Showing papers on "Histone binding published in 2001"

Structure and function of histone acetyltransferases.

Abstract: Histone acetyltranferase (HAT) enzymes are the catalytic subunit of large multisubunit HAT complexes that acetylate the e-amino group of specific lysine residues on histone tails to promote transcriptional activation. Recent structural and functional studies on the divergent HAT enzymes Gcn5/PCAF, Esa1 and Hat1 have provided new insights into the underlying mechanism of histone binding and acetylation by HAT proteins. The three HAT enzymes contain a structurally conserved core domain that plays a functionally conserved role in binding the coenzyme A cofactor and in harboring the putative general base for catalysis. Structurally variable N- and C-terminal domains appear to contain a related scaffold that mediates histone substrate binding. These data provide a framework for understanding the structure and function of other more divergent HAT proteins such as TAFII250 and CBP/p300, and provides a starting point for understanding how HAT proteins may cooperate with other factors within in vivo HAT complexes to promote transcriptional activation.

Multiple Interactions in Sir Protein Recruitment by Rap1p at Silencers and Telomeres in Yeast

Abstract: Initiation of transcriptional silencing at mating type loci and telomeres in Saccharomyces cerevisiae requires the recruitment of a Sir2/3/4 (silent information regulator) protein complex to the chromosome, which occurs at least in part through its association with the silencer- and telomere-binding protein Rap1p. Sir3p and Sir4p are structural components of silent chromatin that can self-associate, interact with each other, and bind to the amino-terminal tails of histones H3 and H4. We have identified a small region of Sir3p between amino acids 455 and 481 that is necessary and sufficient for association with the carboxyl terminus of Rap1p but not required for Sir complex formation or histone binding. SIR3 mutations that delete this region cause a silencing defect at HMR and telomeres. However, this impairment of repression is considerably less than that displayed by Rap1p carboxy-terminal truncations that are defective in Sir3p binding. This difference may be explained by the ability of the Rap1p carboxyl terminus to interact independently with Sir4p, which we demonstrate by in vitro binding and two-hybrid assays. Significantly, the Rap1p-Sir4p two-hybrid interaction does not require Sir3p and is abolished by mutation of the carboxyl terminus of Rap1p. We propose that both Sir3p and Sir4p can directly and independently bind to Rap1p at mating type silencers and telomeres and suggest that Rap1p-mediated recruitment of Sir proteins operates through multiple cooperative interactions, at least some of which are redundant. The physical separation of the Rap1p interaction region of Sir3p from parts of the protein required for Sir complex formation and histone binding raises the possibility that Rap1p can participate directly in the maintenance of silent chromatin through the stabilization of Sir complex-nucleosome interactions.

A homeotic mutation in the trithorax SET domain impedes histone binding

Abstract: The Polycomb group (PcG) of repressors and trithorax group (trxG) of activators target chromatin in order to “freeze” a mitotically stable pattern of gene expression and determined cell fate (Pirrotta 1998; Lyko and Paro 1999; Mahmoudi and Verrijzer 2001). The founding member of the trxG, the Drosophila trx gene, is required throughout development and controls the expression of several developmental regulators, including the homeotic genes (Ingham and Whittle 1980; Ingham 1985; Breen 1999). trx is related to the human Mixed Lineage Leukemia (MLL) gene, which is involved in translocations associated with the majority of cases of infant leukemias (Waring and Cleary 1997). TRX and MLL are part of a highly conserved regulatory network that is required for the correct expression of the homeotic selector genes and determination of segment identity in both mammals and Drosophila. They are very large proteins that contain structural motifs common to chromatin-associated factors such as PHD fingers and a C-terminal SET domain (Fig. ​(Fig.1A;1A; Mazo et al. 1990; Stassen et al. 1995). Figure 1 The TRX SET domain binds histones and nucleosomes. (A) Schematic representation of the domain structure of TRX. Ignoring other conserved regions, only the PHD fingers, and the C-terminal SET domain are indicated. (B) The TRX SET domain interacts preferentially ... The SET domain is a highly conserved 130–150 amino acids motif initially recognized as a common element in chromatin regulators with opposing activities: the suppressor of position affect variegation Su(var)3-9, the PcG protein Enhancer of Zeste [E(z)], and TRX (Jenuwein et al. 1998). The SET domain has been implicated in a multitude of different protein–protein interactions and functions. The SET domains of MLL, yeast Set1p, and E(z) bind to myotubularin-related dual-specificity phosphatases and anti-phosphatases that modulate growth control (Cui et al. 1998). The TRX and MLL SET domains bind to the SNF5 component of the ATP-dependent remodeler SWI/SNF (Rozenblatt-Rosen et al. 1998) and mediate self-association (Rozovskaia et al. 2000). Furthermore, the SET domain of yeast Set1p binds the Mec3p checkpoint protein and has been implicated in DNA repair and telomere function (Corda et al. 1999). The Set1p SET domain alone suffices to mediate telomeric silencing, suggesting that it forms a functional unit (Nislow et al. 1997). Recently, it was shown that SUV39H1, the mammalian homolog of Su(var)3–9, selectively methylates lysine 9 of histone H3 (Rea et al. 2000; Jenuwein 2001). This modification creates a binding site for HP1 and thus can contribute to the propagation of a heterochromatin domain (Bannister et al. 2001; Lachner et al. 2001; Nakayama et al. 2001). Whereas the histone–methylase activity of SUV39H1 was critically dependent on the SET domain, additional protein domains were also required. In contrast to SUV39H1, the SET domains of TRX and E(z) do not appear to mediate histone methylation (Rea et al. 2000; Jenuwein 2001). Thus, the TRX SET domain may form part of a methylase with a substrate other than histones or, alternatively, this SET domain may present a histone-recognizing module that is not a methylase. Here, we report that the TRX SET domain efficiently binds to core histones and to nucleosomes. We found that binding depends on the N-terminal histone tails and investigated the role of their covalent modifications. The effect of a homeotic mutation in the SET domain (trxZ11) on histone binding suggests that histone recognition constitutes an essential step during the in vivo control of gene expression by TRX.