Area of Science: 07 Molecular and Cellular Biology Abstract The eukaryotic genome is present in the nucleus as a complex three-dimensional (3D) entity, the structure of which is disorganized in certain human diseases including various cancers. However, it remains unclear how 3D genome organization influences pathological processes. One impediment is the lack of established methods to investigate higher-order genome organization in three dimensions. We propose to develop a new methodology to map the 3D structure of the genome in vivo. To accomplish this goal, we will first use the chromosome conformation capture (CCC) technique to acquire vast amounts of paired DNA fragments that reflect the physical interactions among multiple genomic loci. The CCC technique involves fixation of the in vivo genome structure by paraformaldehyde (pFA), followed by restriction enzyme digestion and DNA ligation. We will follow this with a newly developed Solexa sequencing technology, which can determine sequences for several million DNA fragments in one experiment. We will create a frequency distribution table indicating the physical interactions between DNA fragments based on the large-scale sequencing results, and model the global 3D genome structure using these data. To accelerate development of this innovative system, we will use the fission yeast Schizosaccharomyces pombe as a simple test model for our technology; then, we will apply this new method to the human genome by analyzing DNA fragments containing Alu repeats, since the human genome is too large to analyze in its entirety. By comparing 3D genome structures sampled from nondiseased and diseased individuals, we will demonstrate the involvement of higher-order genome disorganization in human diseases. This innovative method has the potential to elucidate a novel but poorly understood aspect of pathogenesis, and is also applicable for disease diagnosis by detecting subtle morphological alterations of nuclear structure in diseased individuals. Thus, it has the potential to directly and profoundly affect human health.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
NIH Director’s New Innovator Awards (DP2)
Project #
1DP2OD004348-01
Application #
7597879
Study Section
Special Emphasis Panel (ZGM1-NDIA-G (01))
Program Officer
Basavappa, Ravi
Project Start
2008-09-30
Project End
2013-06-30
Budget Start
2008-09-30
Budget End
2013-06-30
Support Year
1
Fiscal Year
2008
Total Cost
$3,127,500
Indirect Cost
Name
Wistar Institute
Department
Type
DUNS #
075524595
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Noma, Ken-Ichi (2017) The Yeast Genomes in Three Dimensions: Mechanisms and Functions. Annu Rev Genet 51:23-44
Tanizawa, Hideki; Kim, Kyoung-Dong; Iwasaki, Osamu et al. (2017) Architectural alterations of the fission yeast genome during the cell cycle. Nat Struct Mol Biol 24:965-976
Iwasaki, Osamu; Noma, Ken-Ichi (2016) Condensin-mediated chromosome organization in fission yeast. Curr Genet 62:739-743
Gadaleta, Mariana C; Das, Mukund M; Tanizawa, Hideki et al. (2016) Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres. PLoS Genet 12:e1005943
Kim, K-D; Iwasaki, O; Noma, K (2016) An IF-FISH Approach for Covisualization of Gene Loci and Nuclear Architecture in Fission Yeast. Methods Enzymol 574:167-180
Iwasaki, Osamu; Corcoran, Christopher J; Noma, Ken-Ichi (2016) Involvement of condensin-directed gene associations in the organization and regulation of chromosome territories during the cell cycle. Nucleic Acids Res 44:3618-28
Kim, Kyoung-Dong; Tanizawa, Hideki; Iwasaki, Osamu et al. (2016) Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat Genet 48:1242-52
Iwasaki, Osamu; Tanizawa, Hideki; Kim, Kyoung-Dong et al. (2015) Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes. Mol Cell 59:755-67
Gadaleta, Mariana C; Iwasaki, Osamu; Noguchi, Chiaki et al. (2013) New vectors for epitope tagging and gene disruption in Schizosaccharomyces pombe. Biotechniques 55:257-63
Kim, Kyoung-Dong; Tanizawa, Hideki; Iwasaki, Osamu et al. (2013) Centromeric motion facilitates the mobility of interphase genomic regions in fission yeast. J Cell Sci 126:5271-83

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