Biomaterial Database

Xenopus transcription factor IIIA binds to the flanking regions of the 5 S RNA gene intragenic control region in a unique and highly ordered state. 1988

W T Windsor, and T C Lee, and T J Daly, and C W Wu

Department of Pharmacological Sciences, State University of New York, Stony Brook 11794.

The interaction of Xenopus transcription factor IIIA (TFIIIA) with the intragenic control region (ICR) of the 5 S RNA gene was studied by footprinting techniques under conditions which elicited a unique DNase I digestion pattern. Although a typical full footprint at the ICR was apparent at a 5 nM TFIIIA concentration, higher concentrations (greater than or equal to 50 nM) resulted in a decrease in the size of the footprint (on the 5' side of the ICR) concomitant with the appearance of an alternating protection pattern (APP) located both in the 3'- and 5'-flanking regions of the ICR with a periodicity of approximately 10 base pairs. This periodicity indicates that TFIIIA binding occurs on only one side of the DNA helix. The minimum size of the highly ordered and apparently cooperative APP effect was determined to be at least 250 base pairs in length and could be abolished through competition with nonspecific DNA. However, binding of TFIIIA to nonspecific DNA alone was not sufficient to generate the APP effect at any of the TFIIIA concentrations studied. Removal of the C-terminal domain of the protein by either tryptic or papain digestion resulted in the abolition of the APP effect at all concentrations studied, indicating the necessity of the protein-protein interactions for this effect. A nucleation site, most likely at or near the ICR, is proposed to exist through which TFIIIA specifically interacts and orients the binding of additional protein molecules in a cooperative and highly ordered manner to the flanking DNA sequences on either side of the ICR. The APP effect near the ICR may play a role in the initiation and stabilization of 5 S RNA gene transcription.

UI	MeSH Term	Description	Entries
D009865	Oocytes	Female germ cells derived from OOGONIA and termed OOCYTES when they enter MEIOSIS. The primary oocytes begin meiosis but are arrested at the diplotene state until OVULATION at PUBERTY to give rise to haploid secondary oocytes or ova (OVUM).	Ovocytes,Oocyte,Ovocyte
D011485	Protein Binding	The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.	Plasma Protein Binding Capacity,Binding, Protein
D003850	Deoxyribonuclease I	An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.	DNase I,Streptodornase,DNA Endonuclease,DNA Nicking Enzyme,DNAase I,Dornavac,Endonuclease I,Nickase,Pancreatic DNase,T4-Endonuclease II,T7-Endonuclease I,Thymonuclease,DNase, Pancreatic,Endonuclease, DNA,T4 Endonuclease II,T7 Endonuclease I
D004275	DNA, Ribosomal	DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.	Ribosomal DNA,rDNA
D005260	Female		Females
D005809	Genes, Regulator	Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.	Gene, Regulator,Regulator Gene,Regulator Genes,Regulatory Genes,Gene, Regulatory,Genes, Regulatory,Regulatory Gene
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D012335	RNA, Ribosomal	The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)	Ribosomal RNA,15S RNA,RNA, 15S
D012341	RNA, Ribosomal, 5S	Constituent of the 50S subunit of prokaryotic ribosomes containing about 120 nucleotides and 34 proteins. It is also a constituent of the 60S subunit of eukaryotic ribosomes. 5S rRNA is involved in initiation of polypeptide synthesis.	5S Ribosomal RNA,5S rRNA,RNA, 5S Ribosomal,Ribosomal RNA, 5S,rRNA, 5S
D014157	Transcription Factors	Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.	Transcription Factor,Factor, Transcription,Factors, Transcription