Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages.
BACKGROUND
Deficiency 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.


RESULTS
Here, 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.


CONCLUSIONS
These 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.
Department of Anatomy and Embryology, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, 305-8575, Ibaraki, Japan. c0730195@md.tsukuba.ac.jp
Mariko
M
Morita
Megumi
M
Nakamura
Michito
M
Hamada
Satoru
S
Takahashi
D020816:Amino Acid Motifs; D000818:Animals; D002454:Cell Differentiation; D015922:Complement C1q / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D050982:GATA1 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D008264:Macrophages / Q000166:cytology* / Q000378:metabolism; D051258:MafB Transcription Factor / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D050982:GATA1 Transcription Factor; C494689:Gata1 protein, mouse; D051258:MafB Transcription Factor; D015922:Complement C1q