Name
Abstract | ||
|---|---|---|
Evolutionary trends have been examined in 146 HIV-1 forms (2662 copies, 2311 isolates) polymorphic for the TATA box using the "DNA sequence-->affinity for TBP" regression (TBP is the TATA binding protein). As a result, a statistically significant excess of low-affinity TATA box HIV-1 variants corresponding to a low level of both basal and TAT-dependent expression and, consequently, slow replication of HIV-1 have been detected. A detailed analysis revealed that the excess of slowly replicating HIV-1 is associated with the subtype E-associated TATA box core sequence "CATAAAA". Principal Component Analysis performed on 2662 HIV-1 TATA box copies in 70 countries revealed the presence of two principal components, PC1 (75.7% of the variance) and PC2 (23.3% of the variance). They indicate that each of these countries is specifically associated with one of the following trends in HIV-1 evolution: neutral drift around the normal TATA box; neutral drift around the slowly replicating TATA box core sequence (phylogenetic inertia); an adaptive increase in the frequency of the slowly replicating form. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1142/S0219720010004677 | J. Bioinformatics and Computational Biology |
Keywords | Field | DocType |
snp,tata box,prediction | TATA box,Biology,TATA-binding protein,DNA,Single-nucleotide polymorphism,Bioinformatics,Genetics | Journal |
Volume | Issue | ISSN |
8 | 3 | 1757-6334 |
Citations | PageRank | References |
1 | 0.36 | 3 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Valentin V Suslov | 1 | 3 | 1.08 |
| Petr M Ponomarenko | 2 | 2 | 0.72 |
| Vadim M Efimov | 3 | 1 | 0.36 |
| Ludmila K Savinkova | 4 | 1 | 0.36 |
| Mikhail P Ponomarenko | 5 | 131 | 27.97 |
| Nikolay A. Kolchanov | 6 | 470 | 105.75 |