Edward Trifonov
Edward Trifonov
Project: CHROMPLANT - Plant chromatin, structure and fiction at single base resolution
Person in Charge: prof. RNDr. Jiří Fajkus, CSc.
Host institution: Department of Experimental Biology, Faculty of Science, Masaryk University
Country of Origin: Israel
Project duration: 15 months
Scientific panel: Life sciences
Abstract:
Recent developments in high throughput sequencing and sequence analyses make possible increasingly detailed studies of chromatin. In particular, the first computer program has been developed in the Genome Diversity Center, Haifa University, that allows to map the nucleosomes on the sequences with single base resolution. This opens a unique possibility to study 3D structure and function of chromatin. Indeed, knowing exact positions of the nucleosomes on the sequence, one can calculate from the lengths of the linkers between the nucleosomes their mutual orientation and, hence, local architecture of chromatin. This is especially important for chromatin that involves promoters, telomeres, centromeres, origins of replication etc. The project is aimed to, specifically, plant chromatin studies. First, for computational generation of DNA bendability matrix for plants (Arabidopsis to begin with) a large experimentally derived database of the nucleosome sequences will be constructed in the laboratory of Prof. J. Fajkus (Masaryk Univ.) with whom we have a long standing scientific collaboration. The nucleosome mapping procedure will be then developed, similar to currently used program, available on public server. The 3D reconstruction of chromatin segments of interest on the basis of the accurate nucleosome maps will be conducted by an original program under development in the Genome Diversity Center. The standard architectural elements of plant chromatin will be revealed, for the first time with high resolution, comparable to resolution of x-ray crystallography. The sequence-directed reconstruction of the chromatin 3D structure will be possible for every segment of natural chromatin which cannot be done by means of crystallography. Knowing the architecture of promoter chromatin one would be able to rationalize interactions of promoters with transcription factors, their spatial distribution around promoters and details of regulation of gene expression.
The ongoing project summary:
One of the main research objectives of the project is to derive the nucleosome positioning (bendability) sequence patterns for various genomes of general interest, including the plant genomes. During the first year of the project a significant progress was achieved both in results and in pattern derivation techniques, involving several species, by a whole genome analyses. We have reconstructed the bendability patterns for 13 complete genomes by a novel approach, never used before in bioinformatics studies – extension of highest frequency trinucleotides (Shannon N‐gram extension). The consensus of the patterns reconstructed is derived: CRAAAATTTTYG, and, in binary form: YRRRRRYYYYYR. The Table 1 summarizes the results of the studies during the first year of the project.
Table 1. Nucleosome positioning [patterns derived by various means from various sequences
Pattern technique/sequences reference
CC GGRAA TTYCC GG theoretical, bendability [1]
C GGAAA TTTCC G reconstruction from partial signal [11]
C.elegans, nucleosome database.
C AAAAA TTTTT G Shannon N-gram extension, AT-based, [5]
13 genomes, incl. A.thaliana
C GAAAA TTTTT R Same, CG-based
T AAAAA TTTTT A Shannon extension, isochores L1, L2, [8]
human, mouse, chicken genomes.
C AGAAA TTTCT G Same, isochores H1
Y RGGGR YCCCY R Same, isochores H2
Y RGGGG CCCCY R Same, isochores H3
C GGGGG CCCCC G Same, isochores H4
T AAAAA TTTTT A signal reconstruction, human L1 [13]
C AGGGG CCCCT G same, human H3
General consensus:
Y RRRRR YYYYY R
The results above clearly demonstrate universality of the pattern Y RRRRR YYYYY R, and make us confident that the forthcoming nucleosome database for A.thaliana will generate the same pattern as provided by a whole genome analysis. The data above also demonstrated for the first time that the nucleosome positioning pattern is substantially different in different isochores.