The H2A/H2B-like histone-fold domain proteins at the crossroad between chromatin and different DNA metabolisms

References

• Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389:251 - 60; http://dx.doi.org/10.1038/38444; PMID: 9305837
   PubMed Web of Science ®Google Scholar
• Suganuma T, Workman JL. Signals and combinatorial functions of histone modifications. Annu Rev Biochem 2011; 80:473 - 99; http://dx.doi.org/10.1146/annurev-biochem-061809-175347; PMID: 21529160
   PubMed Web of Science ®Google Scholar
• Werten S, Mitschler A, Romier C, Gangloff YG, Thuault S, Davidson I, et al. Crystal structure of a subcomplex of human transcription factor TFIID formed by TATA binding protein-associated factors hTAF4 (hTAF(II)135) and hTAF12 (hTAF(II)20). J Biol Chem 2002; 277:45502 - 9; http://dx.doi.org/10.1074/jbc.M206587200; PMID: 12237304
   PubMed Web of Science ®Google Scholar
• Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, et al. Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex. Cell 2001; 106:71 - 81; http://dx.doi.org/10.1016/S0092-8674(01)00417-2; PMID: 11461703
   PubMed Web of Science ®Google Scholar
• Hartlepp KF, Fernández-Tornero C, Eberharter A, Grüne T, Müller CW, Becker PB. The histone fold subunits of Drosophila CHRAC facilitate nucleosome sliding through dynamic DNA interactions. Mol Cell Biol 2005; 25:9886 - 96; http://dx.doi.org/10.1128/MCB.25.22.9886-9896.2005; PMID: 16260604
   PubMed Web of Science ®Google Scholar
• Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, et al. Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Cell 2013; 152:132 - 43; http://dx.doi.org/10.1016/j.cell.2012.11.047; PMID: 23332751
   PubMed Web of Science ®Google Scholar
• Dolfini D, Gatta R, Mantovani R. NF-Y and the transcriptional activation of CCAAT promoters. Crit Rev Biochem Mol Biol 2012; 47:29 - 49; http://dx.doi.org/10.3109/10409238.2011.628970; PMID: 22050321
   PubMed Web of Science ®Google Scholar
• Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2012; 22:1798 - 812; http://dx.doi.org/10.1101/gr.139105.112; PMID: 22955990
   PubMed Web of Science ®Google Scholar
• Imbriano C, Gnesutta N, Mantovani R. The NF-Y/p53 liaison: well beyond repression. Biochim Biophys Acta 2011; 1825:131-39.
   Google Scholar
• Frontini M, Imbriano C, diSilvio A, Bell B, Bogni A, Romier C, et al. NF-Y recruitment of TFIID, multiple interactions with histone fold TAF(II)s. J Biol Chem 2002; 277:5841 - 8; http://dx.doi.org/10.1074/jbc.M103651200; PMID: 11689552
   PubMed Web of Science ®Google Scholar
• Inostroza JA, Mermelstein FH, Ha I, Lane WS, Reinberg D. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. Cell 1992; 70:477 - 89; http://dx.doi.org/10.1016/0092-8674(92)90172-9; PMID: 1339312
   PubMed Web of Science ®Google Scholar
• Goppelt A, Stelzer G, Lottspeich F, Meisterernst M. A mechanism for repression of class II gene transcription through specific binding of NC2 to TBP-promoter complexes via heterodimeric histone fold domains. EMBO J 1996; 15:3105 - 16; PMID: 8670811
   PubMed Web of Science ®Google Scholar
• Tora L, Timmers HT. The TATA box regulates TATA-binding protein (TBP) dynamics in vivo. Trends Biochem Sci 2010; 35:309 - 14; http://dx.doi.org/10.1016/j.tibs.2010.01.007; PMID: 20176488
   PubMed Web of Science ®Google Scholar
• Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, et al. Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε. PLoS Genet 2010; 6:e1001209; http://dx.doi.org/10.1371/journal.pgen.1001209; PMID: 21124948
   PubMed Web of Science ®Google Scholar
• Wang YL, Faiola F, Xu M, Pan S, Martinez E. Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein. J Biol Chem 2008; 283:33808 - 15; http://dx.doi.org/10.1074/jbc.M806936200; PMID: 18838386
   PubMed Web of Science ®Google Scholar
• Suganuma T, Gutiérrez JL, Li B, Florens L, Swanson SK, Washburn MP, et al. ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding. Nat Struct Mol Biol 2008; 15:364 - 72; http://dx.doi.org/10.1038/nsmb.1397; PMID: 18327268
   PubMed Web of Science ®Google Scholar
