The Histone Database

Sullivan, Steven A.; Sink, Daniel W.; Trout, Kenneth L.; Makałowska, Izabela; Taylor, Patrick M.; Baxevanis, Andreas D.; Landsman, David

doi:10.1093/nar/30.1.341

Cited by 60 publications

(39 citation statements)

References 16 publications

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“…1C). The three variants with wild type affinity had large conservative side chain substitutions (L46F and L62Y) or a cysteine (L46C) residue at precisely the location of Cys-110 in histone H3 (42). Presumably, the side chains of these residues must still provide fully effective hydrophobic stabilizing interactions within the 4HB formed between the two (HMfB) 2 dimers.…”

Section: Discussionmentioning

confidence: 99%

“…The hTAF II 31 human homolog of dTAF II 42 does, for example, have such a histidine that could stabilize (hTAF II 31ϩhTAF II 80) 2 tetramers, whereas the predicted yeast homolog, yTAF II 17, lacks an appropriately positioned histidine, arguing against (yTAF II 17ϩyTAF II 60) 2 tetramer stabilization (3, 6 -8). The aspartate in ␣3 is conserved in virtually all histone folds (42), but because this is also required to stabilize the histone fold monomer (18,22), the presence of this residue is more a predictor of a histone fold than of tetramerization.…”

Section: Discussionmentioning

confidence: 99%

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Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Frederic¹,

Sandman²,

Lurz³

et al. 2002

Journal of Biological Chemistry

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DNA binding and the topology of DNA have been determined in complexes formed by >20 archaeal histone variants and archaeal histone dimer fusions with residue replacements at sites responsible for histone fold dimer:dimer interactions. Almost all of these variants have decreased affinity for DNA. They have also lost the flexibility of the wild type archaeal histones to wrap DNA into a negative or positive supercoil depending on the salt environment; they wrap DNA into positive supercoils under all salt conditions. The histone folds of the archaeal histones, HMfA and HMfB, from Methanothermus fervidus are almost identical, but (HMfA) 2 and (HMfB) 2 homodimers assemble into tetramers with sequence-dependent differences in DNA affinity. By construction and mutagenesis of HMfA؉HMfB and HMfB؉HMfA histone dimer fusions, the structure formed at the histone dimer:dimer interface within an archaeal histone tetramer has been shown to determine this difference in DNA affinity. Therefore, by regulating the assembly of different archaeal histone dimers into tetramers that have different sequence affinities, the assembly of archaeal histone-DNA complexes could be localized and used to regulate gene expression.The histone fold, three ␣-helices (␣1, ␣2, and ␣3) 1 separated by two ␤-strand loops (L1 and L2), was first identified in the four nucleosome core histones and shown to direct their assembly into (H2AϩH2B) and (H3ϩH4) heterodimers (1). Histone folds have since been found to direct the pairwise assembly of subunits in many transcription regulators, including TFIID, CBF, CHRAC, PCAF, SAGA, STAGA, and TFTC, and considerable effort has been focused on establishing the determinants of specific histone fold partnerships (2-8). In contrast, relatively few studies have investigated how such histone fold dimers are further assembled and whether alternative higher order structures might be formed with different functions or properties. It has been shown that the interface between the two (H3ϩH4) histone dimers in an (H3ϩH4) 2 tetramer is flexible and that alternative tetramer structures can result that wrap DNA in either a negative or positive DNA supercoil (9, 10). Nucleosomes containing the histone H3 variant alternatively designated CENP-A, CSE4p, CID, HCP-3, or SpCENP-A (11) assemble only at centromeric DNA. Mutagenesis and domain-swap experiments have revealed that this localization is similarly dependent on a difference at the histone dimer:dimer interface in (CENPϪAϩH4) 2 and (CSE4pϩH4) 2 versus (H3ϩH4) 2 tetramers (12-17). Based on their crystal structures, nucleosomes assembled with histones from different species or histone variants do exhibit higher order structural differences, again most notably at the sites of histone dimer:dimer interactions (18-21).Archaeal histones are only histone folds with structures almost identical to the histone folds in eukaryotic histones and transcription factors (22). They are dimers in solution but must assemble into tetramers to bind DNA (23,24). By mutagenesis, the residues have been i...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Frederic¹,

Sandman²,

Lurz³

et al. 2002

Journal of Biological Chemistry

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“…Alterations in histone PTMs have been documented in many types of cancer and may in fact play an important role in tumorogenesis [2]. The National Human Genome Research Institute (NHGRI) maintains a histone database (http://research.nhgri.nih.gov/histones/) that list 21 variants of human H2A, 14 of H2B, and at least three variants of H3 [3], in addition to proteins similar to core histones or histone-like.…”

