Regulation of Gene Transcription by the Histone H2A N-Terminal Domain

Abstract

Histone N-terminal domains play critical roles in regulating chromatin structure and gene transcription. Relatively little is known, however, about the role of the histone H2A N-terminal domain in transcription regulation. We have used DNA microarrays to characterize the changes in genome-wide expression caused by mutations in the N-terminal domain of histone H2A. Our results indicate that the N-terminal domain of histone H2A functions primarily to repress the transcription of a large subset of the Saccharomyces cerevisiae genome and that most of the H2A-repressed genes are also repressed by the histone H2B N-terminal domain. Using the histone H2A microarray data, we selected three reporter genes (BNA1, BNA2, and GCY1), which we subsequently used to map regions in the H2A N-terminal domain responsible for this transcriptional repression. These studies revealed that a small subdomain in the H2A N-terminal tail, comprised of residues 16 to 20, is required for the transcriptional repression of these reporter genes. Deletion of either the entire histone H2A N-terminal domain or just this small subdomain imparts sensitivity to UV irradiation. Finally, we show that two residues in this H2A subdomain, serine-17 and arginine-18, are specifically required for the transcriptional repression of the BNA2 reporter gene.The packaging of DNA into chromatin has profound consequences on the regulation of gene transcription. The principal packaging unit of chromatin is the nucleosome core particle, consisting of two copies each of histones H2A, H2B, H3, and H4 and 147 bp of DNA (16). The arrangement and organization of genomic DNA into nucleosomes are not random processes, but instead appear to play an important regulatory function in transcription (14). Regions of genomic DNA are also distinguished by distinct patterns of posttranslational modifications that decorate the associated histone proteins (11). A large body of scientific literature has shown that histone posttranslational modifications are important regulators of transcription (2).The N-terminal domains of histone proteins play critical roles in both the organization and posttranslational modification of chromatin. Previous studies have shown that the histone N-terminal domains function to control the translational positioning of nucleosomes in vitro (24). Histone N-terminal domains can mediate internucleosome interactions that are required for the formation of higher-order chromatin structures (4, 25). Histone Nterminal domains are also primary sites of posttranslational modifications. These modifications, such as lysine acetylation, lysine and arginine methylation, and serine phosphorylation, can alter the stability of the nucleosome and regulate the association of transcriptional regulatory proteins (2, 6, 21).In Saccharomyces cerevisiae, a single histone H2A N-terminal modification has been verified, i.e., acetylation of H2A K7 (20,22). An additional acetylation site at H2A K4 is suspected (3, 18); however, this modification has yet to be verified in vivo.Both H2A ...

Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination

“…Deleting the H2A N-terminal tail (residues 4 -20) decreased the expression of certain Jhd2 target genes (e.g. SPL2 and CAR1) (65). Furthermore, residues 16 -20 within the H2A N-terminal tail, which constitute the H2A repression domain (65), were shown to be important for H2B ubiquitination and H3K4 methylation (67).…”

“…SPL2 and CAR1) (65). Furthermore, residues 16 -20 within the H2A N-terminal tail, which constitute the H2A repression domain (65), were shown to be important for H2B ubiquitination and H3K4 methylation (67). In a library screen of H2A mutants, alanine substitutions in certain H2A acidic patch residues reduced H3K4 methylation without affecting H2B ubiquitination (68).…”

Chromatin and Transcription in Yeast

“…Other studies addressed specific issues regarding histone function, such as functional interactions with the chromatinremodeling complex Swi/Snf (Prelich and Winston 1993;Hirschhorn et al 1995;Kruger et al 1995;Recht and Osley 1999;Duina and Winston 2004;He et al 2008), histonehistone interactions (Santisteban et al 1997;Glowczewski et al 2000), and the requirements for N-terminal lysines . Genome-wide expression analysis of histone mutants has provided broader understanding of the impact of specific histone mutants (e.g., see Wyrick et al 1999;Sabet et al 2004;Dion et al 2005;Parra et al 2006;Parra and Wyrick 2007;Nag et al 2010). Recently, large-scale studies have systematically constructed and analyzed hundreds of mutations in histone genes, providing a comprehensive data set of the histone residues that are required for normal transcription in vivo (Matsubara et al 2007;Dai et al 2008;Nakanishi et al 2008;Seol et al 2008;Kawano et al 2011).…”

Overexpression of SeveralArabidopsisHistone Genes IncreasesAgrobacterium-Mediated Transformation and Transgene Expression in Plants

“…Genome-wide expression profiling was used to identify yeast genes whose expression was altered by mutation or deletion of the N-terminal domain of histone H2A. These experimental results indicated that a small subdomain, 16 to 20 amino acid residues from the N terminus, is required for transcriptional repression of a BNA2 reporter gene (Parra and Wyrick, 2007). Our results indicate that specific regions within the N-terminal region of H2A-1 are important for increasing both transgene expression and stability.…”

“…Histone N-terminal domains may also function to control the translational positioning of nucleosomes in vitro (Parra and Wyrick, 2007) and can mediate internucleosome interactions that are required for the formation of higher-order chromatin structures.…”