Promoter modeling: the case study of mammalian histone promoters

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Bioinform.

• Publication date

  2005-06-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/bti387PMID 15769833
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Assessing computational tools for the discovery of transcription factor binding sites

  2005cited by this paper
• PromoSer: improvements to the algorithm, visualization and accessibility

  2004influential reference
• Human replication-dependent histone H3 genes are activated by a tandemly arranged pair of two CCAAT boxes.

  2004cited by this paper
• Promoters can contribute to the elucidation of protein function.

  2003cited by this paper
• Specific Binding of Nuclear Proteins to a Bifunctional Promoter Element Upstream of the H1/AC Box of the Testis-Specific Histone H1t Gene1

  2003cited by this paper
• Transcriptional repression of the testis-specific histone H1t gene mediated by an element upstream of the H1/AC box.

  2003cited by this paper
• Identification of HiNF-P, a Key Activator of Cell Cycle-Controlled Histone H4 Genes at the Onset of S Phase

  2003cited by this paper
• Transcriptional control of the testis-specific histone H1t gene.

  2003cited by this paper
• Differential expression of human replacement and cell cycle dependent H3 histone genes.

  2003cited by this paper
• TRANSFAC®: transcriptional regulation, from patterns to profiles

  2003cited by this paper
• FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes

  2003cited by this paper
• H1oo: a pre-embryonic H1 linker histone in search of a function.

  2003cited by this paper
• Aberrant Expression Pattern of Replication-Dependent Histone H3 Subtype Genes in Human Tumor Cell Lines

  2003cited by this paper
• The Stem-Loop Binding Protein Is Required for Efficient Translation of Histone mRNA In Vivo and In Vitro

  2002cited by this paper
• The human and mouse replication-dependent histone genes.

  2002cited by this paper
• Regulatory Modules Shared within Gene Classes as Well as Across Gene Classes Can Be Detected by the Same in Silico Approach

  2002cited by this paper
• Finding and Decrypting of Promoters Contributes to the Elucidation of Gene Function

  2002cited by this paper
• Modifications of the histone N-terminal domains

  2001cited by this paper
• Target gene identification from expression array data by promoter analysis.

  2001cited by this paper
• A predictive model for regulatory sequences directing liver-specific transcription.

  2001cited by this paper
• Chromatin: the second wave. Chromatin structure and function (3rd edn) Academic Press, Cambridge, UK. 447 pp. Alan P. Wolffe.

  2000cited by this paper
• The Human H2A and H2B Histone Gene Complement

  1999cited by this paper
• The expression of human H2A-H2B histone gene pairs is regulated by multiple sequence elements in their joint promoters.

  1999cited by this paper
• Chromatin remodeling and transcriptional regulation.

  1999cited by this paper
• Mammalian Krüppel-like transcription factors: more than just a pretty finger.

  1999cited by this paper
• The molecular biology of the CCAAT-binding factor NF-Y.

  1999influential reference
• cAMP/phorbol ester response element is involved in transcriptional regulation of the human replacement histone gene H3.3B.

  1998cited by this paper
• Conserved sequence elements in human main type-H1 histone gene promoters: their role in H1 gene expression.

  1998influential reference
• Combining evidence using p-values: application to sequence homology searches

  1998cited by this paper
• Identification of regulatory regions which confer muscle-specific gene expression.

  1998cited by this paper
• Repressor elements in the coding region of the human histone H4 gene interact with the transcription factor CDP/cut.

  1998cited by this paper
• Histones: genetic diversity and tissue-specific gene expression

  1997cited by this paper
• The human histone gene cluster at the D6S105 locus

  1997cited by this paper
• Transcriptional regulation of the human replacement histone gene H3.3B

  1997cited by this paper
• The Evolution of the Differentiation-Specific Histone H1 Gene Basal Promoter

  1997cited by this paper
• [Adverse reactions to contrast media].

  1997cited by this paper
• Organization and expression of the developmentally regulated H1(o) histone gene in vertebrates.

  1996influential reference
• Cloning of the cDNA encoding a novel subtype of histone H1.

  1996cited by this paper
• Functional domains for assembly of histones H3 and H4 into the chromatin of Xenopus embryos.

  1996cited by this paper
• The E2F transcription factor activates a replication-dependent human H2A gene in early S phase of the cell cycle

  1996cited by this paper
• TRANSCRIPTIONAL CONTROL OF CELL CYCLE PROGRESSION: THE HISTONE GENE IS A PARADIGM FOR THE G1/S PHASE AND PROLIFERATION/DIFFERENTIATION TRANSITIONS

  1996cited by this paper
• CDP/cut is the DNA-binding subunit of histone gene transcription factor HiNF-D: a mechanism for gene regulation at the G1/S phase cell cycle transition point independent of transcription factor E2F.

