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Abstract:
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Identification of common sub-sequences for a group of functionally
related DNA sequences can shed light on the role of such elements in cell-specific gene
expression. In the megakaryocytic lineage, no one single unique transcription factor was
described as linage specific, raising the possibility that a cluster of gene promoter
sequences presents a unique signature. Here, the megakaryocytic gene promoter group, which
consists of both human and mouse 5' non-coding regions, served as a case study. A
methodology for group-combinatorial search has been implemented as a customized software
platform. It extracts the longest common sequences for a group of related DNA sequences and
allows for single gaps of varying length, as well as double- and multiple-gap sequences. The
results point to common DNA sequences in a group of genes that is selectively expressed in
megakaryocytes, and which does not appear in a large group of control, random and specific
sequences. This suggests a role for a combination of these sequences in cell-specific gene
expression in the megakaryocytic lineage. The data also point to an intrinsic cross-species
difference in the organization of 5' non-coding sequences within the mammalian genomes. This
methodology may be used for the identification of regulatory sequences in other
lineages. |
