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Indian Journal of Biochemistry and Biophysics (IJBB) >
IJBB Vol.48 [2011] >
IJBB Vol.48(1) [February 2011] >
| Title: | Signals in the promoter regions of several cancerous genes |
| Authors: | Das, Dibyajyoti
Mitra, Chanchal K |
| Keywords: | Transcription factor
Promoter
miRNA
Cancerous gene
Nucleotide hexamer |
| Issue Date: | Feb-2011 |
| Publisher: | NISCAIR-CSIR, India |
| Abstract: | The eukaryotic core promoter regions are
complex and fuzzy, usually lacking any conserved regions. However, they contain
signals in the form of short stretches of nucleic acid sequences, for
transcription start sites (TSS) that are recognized by the transcription
factors (TFs). The core promoter region thus plays an important role in
biological pathways (gene network and activation). It has been reported that
these signals are composed of nucleotide hexamers in the promoter sequence
(smaller sequences are likely to have too little information to be useful and
longer sequences are too complex to be recognized by proteins) reasonably close
to the TSS. The signals (nucleotide hexamers) have been identified by a
similarity search on the eukaryotic promoter database (EPD, Homo sapiens).
The signals have been classified, depending on their base composition. They
have been have clustered using an algorithm, such that there are two and three
nucleotide differences between the classes and a single nucleotide difference
within a class. We have reclassified the hexamers taking the highest frequent
hexamers present in the EPD (Homo sapiens) as the class representatives.
Also we have tried to find whether the same composition is reflected on the
miRNAs but found that they probably have other functions unrelated to promoter
recognition. In this report melanoma carcinoma pathway has been chosen as the
reference pathway and the promoters of the driver genes has been searched for
the presence of the major classes. A few of these were found and are reported
here. Several non-cancerous genes have also been studied as reference and
comparison. |
| Page(s): | 14-21 |
| CC License: |  CC Attribution-Noncommercial-No Derivative Works 2.5 India |
| ISSN: | 0975-0959 (Online); 0301-1208 (Print) |
| Source: | IJBB Vol.48(1) [February 2011]
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