  1996cited by this paper
• Testis-specific expression of a novel human H3 histone gene.

  1996cited by this paper
• A H1 histone gene-specific AC-box-related element influences transcription from a major chicken H1 promoter.

  1995cited by this paper
• Sp1 trans-activation of cell cycle regulated promoters is selectively repressed by Sp3.

  1995cited by this paper
• Regulation of the Mouse Histone H2A.X Gene Promoter by the Transcription Factor E2F and CCAAT Binding Protein (*)

  1995cited by this paper
• The human replacement histone H3.3B gene (H3F3B).

  1995cited by this paper
• An upstream control region required for inducible transcription of the mouse H1(zero) histone gene during terminal differentiation

  1995cited by this paper
• Sp1‐mediated transcriptional activation is repressed by Sp3.

  1994cited by this paper
• Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer

  1994cited by this paper
• Organization and expression of H1 histone and H1 replacement histone genes

  1994cited by this paper
• Cell cycle controlled histone H1, H3, and H4 genes share unusual arrangements of recognition motifs for HiNF‐D supporting a coordinate promoter binding mechanism

  1994cited by this paper
• H1TF2A, the large subunit of a heterodimeric, glutamine-rich CCAAT-binding transcription factor involved in histone H1 cell cycle regulation

  1994influential reference
• Overlapping and CpG methylation-sensitive protein-DNA interactions at the histone H4 transcriptional cell cycle domain: distinctions between two human H4 gene promoters

  1992cited by this paper
• The regulation of histone synthesis in the cell cycle.

  1991cited by this paper
• Histone gene transcription factor binding in extracts of normal human cells

  1991cited by this paper
• Human H4 histone gene transcription requires the proliferation-specific nuclear factor HiNF-D. Auxiliary roles for HiNF-C (Sp1-like) and HiNF-A (high mobility group-like).

  1989cited by this paper
• Characterization and purification of H1TF2, a novel CCAAT-binding protein that interacts with a histone H1 subtype-specific consensus element

  1989cited by this paper
• Histone H1 subtype-specific consensus elements mediate cell cycle-regulated transcription in vitro.

  1989cited by this paper
• Human H1 histone gene promoter CCAAT box binding protein HiNF-B is a mosaic factor.

  1988cited by this paper
• A gene‐specific promoter element is required for optimal expression of the histone H1 gene in S‐phase.

  1988cited by this paper
• Analysis of Sp1 in vivo reveals mutiple transcriptional domains, including a novel glutamine-rich activation motif

  1988influential reference
• Methods to define and locate patterns of motifs in sequences

  1988cited by this paper
• Factors involved in specific transcription by mammalian RNA polymerase II: purification, genetic specificity, and TATA box-promoter interactions of TFIID

  1988cited by this paper
• Two target sites for protein binding in the promoter region of a cell cycle regulated human H1 histone gene.

  1988cited by this paper
• Purification and characterization of OTF-1, a transcription factor regulating cell cycle expression of a human histone H2b gene.

  1987cited by this paper
• Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family.

  1987cited by this paper
• Protein-DNA interactions in vivo upstream of a cell cycle-regulated human H4 histone gene.

  1987cited by this paper
• Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters

  1985cited by this paper

• Gene expression dynamics underlying diversification and expansion of an actin gene family

  2018cites this paper
• Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications

  2015cites this paper
• Chromatin Dynamics in Pluripotency and Differentiation: A Dissertation

  2012cites this paper
• Nucleus‐ and nucleomorph‐targeted histone proteins in a chlorarachniophyte alga

  2011influential citation
• Genome-wide analysis of regions similar to promoters of histone genes

  2010cites this paper
• Screening of the osmotic pressure-inducible promoter regions from the whole genome of Escherichia coli by using a novel cloning method

  2008cites this paper
• Anàlisi bioinformàtica de seqüències reguladores de l'expressió gènica en eucariotes.

  2008cites this paper
• Identification of novel target genes for the plasticity-related transcription factor Zif268.

  2007cites this paper
• Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

  2007cites this paper
• Cellular / Molecular Regulation of the Neuronal Proteasome by Zif 268 ( Egr 1 )

  2006cites this paper
• Multiple independent evolutionary solutions to core histone gene regulation

  2006cites this paper
• Regulation of the Neuronal Proteasome by Zif268 (Egr1)

  2006cites this paper
• A BAYESIAN SYSTEM FOR MODELING PROMOTER STRUCTURE : A CASE STUDY OF HISTONE PROMOTERS

  2006cites this paper
• Predicting transcription factor binding sites using local over-representation and comparative genomics

  2006cites this paper
• Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves

  2006cites this paper
• Algorithmes pour l'analyse de régions régulatrices dans le génome d'eucaryotes supérieurs

  2006cites this paper