Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages

Mariko Morita,Megumi Nakamura,Michito Hamada,Satoru Takahashi

doi:10.1186/1752-0509-5-s2-s7

Abstract

BackgroundDeficiency of the transcription factor MafB, which is normally expressed in macrophages, can underlie cellular dysfunction associated with a range of autoimmune diseases and arteriosclerosis. MafB has important roles in cell differentiation and regulation of target gene expression; however, the mechanisms of this regulation and the identities of other transcription factors with which MafB interacts remain uncertain. Bioinformatics methods provide a valuable approach for elucidating the nature of these interactions with transcriptional regulatory elements from a large number of DNA sequences. In particular, identification of patterns of co-occurrence of regulatory cis-elements (motifs) offers a robust approach.ResultsHere, the directional relationships among several functional motifs were evaluated using the Log-linear Graphical Model (LGM) after extraction and search for evolutionarily conserved motifs. This analysis highlighted GATA-1 motifs and 5’AT-rich half Maf recognition elements (MAREs) in promoter regions of 18 genes that were down-regulated in Mafb deficient macrophages. GATA-1 motifs and MafB motifs could regulate expression of these genes in both a negative and positive manner, respectively. The validity of this conclusion was tested with data from a luciferase assay that used a C1qa promoter construct carrying both the GATA-1 motifs and MAREs. GATA-1 was found to inhibit the activity of the C1qa promoter with the GATA-1 motifs and MafB motifs.ConclusionsThese observations suggest that both the GATA-1 motifs and MafB motifs are important for lineage specific expression of C1qa. In addition, these findings show that analysis of combinations of evolutionarily conserved motifs can be successfully used to identify patterns of gene regulation.

Highlights

In recent years, genomic analyses have identified many short DNA sequences that function as transcriptional regulatory elements and show evolutionary conservation
In an attempt to understand the motif information, we focused on our analysis of MafB, which is bound to the Maf recognition elements (MAREs) in the promoter region of genes that are down-regulated in Mafb deficient macrophages
Postulates that ”GATA-1 motifs and MafB motifs negatively and positively regulate expression of 18 genes that are down-regulated in Mafb deficient macrophages, respectively”

Summary

Introduction

Genomic analyses have identified many short DNA sequences that function as transcriptional regulatory elements and show evolutionary conservation. These signature sequences are usually referred to as ”motifs”. In order to expedite investigation of long and complex mammalian genomes, it was necessary to develop computer science methods that permitted analyses to be performed in real-time with high-sensitivity and high-precision. One such approach is the Smith-Waterman algorithm [3], which permits sequence ambiguity, and provides high accuracy and flexibility, not with high processing speed. Identification of patterns of co-occurrence of regulatory cis-elements (motifs) offers a robust approach

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Discussion

Conclusion