We have introduced the histone variant H3.3 into chicken erythroid cell lines and examined its distribution in the neighborhood of the folate receptor (FR) and -globin genes by using high-resolution chromatin immunoprecipitation (ChIP). Marked incorporation of tagged H3.3 into the FR gene is confined to its upstream regulatory region and is observed whether or not the gene is transcriptionally active. Incorporation is also observed over locus control regulatory elements in the absence of transcription of genes regulated by these elements, suggesting that gene activity per se is not necessarily required to replace H3 with H3.3. Other active genes display various behaviors, either incorporating H3.3 over both the coding region and upstream regulatory region or over upstream sequences only. There is, however, no straightforward correlation between sites of H3.3 incorporation and regions of enrichment in H3 acetylation and lysine-4 methylation. In the case of FR and VEGF-D, in which incorporation is confined to upstream regions, the presence of exogenous H3 results in reduced expression, whereas H3.3 stimulates expression. This finding suggests that these histone variants can be active rather than passive participants in regulation of expression.folate receptor ͉ vascular endothelial growth factor D ͉ globin ͉ chromatin H istone variants are incorporated into chromatin at sites that suggest that the variants play an important role as epigenetic marks. Among these, the variants of histone H3 have been the focus of considerable attention. A family of H3-like proteins (CenH3) is localized at the centromeres of eukaryotes, where it replaces histone H3 and appears to play a critical role in defining centromeric identity (1, 2). Recently, it has been shown that another H3 variant, H3.3, is incorporated into chromatin throughout the cell cycle, in contrast to H3, which is incorporated only during S phase (3). This constraint ensures that if nucleosomes that are disrupted or lost during transcription must be replaced, the new nucleosomes will contain H3.3. Presumably, as a result, H3.3-containing nucleosomes are enriched in euchromatin (3). Consistent with this view, H3.3 isolated from a Drosophila cell line is enriched in covalent modifications associated with transcriptionally active chromatin such as acetylation at multiple lysines and methylation at Lys-4 (K4) (4). The mechanism of H3.3 deposition involves a specialized chaperone complex containing the protein HIRA. In contrast, the replication-dependent incorporation of H3 is effected by a replication-specific complex that includes CAF-1 (5).Recent microarray studies in Drosophila provide strong evidence for a correlation between transcriptional activity and H3.3 incorporation (6). Because of the association of H3.3 with transcriptionally active chromatin domains, it has been suggested that there is a causal relationship between the presence of H3.3 and the accessibility of the chromatin template for transcription. It has been noted that if H3.3-containing chromatin i...