macroH2A1 Histone Variants Are Depleted on Active Genes but Concentrated on the Inactive X Chromosome

Abstract

Using a novel thiol affinity chromatography approach to purify macroH2A1-containing chromatin fragments, we examined the distribution of macroH2A1 histone variants in mouse liver chromatin. We found that macroH2A1 was depleted on the transcribed regions of active genes. This depletion was observed on all of the 20 active genes that we probed, with only one site showing a small amount of enrichment. In contrast, macroH2A1 was concentrated on the inactive X chromosome, consistent with our previous immunofluorescence studies. This preferential localization was seen on genes that are active in liver, genes that are inactive in liver, and intergenic regions but was absent from four regions that escape X inactivation. These results support the hypothesis that macroH2As function as transcriptional repressors. Also consistent with this hypothesis is our finding that the heterochromatin protein HP1β copurifies with the macroH2A1-containing chromatin fragments. This study presents the first detailed examination of the distribution of macroH2A1 variants on specific sequences. Our results indicate that macroH2As have complex distribution patterns that are influenced by both local factors and long-range mechanisms.

Supplemental material for this article may be found at http://mcb.asm.org/.

We thank Steve Seeholzer for the identification of proteins by mass spectrometry; Chhaya Dharia, Leslie Taylor, Dannee Chen, Carl Costanzi, and Denys Volgin for technical help and suggestions; Mike Atchison and Narayan Avadhani for comments on the manuscript; and Sandra Martin for LINE L1 clones.

This work was supported by Public Health Service grant GM49351 from the NIH.