title: Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome.
abstract: Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by cysteines and histidines. The zinc finger domain defines one of the largest protein superfamilies in mammalian genomes;46 different conserved zinc finger domains are listed in InterPro (http://www.ebi.ac.uk/InterPro). Zinc finger proteins can bind to DNA, RNA, other proteins, or lipids as a modular domain in combination with other conserved structures. Owing to this combinatorial diversity, different members of zinc finger superfamilies contribute to many distinct cellular processes, including transcriptional regulation, mRNA stability and processing, and protein turnover. Accordingly, mutations of zinc finger genes lead to aberrations in a broad spectrum of biological processes such as development, differentiation, apoptosis, and immunological responses. This study provides the first comprehensive classification of zinc finger proteins in a mammalian transcriptome. Specific detailed analysis of the SP/Krüppel-like factors and the E3 ubiquitin-ligase RING-H2 families illustrates the importance of such an analysis for a more comprehensive functional classification of large protein families. We describe the characterization of a new family of C2H2 zinc-finger-containing proteins and a new conserved domain characteristic of this family, the identification and characterization of Sp8, a new member of the Sp family of transcriptional regulators, and the identification of five new RING-H2 proteins.
authors.affiliation: Institute for Molecular Bioscience, Brisbane, Australia. t.ravasi@imb.uq.edu.au
authors.forename: Timothy
authors.initials: T
authors.lastname: Ravasi
authors.forename: Thomas
authors.initials: T
authors.lastname: Huber
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.forename: Alistair
authors.initials: A
authors.lastname: Forrest
authors.forename: Terry
authors.initials: T
authors.lastname: Gaasterland
authors.forename: Sean
authors.initials: S
authors.lastname: Grimmond
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D002874:Chromosome Mapping; D016000:Cluster Analysis; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic / Q000706:statistics & numerical data; D006801:Humans; D051741:Kruppel-Like Transcription Factors; D008025:Ligases / Q000737:chemistry / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D012097:Repressor Proteins; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*; D025801:Ubiquitin / Q000378:metabolism; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D051741:Kruppel-Like Transcription Factors; D011506:Proteins; D020543:Proteome; D012097:Repressor Proteins; D014157:Transcription Factors; D025801:Ubiquitin; D008025:Ligases