The Histone Variant MacroH2A1 Regulates Target Gene Expression in Part by Recruiting the Transcriptional Coregulator PELP1

Abstract

MacroH2A1 is a histone variant harboring an ∼25-kDa carboxyl-terminal macrodomain. Due to its enrichment on the inactive X chromosome, macroH2A1 was thought to play a role in transcriptional repression. However, recent studies have shown that macroH2A1 occupies autosomal chromatin and regulates genes in a context-specific manner. The macrodomain may play a role in the modulation of gene expression outcomes via physical interactions with effector proteins, which may depend on the ability of the macrodomain to bind NAD⁺ metabolite ligands. Here, we identify proline, glutamic acid, and leucine-rich protein 1 (PELP1), a chromatin-associated factor and transcriptional coregulator, as a ligand-independent macrodomain-interacting factor. We used chromatin immunoprecipitation coupled with tiling microarrays (ChIP-chip) to determine the genomic localization of PELP1 in MCF-7 human breast cancer cells. We find that PELP1 genomic localization is highly correlated with that of macroH2A1. Additionally, PELP1 positively correlates with heterochromatic chromatin marks and negatively correlates with active transcription marks, much like macroH2A1. MacroH2A1 specifically recruits PELP1 to the promoters of macroH2A1 target genes, but macroH2A1 occupancy occurs independent of PELP1. This recruitment allows macroH2A1 and PELP1 to cooperatively regulate gene expression outcomes.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.01315-13.

ACKNOWLEDGMENTS

We thank Shrikanth Gadad and Xin Luo for critical reading of the manuscript, Trevor Halle for assistance in making the MCF-7 TetR cell line, Lynne Lacomis for help with mass spectrometry and sample preparation, Rosemary Conry for preparing the GST-macrodomain fusions, and Hans Clevers and Marc Timmers for the Tet-inducible expression constructs.

This work was supported by grants from the NIH/NIDDK (DK069710), Cornell University's NanoBiotechnology Center (an STC Program of the NSF, agreement no. ECS-9876771), and the Endocrine Society to W.L.K., by a predoctoral fellowship from the American Heart Association to K.M.H., by postdoctoral fellowships from the American Heart Association and the NIH/NIDDK (F32DK079847) and a grant from the NIH/NCI (R01CA155232) to M.J.G., and by an NIH/NCI Cancer Center Support Grant (P30 CA08748) to P.T.