Literature DB >> 11752331

The Histone Database.

Steven Sullivan1, Daniel W Sink, Kenneth L Trout, Izabela Makalowska, Patrick M Taylor, Andreas D Baxevanis, David Landsman.   

Abstract

Histone proteins are often noted for their high degree of sequence conservation. It is less often recognized that the histones are a heterogeneous protein family. Furthermore, several classes of non-histone proteins containing the histone fold motif exist. Novel histone and histone fold protein sequences continue to be added to public databases every year. The Histone Database (http://genome.nhgri.nih.gov/histones/) is a searchable, periodically updated collection of histone fold-containing sequences derived from sequence-similarity searches of public databases. Sequence sets are presented in redundant and non-redundant FASTA form, hotlinked to GenBank sequence files. Partial sequences are also now included in the database, which has considerably augmented its taxonomic coverage. Annotated alignments of full-length non-redundant sets of sequences are now available in both web-viewable (HTML) and downloadable (PDF) formats. The database also provides summaries of current information on solved histone fold structures, post-translational modifications of histones, and the human histone gene complement.

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Year:  2002        PMID: 11752331      PMCID: PMC99096          DOI: 10.1093/nar/30.1.341

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  16 in total

Review 1.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Authors:  A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul
Journal:  Nucleic Acids Res       Date:  2001-07-15       Impact factor: 16.971

2.  The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger.

Authors:  Y G Gangloff; J C Pointud; S Thuault; L Carré; C Romier; S Muratoglu; M Brand; L Tora; J L Couderc; I Davidson
Journal:  Mol Cell Biol       Date:  2001-08       Impact factor: 4.272

3.  The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins.

Authors:  S A Sullivan; L Aravind; I Makalowska; A D Baxevanis; D Landsman
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

4.  The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix.

Authors:  G Arents; R W Burlingame; B C Wang; W E Love; E N Moudrianakis
Journal:  Proc Natl Acad Sci U S A       Date:  1991-11-15       Impact factor: 11.205

Review 5.  Histones and nucleosomes in Archaea and Eukarya: a comparative analysis.

Authors:  S L Pereira; J N Reeve
Journal:  Extremophiles       Date:  1998-08       Impact factor: 2.395

6.  A histone fold TAF octamer within the yeast TFIID transcriptional coactivator.

Authors:  W Selleck; R Howley; Q Fang; V Podolny; M G Fried; S Buratowski; S Tan
Journal:  Nat Struct Biol       Date:  2001-08

7.  Spheroid chromatin units (v bodies).

Authors:  A L Olins; D E Olins
Journal:  Science       Date:  1974-01-25       Impact factor: 47.728

8.  Histone variant H2A.Z is required for early mammalian development.

Authors:  R Faast; V Thonglairoam; T C Schulz; J Beall; J R Wells; H Taylor; K Matthaei; P D Rathjen; D J Tremethick; I Lyons
Journal:  Curr Biol       Date:  2001-08-07       Impact factor: 10.834

9.  Calf and pea histone IV. 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone.

Authors:  R J DeLange; D M Fambrough; E L Smith; J Bonner
Journal:  J Biol Chem       Date:  1969-10-25       Impact factor: 5.157

Review 10.  Histone variants: are they functionally heterogeneous?

Authors:  D T Brown
Journal:  Genome Biol       Date:  2001-07-05       Impact factor: 13.583

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  22 in total

1.  Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions.

Authors:  Uma M Muthurajan; Yunhe Bao; Lawrence J Forsberg; Rajeswari S Edayathumangalam; Pamela N Dyer; Cindy L White; Karolin Luger
Journal:  EMBO J       Date:  2004-01-22       Impact factor: 11.598

2.  Mining core histone sequences from public protein databases.

Authors:  Steven A Sullivan; David Landsman
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

3.  The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.

Authors:  Yang Qiu; Valentina Tereshko; Youngchang Kim; Rongguang Zhang; Frank Collart; Mohammed Yousef; Anthony Kossiakoff; Andrzej Joachimiak
Journal:  Proteins       Date:  2006-01-01

4.  The Histone Database: a comprehensive resource for histones and histone fold-containing proteins.

Authors:  Leonardo Mariño-Ramírez; Benjamin Hsu; Andreas D Baxevanis; David Landsman
Journal:  Proteins       Date:  2006-03-01

5.  Common evolutionary origin and birth-and-death process in the replication-independent histone H1 isoforms from vertebrate and invertebrate genomes.

Authors:  José M Eirín-López; M Fernanda Ruiz; Ana M González-Tizón; Andrés Martínez; Juan Ausió; Lucas Sánchez; Josefina Méndez
Journal:  J Mol Evol       Date:  2005-07-28       Impact factor: 2.395

6.  Histones in crenarchaea.

Authors:  L'ubomíra Cubonová; Kathleen Sandman; Steven J Hallam; Edward F Delong; John N Reeve
Journal:  J Bacteriol       Date:  2005-08       Impact factor: 3.490

Review 7.  Dynamic nucleosomes.

Authors:  Karolin Luger
Journal:  Chromosome Res       Date:  2006       Impact factor: 5.239

8.  Liquid chromatography mass spectrometry profiling of histones.

Authors:  Xiaodan Su; Naduparambil K Jacob; Ravindra Amunugama; David M Lucas; Amy R Knapp; Chen Ren; Melanie E Davis; Guido Marcucci; Mark R Parthun; John C Byrd; Richard Fishel; Michael A Freitas
Journal:  J Chromatogr B Analyt Technol Biomed Life Sci       Date:  2007-01-07       Impact factor: 3.205

9.  Dispersed mutations in histone H3 that affect transcriptional repression and chromatin structure of the CHA1 promoter in Saccharomyces cerevisiae.

Authors:  Qiye He; Cailin Yu; Randall H Morse
Journal:  Eukaryot Cell       Date:  2008-07-25

10.  EPITRANS: a database that integrates epigenome and transcriptome data.

Authors:  Soo Young Cho; Jin Choul Chai; Soo Jun Park; Hyemyung Seo; Chae-Bong Sohn; Young Seek Lee
Journal:  Mol Cells       Date:  2013-11-08       Impact factor: 5.034

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