The short-sequence designs of isochores from the human genome.
The human genome, a typical mammalian genome, is made up of long (approximately 1-Mb, on average) regions, the isochores, that are fairly homogeneous in base composition and belong in five families characterized by different GC levels. An analysis of di- and tri-nucleotide densities in the isochores from the five families has shown large differences. These different "short-sequence designs:" (i) account for the fractionation of human DNA (and vertebrate DNA in general) when using sequence-specific ligands in density gradients, (ii) are very similar in whole isochores and in the corresponding intergenic sequences and introns, (iii) are reflected in different codon usages, (iv) lead to amino acid differences that increase the thermal stability of the proteins encoded by genes located in increasingly GC-rich isochore families, and (v) correspond to different chromatin structures.
Costantini
Maria
M
Laboratory of Molecular Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
Bernardi
Giorgio
G
D001483:Base Sequence; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D032085:Isochores / Q000145:classification / Q000235:genetics*
D032085:Isochores
Genome Res. 2006 Apr;16(4):536-41
16597586
Biochemistry. 1979 Dec 11;18(25):5698-703
518863
Genome Res. 2003 Jul;13(7):1572-9
12840036
Gene. 1991 Oct 15;106(2):185-95
1937049
J Mol Biol. 1973 Oct 15;80(1):177-97
4798988
Gene. 1996 Sep 26;174(1):95-102
8863734
Genome Res. 2001 Apr;11(4):540-6
11282969
Gene. 2002 Oct 30;300(1-2):169-78
12468098
Science. 1985 May 24;228(4702):953-8
4001930
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3433-7
18305168
Gene. 1997 Dec 31;205(1-2):109-18
9461384
J Mol Evol. 1986;24(1-2):28-38
3104616
J Mol Biol. 1976 Nov;108(1):1-23
1003479
Nature. 2006 Aug 17;442(7104):772-8
16862119
J Biol Chem. 1961 Mar;236:864-75
13790780
J Biol Chem. 1962 Jun;237:1961-7
13918810
Gene. 2008 Aug 1;419(1-2):62-5
18436395
Gene. 1998 Dec 11;224(1-2):123-7
9931467
J Mol Biol. 1976 Nov;108(1):237-54
826644
Trends Genet. 1995 Jul;11(7):283-90
7482779
Methods Enzymol. 1992;211:67-111
1406328
Biochemistry. 1968 Dec;7(12):4373-9
5700661
Genome Res. 2002 Jun;12(6):996-1006
12045153
Eur J Biochem. 1981 Apr;115(2):227-33
7238506
Nature. 2001 Feb 15;409(6822):860-921
11237011
Nature. 2003 Jan 23;421(6921):448-53
12540921
Gene. 2004 May 26;333:143-9
15177689
Nature. 2004 Oct 21;431(7011):931-45
15496913
Gene. 2001 Oct 3;276(1-2):3-13
11591466
Eur J Biochem. 1980 Nov;112(2):203-10
7460919
J Mol Evol. 1986;24(1-2):1-11
3104608
J Mol Biol. 1976 Nov;108(1):219-35
826643
Proc Natl Acad Sci U S A. 1959 Jul;45(7):1039-43
16590475