, T ;

Kubista, M .

JOURNAL OF MOLECULAR BIOLOGY, 1998, 281 (02) :253-260

[6] A LEISURELY LOOK AT THE BOOTSTRAP, THE JACKKNIFE, AND CROSS-VALIDATION [J].

EFRON, B ;

GONG, G .

AMERICAN STATISTICIAN, 1983, 37 (01) :36-48

[7] The use of multiple measurements in taxonomic problems [J].

Fisher, RA .

ANNALS OF EUGENICS, 1936, 7 :179-188

[8]

FITZGERALD DJ, 1994, J BIOL CHEM, V269, P21303

[9] NUCLEOSOME POSITIONING ON THE MMTV LTR RESULTS FROM THE FREQUENCY-BIASED OCCUPANCY OF MULTIPLE FRAMES [J].

FRAGOSO, G ;

JOHN, S ;

ROBERTS, MS ;

HAGER, GL .

GENES & DEVELOPMENT, 1995, 9 (15) :1933-1947

[10] Chromatin structure analysis of the human c-fos promoter reveals a centrally positioned nucleosome [J].

Herrera, RE ;

Nordheim, A ;

Stewart, AF .

CHROMOSOMA, 1997, 106 (05) :284-292

← 1 2 3 4 5 →