Delineation of the Protein Module That Anchors HMGN Proteins to Nucleosomes in the Chromatin of Living Cells

Abstract

Numerous nuclear proteins bind to chromatin by targeting unique DNA sequences or specific histone modifications. In contrast, HMGN proteins recognize the generic structure of the 147-bp nucleosome core particle. HMGNs alter the structure and activity of chromatin by binding to nucleosomes; however, the determinants of the specific interaction of HMGNs with chromatin are not known. Here we use systematic mutagenesis, quantitative fluorescence recovery after photobleaching, fluorescence imaging, and mobility shift assays to identify the determinants important for the specific binding of these proteins to both the chromatin of living cells and to purified nucleosomes. We find that several regions of the protein affect the affinity of HMGNs to chromatin; however, the conserved sequence RRSARLSA, is the sole determinant of the specific interaction of HMGNs with nucleosomes. Within this sequence, each of the 4 amino acids in the R-S-RL motif are the only residues absolutely essential for anchoring HMGN protein to nucleosomes, both in vivo and in vitro. Our studies identify a new chromatin-binding module that specifically recognizes nucleosome cores independently of DNA sequence or histone tail modifications.

ACKNOWLEDGMENTS

We thank David Landsman, National Center for Biotechnology Information, National Institutes of Health (NIH), for numerous helpful comments on the manuscript and S. Garfield, Confocal Core Facility, LEC, National Cancer Institute (NCI), for help with imaging experiments.

This research was supported by the intramural program of the NCI, by a JSPS research fellowship for Japanese Biomedical and Behavioral Research at NIH to T.U., and by a Jacob and Lena Joels Foundation visiting professorship from the Hebrew University, Jerusalem, Israel, to M.B.