Section: Introductionmentioning

confidence: 99%

Liquid chromatography mass spectrometry profiling of histones

Jacob

Amunugama

et al. 2007

Journal of Chromatography B

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Here we describe the use of reverse-phase liquid chromatography mass spectrometry (RP-LC-MS) to simultaneously characterize variants and post-translationally modified isoforms for each histone. The analysis of intact proteins significantly reduces the time of sample preparation and simplifies data interpretation. LC-MS analysis and peptide mass mapping have previously been applied to identify histone proteins and to characterize their post-translational modifications. However, these studies provided limited characterization of both linker histones and core histones. The current LC-MS analysis allows for the simultaneous observation of all histone PTMs and variants (both replacement and bulk histones) without further enrichment, which will be valuable in comparative studies. Protein identities were verified by the analysis of histone H2A species using RPLC fractionation, AU-PAGE separation and nano-LC-MS/MS.

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“…It was originally hypothesized by Roeder and coworkers (29,53) that a subset of TFIID subunits, those containing the helix-loop-helix-loop-helix or histone fold domain (HFD), could assemble to form a complex resembling the histone nucleosome octamer (1,29,53,60). This core structure was suggested to depend upon the HFD, a structural motif shared by the core histones (22) and many other proteins (70). Nine of 14 yeast Tafps appear to contain HFDs, and subsets of these can form dimers with specific partner HFD Tafps (3,6,9,23,24,29,45,47,80).…”

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confidence: 99%

Molecular and Genetic Characterization of a Taf1p Domain Essential for Yeast TFIID Assembly

Singh

Bland

Weil

2004

Molecular and Cellular Biology

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Yeast Taf1p is an integral component of the multiprotein transcription factor TFIID. By using coimmunoprecipitation assays, coupled with a comprehensive set of deletion mutants encompassing the entire open reading frame of TAF1, we have discovered an essential role of a small portion of yeast Taf1p. This domain of Taf1p, termed region 4, consisting of amino acids 200 to 303, contributes critically to the assembly and stability of the 15-subunit TFIID holocomplex. Region 4 of Taf1p is mutationally sensitive, can assemble several Tafps into a partial TFIID complex, and interacts directly with Taf4p and Taf6p. Mutations in Taf1p-region 4 induce temperature-conditional growth of yeast cells. At the nonpermissive temperature these mutations have drastic effects on both TFIID integrity and mRNA synthesis. These data are consistent with the hypothesis that Taf1p subserves a critical scaffold function within the TFIID complex. The significance of these data with regard to TFIID structure and function is discussed.TFIID, one of several multiprotein general transcription factors required for RNA polymerase II (PolII)-catalyzed mRNA gene transcription, is comprised of the TATA-binding protein (TBP) and 14 distinct TBP-associated factors (TAFs or Tafps) that range in M r from 17,000 to 150,000 in Saccharomyces cerevisiae (62,63,65,75). These TFIID subunits share significant sequence conservation with their metazoan orthologs (1,22,26). In vitro, PolII needs six general transcription factors, TFIIA, -B, -D, -E, -F, and -H, to form functional preinitiation complexes (PICs) (12, 51, 54); TFIID plays several critical roles in this process. First, TFIID functions during promoter recognition by binding directly to the promoter (67,76,77). On promoters containing a TATA box, Tafps help stabilize TBP binding to the TATA element via interaction with TATA-proximal initiator DNA sequences (69). Tafp-DNA interactions may be particularly important for TFIID binding to promoters that lack a canonical TATA element and contain TATA-proximal initiator and distal promoter element sequences (13,15,42,69,76). Second, Tafps can function as coactivators during transcriptional activation by making direct contacts with specific activators leading to an increase in PolII PIC formation (1, 16). Finally, Taf1p contains several distinct enzymatic activities, those of histone acetyltransferase (HAT) (46), protein kinase (19), and ubiquitin ligase (55). These enzymatic activities presumably modify proteins that stimulate PIC formation and/or function, leading to PolII transcription initiation.In most contexts, the Tafp subunits of TFIID are essential for survival, as Tafp inactivation or depletion results in cessation of specific mRNA synthesis and loss of cell viability (3,4,33,34,56,59,64,65,78). Because of these critical roles, the composition, organization, assembly, structure, and function of the TFIID complex have been topics of great interest. TBP appears to be incorporated into the TFIID complex primarily through its interaction with the biparti...

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The Histone Database

Cited by 60 publications

References 16 publications

Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Liquid chromatography mass spectrometry profiling of histones

Molecular and Genetic Characterization of a Taf1p Domain Essential for Yeast TFIID Assembly

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