• Spedale G, Timmers HT, Pijnappel WW. ATAC-king the complexity of SAGA during evolution. Genes Dev 2012; 26:527 - 41; http://dx.doi.org/10.1101/gad.184705.111; PMID: 22426530
   PubMed Web of Science ®Google Scholar
• Kukimoto I, Elderkin S, Grimaldi M, Oelgeschläger T, Varga-Weisz PD. The histone-fold protein complex CHRAC-15/17 enhances nucleosome sliding and assembly mediated by ACF. Mol Cell 2004; 13:265 - 77; http://dx.doi.org/10.1016/S1097-2765(03)00523-9; PMID: 14759371
   PubMed Web of Science ®Google Scholar
• Tsubota T, Tajima R, Ode K, Kubota H, Fukuhara N, Kawabata T, et al. Double-stranded DNA binding, an unusual property of DNA polymerase epsilon, promotes epigenetic silencing in Saccharomyces cerevisiae. J Biol Chem 2006; 281:32898 - 908; http://dx.doi.org/10.1074/jbc.M606637200; PMID: 16916794
   PubMed Web of Science ®Google Scholar
• Spiga MG, D’Urso G. Identification and cloning of two putative subunits of DNA polymerase epsilon in fission yeast. Nucleic Acids Res 2004; 32:4945 - 53; http://dx.doi.org/10.1093/nar/gkh811; PMID: 15388803
   PubMed Web of Science ®Google Scholar
• Nagy Z, Tora L. Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation. Oncogene 2007; 26:5341 - 57; http://dx.doi.org/10.1038/sj.onc.1210604; PMID: 17694077
   PubMed Web of Science ®Google Scholar
• Gazit K, Moshonov S, Elfakess R, Sharon M, Mengus G, Davidson I, et al. TAF4/4b x TAF12 displays a unique mode of DNA binding and is required for core promoter function of a subset of genes. J Biol Chem 2009; 284:26286 - 96; http://dx.doi.org/10.1074/jbc.M109.011486; PMID: 19635797
   PubMed Web of Science ®Google Scholar
• Wright KJ, Marr MT 2nd, Tjian R. TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter. Proc Natl Acad Sci U S A 2006; 103:12347 - 52; http://dx.doi.org/10.1073/pnas.0605499103; PMID: 16895980
   PubMed Web of Science ®Google Scholar
• Bieniossek C, Papai G, Schaffitzel C, Garzoni F, Chaillet M, Scheer E, et al. The architecture of human general transcription factor TFIID core complex. Nature 2013; 493:699 - 702; http://dx.doi.org/10.1038/nature11791; PMID: 23292512
   PubMed Web of Science ®Google Scholar
• Burke TW, Kadonaga JT. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 1997; 11:3020 - 31; http://dx.doi.org/10.1101/gad.11.22.3020; PMID: 9367984
   PubMed Web of Science ®Google Scholar
• Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, et al. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell 2013; 152:120 - 31; http://dx.doi.org/10.1016/j.cell.2012.12.005; PMID: 23332750
   PubMed Web of Science ®Google Scholar
• Creton S, Svejstrup JQ, Collart MA. The NC2 alpha and beta subunits play different roles in vivo. Genes Dev 2002; 16:3265 - 76; http://dx.doi.org/10.1101/gad.234002; PMID: 12502746
   PubMed Web of Science ®Google Scholar
• Petroni K, Kumimoto RW, Gnesutta N, Calvenzani V, Fornari M, Tonelli C, et al. The promiscuous life of plant NUCLEAR FACTOR Y transcription factors. Plant Cell 2012; 24:4777 - 92; http://dx.doi.org/10.1105/tpc.112.105734; PMID: 23275578
   PubMed Web of Science ®Google Scholar
• Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics 2011; 10:M111.013284.
   Google Scholar
• Lan L, Ui A, Nakajima S, Hatakeyama K, Hoshi M, Watanabe R, et al. The ACF1 complex is required for DNA double-strand break repair in human cells. Mol Cell 2010; 40:976 - 87; http://dx.doi.org/10.1016/j.molcel.2010.12.003; PMID: 21172662
   PubMed Web of Science ®Google Scholar
• Schmitz KM, Schmitt N, Hoffmann-Rohrer U, Schäfer A, Grummt I, Mayer C. TAF12 recruits Gadd45a and the nucleotide excision repair complex to the promoter of rRNA genes leading to active DNA demethylation. Mol Cell 2009; 33:344 - 53; http://dx.doi.org/10.1016/j.molcel.2009.01.015; PMID: 19217408
   PubMed Web of Science ®Google Scholar
• Puddu F, Piergiovanni G, Plevani P, Muzi-Falconi M. Sensing of replication stress and Mec1 activation act through two independent pathways involving the 9-1-1 complex and DNA polymerase ε. PLoS Genet 2011; 7:e1002022; http://dx.doi.org/10.1371/journal.pgen.1002022; PMID: 21436894
   PubMedGoogle Scholar