[en] We use the wavelet transform modulus maxima method to investigate the multifractal properties of strand-asymmetry DNA walk profiles in the human genome. This study reveals the bifractal nature of these profiles, which involve two competing scale-invariant (up to repeat-masked distances less than or similar to 40 kbp) components characterized by Holder exponents h(1)=0.78 and h(2)=1, respectively. The former corresponds to the long-range-correlated homogeneous fluctuations previously observed in DNA walks generated with structural codings. The latter is associated with the presence of jumps in the original strand-asymmetry noisy signal S. We show that a majority of upward (downward) jumps colocate with gene transcription start (end) sites. Here 7228 human gene transcription start sites from the refGene database are found within 2 kbp from an upward jump of amplitude Delta S >= 0.1 which suggests that about 36% of annotated human genes present significant transcription-induced strand asymmetry and very likely high expression rate.
Disciplines :
Physics
Author, co-author :
Nicolay, Samuel ; Université de Liège - ULiège > Département de mathématique > Analyse, analyse fonctionnelle, ondelettes
A. Arneodo, in The Science of Disasters: Climate Disruptions, Heart Attacks, and Market Crashes, edited by, A. Bunde, J. Kropp, and, H. Schellnhuber, (Springer-Verlag, Berlin, 2002), p. 26.
A. Arneodo, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.74.3293 74, 3293 (1995);
A. Arneodo, Physica D PDNPDT 0167-2789 10.1016/0167-2789(96)00029-2 96, 291 (1996).
B. Audit, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.86.2471 86, 2471 (2001);
B. Audit, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.2001.5363 316, 903 (2002).
C. Vaillant, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95. 068101 95, 068101 (2005);
C. Vaillant, Eur. Phys. J. E EPJSFH 1292-8941 19, 263 (2006).
E. Chargaff, Fed. Proc. FEPRA7 0014-9446 10, 654 (1951);
R. Rudner, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 60, 921 (1968).
J. W. Fickett, Genomics GNMCEP 0888-7543 10.1016/0888-7543(92)90019-O 13, 1056 (1992);
J. R. Lobry, J. Mol. Evol. JMEVAU 0022-2844 10.1007/BF00163237 40, 326 (1995).
J. M. Freeman, Science SCIEAS 0036-8075 279, 1827 (1998);
A. Beletskii, J. Mol. Biol. JMOBAK 0022-2836 300, 1057 (2000);
M. P. Francino and H. Ochman, J. Mol. Evol. JMEVAU 0022-2844 18, 1147 (2001).
J. Mrázek and S. Karlin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.7.3720 95, 3720 (1998);
A. C. Frank and J. R. Lobry, Gene GENED6 0378-1119 10.1016/S0378-1119(99) 00297-8 238, 65 (1999);
E. P. Rocha, Mol. Microbiol. MOMIEE 0950-382X 10.1046/j.1365-2958.1999. 01334.x 32, 11 (1999);
E. R. M. Tillier and R. A. Collins, J. Mol. Evol. JMEVAU 0022-2844 50, 249 (2000).
P. Green, Nat. Genet. NGENEC 1061-4036 10.1038/ng1103 33, 514 (2003).
M. Touchon, FEBS Lett. FEBLAL 0014-5793 10.1016/S0014-5793(03)01306-1 555, 579 (2003);
