Title: Prsentation PowerPoint
1DNA in chromatin
how to extract structural, dynamical and
functional information from the analysis of
genomic sequences using space-scale wavelet
techniques
Alain Arneodo Laboratoire de Physique, Ecole
Normale Supérieure de Lyon 46 allée dItalie,
69364 Lyon Cedex 07, FRANCE
Françoise Argoul Benjamin Audit Samuel
Nicolay ENS de Lyon, France Edward-Benedict
Brodie of Brodie Cédric
Vaillant EPF Lausanne,
Switzerland Marie Touchon
Yves dAubenton-Carafa CGM, Gif-sur-Yvette,
France Claude Thermes
2(No Transcript)
3DeoxyriboNucleic Acid
- Double helix macromolecule
- Each strand consists of an oriented sequence of
four possible nucleotides - Adenine, Thymine, Guanine Cytosine
- Complementary strands
- AT GC over the sum of both strands
4(No Transcript)
5Sequencing projects result in 4 letter texts
6(No Transcript)
7(No Transcript)
8(No Transcript)
9(No Transcript)
10(No Transcript)
11(No Transcript)
12(No Transcript)
13(No Transcript)
14(No Transcript)
15(No Transcript)
16(No Transcript)
17(No Transcript)
18(No Transcript)
19SYNTHETIC DNA SEQUENCES
n
n
20SYNTHETIC DNA WALKS
Fractional Brownian motions BH
n
21(No Transcript)
22(No Transcript)
23G C poor
G C rich
24(No Transcript)
25(No Transcript)
26(No Transcript)
27(No Transcript)
28(No Transcript)
29(No Transcript)
30(No Transcript)
31(No Transcript)
32(No Transcript)
33AFM visualisation of a reconstituted chromatin
fiber Pierre-Louis Porté, Emeline Fontaine,
Cendrine Moskalenko
Images obtained in Tapping Mode in air
34Linear DNA (2500 bp) positioning nucleosomes
Image obtained in Tapping Mode in air
35Linear DNA (2500 bp) positioning nucleosomes
Image obtained in Tapping Mode in air
36Plasmid DNA (3200 bp) nucleosomes
Images obtained in Tapping Mode in air
37Plasmid DNA (3200 bp) nucleosomes
Images obtained in Tapping Mode in air
38(No Transcript)
39(No Transcript)
40Chromosome 22 (Human)
41 Transcription
Replication
Opening of the double helix with a different
environment for each strand gt asymmetrical
process
42Symmetrical properties of the strands Parity
Rule type 2
A T G C in each strand
Deviations from this property estimated by the
compositional skews
Compositional skew due to local biases in a
strand in the course of biological mechanisms
43Strand Compositional Asymmetry
44A wavelet based methodology to detect gene
clusters Chromosome 22 (Human)
Scale (bp) A/T C/G skew
45A wavelet based methodology to detect replication
origins
Experimentaly observed replication origin in the
human genome Globin 4008 kb Chromosome
11 Predicted RO 4009 kb
Scale (bp) A/TC/G skew
46A wavelet based methodology to detect replication
origins
Experimentaly observed replication origin in the
human genome Lamin B2 2368 kb Chromosome
19 Predicted RO 2365 kb
Scale (bp) A/TC/G skew
47Transcription bias
48Transcription bias
Detecting discontinuities using the wavelet
transform
49Application to a known human replication origin
First evidence of a replication bias in human DNA
50Application to a known human replication origin
First evidence of a replication bias in human DNA
51Application to a known human replication origin
First evidence of a replication bias in human DNA
Our model well defined replication origins,
separated by diffuse terminuses
52Profile detection using an analyzing wavelet
adapted to the shape of replicons
53Profile detection using an analyzing wavelet
adapted to the shape of replicons
54Deterministic Chaos in DNA Sequences
55SHILNIKOV HOMOCLINIC CHAOS
56(No Transcript)
57Strand Compositional Asymmetry
58Phase Portrait Representation of ATCG skew
59(No Transcript)
60(No Transcript)