| RRC ID |
36994
|
| Author |
Ohta S, Montaño-Gutierrez LF, de Lima Alves F, Ogawa H, Toramoto I, Sato N, Morrison CG, Takeda S, Hudson DF, Rappsilber J, Earnshaw WC.
|
| Title |
Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes.
|
| Journal |
Mol Cell Proteomics
|
| Abstract |
Packaging of DNA into condensed chromosomes during mitosis is essential for the faithful segregation of the genome into daughter nuclei. Although the structure and composition of mitotic chromosomes have been studied for over 30 years, these aspects are yet to be fully elucidated. Here, we used stable isotope labeling with amino acids in cell culture to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes. Our analysis revealed that these complexes associate with chromosomes independently of each other, with the SMC5/6 complex showing no significant dependence on any other chromosomal proteins during mitosis. To identify subtle relationships between chromosomal proteins, we employed a nano Random Forest (nanoRF) approach to detect protein complexes and the relationships between them. Our nanoRF results suggested that as few as 113 of 5058 detected chromosomal proteins are functionally linked to chromosome structure and segregation. Furthermore, nanoRF data revealed 23 proteins that were not previously suspected to have functional interactions with complexes playing important roles in mitosis. Subsequent small-interfering-RNA-based validation and localization tracking by green fluorescent protein-tagging highlighted novel candidates that might play significant roles in mitotic progression.
|
| Volume |
15(8)
|
| Pages |
2802-18
|
| Published |
2016-8-1
|
| DOI |
10.1074/mcp.M116.057885
|
| PII |
S1535-9476(20)33505-2
|
| PMID |
27231315
|
| PMC |
PMC4974353
|
| MeSH |
Adenosine Triphosphatases / genetics
Adenosine Triphosphatases / metabolism
Animals
Cell Culture Techniques
Cell Cycle Proteins / genetics*
Cell Cycle Proteins / metabolism
Cell Line
Chickens
Chromosomal Proteins, Non-Histone / genetics
Chromosomal Proteins, Non-Histone / metabolism
Chromosomes / genetics*
Chromosomes / metabolism
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
Isotope Labeling
Mitosis*
Multiprotein Complexes / genetics
Multiprotein Complexes / metabolism
Proteomics / methods*
|
| IF |
4.87
|
| Times Cited |
12
|
|
WOS Category
|
BIOCHEMICAL RESEARCH METHODS
|
| Resource |
| DNA material |
Genome Network Project Clone IRAL004E22 (HGY081718). |
