Serum Response Factor Utilizes Distinct Promoter- and Enhancer-Based Mechanisms To Regulate Cytoskeletal Gene Expression in Macrophages

Abstract

Cells of the monocyte/macrophage lineage play essential roles in tissue homeostasis and immune responses, but mechanisms underlying the coordinated expression of cytoskeletal genes required for specialized functions of these cells, such as directed migration and phagocytosis, remain unknown. Here, using genetic and genomic approaches, we provide evidence that serum response factor (SRF) regulates both general and cell type-restricted components of the cytoskeletal gene expression program in macrophages. Genome-wide location analysis of SRF in macrophages demonstrates enrichment of SRF binding at ubiquitously expressed target gene promoters, as expected, but also reveals that the majority of SRF binding sites associated with cell type-restricted target genes are at distal inter- and intragenic locations. Most of these distal SRF binding sites are established by the prior binding of the macrophage- and the B cell-specific transcription factor PU.1 and exhibit histone modifications characteristic of enhancers. Consistent with this, representative cytoskeletal target genes associated with these elements require both SRF and PU.1 for full expression. These findings suggest that SRF uses two distinct molecular strategies to regulate programs of cytoskeletal gene expression: a promoter-based strategy for ubiquitously expressed target genes and an enhancer-based strategy at target genes that exhibit cell type-restricted patterns of expression.

ACKNOWLEDGMENTS

A.L.S. was supported by a grant from the American Heart Association. These studies were also supported by NIH grants P01-HC088093 and R01 CA52599 to C.K.G. and HL091168 to J.M.M. C.K.G. acknowledges support from a Leducq Transatlantic Network grant. We also acknowledge the UCSD Neuroscience Microscopy Shared Facility (grant P30 NS047101).

We thank James Sprague, Roman Sasik, and Colleen Ludka of the UCSD Biogem Core facility for their microarray and ChIP sequencing services and M. G. Farquhar for microscope access. Mx-CRE mice were a kind gift of L. Goldstein. We thank Lynn Bautista for her assistance with preparation of the figures.

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00836-10.