ABSTRACT
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
Subject(s)
Gene Expression Regulation , Gene Regulatory Networks , Transcription Factors/metabolism , Animals , Cell Differentiation , Evolution, Molecular , Humans , Mice , Monocytes/cytology , Organ Specificity , Smad3 Protein/metabolism , Trans-Activators/metabolismABSTRACT
It has been suggested that the oxidase activity of NADH dehydrogenase of an alkaliphilic Bacillus YN-1 is markedly increased by the addition of free FAD. Site-directed mutagenesis of Lys-306, Lys-308, Arg-317, Arg-319 and Lys-332 of the enzyme was attempted to determine whether the basic amino acid residues are involved in FAD-dependent oxidase activity. Replacement of Arg-317, Arg-319 and Lys-332 by Ala had almost no effect on activity. Substitution of Lys-306 by Ala caused complete loss of the activity. When Lys-308 was replaced by Ala, the extent of FAD stimulation of the oxidase activity of the mutant (K308A) was only one-third that of the wild-type enzyme. FAD stimulation of oxidase activity of the wild-type enzyme was competitively inhibited by NAD. Although the K308A enzyme was also inhibited by NAD, this inhibition was significantly lower than that of the wild-type enzyme. It is likely that Lys-308 plays an important role in regulation of oxidase activity.
Subject(s)
Bacillus/enzymology , Flavin-Adenine Dinucleotide/metabolism , Lysine/metabolism , NADH Dehydrogenase/metabolism , Amino Acid Sequence , Amino Acid Substitution , Molecular Sequence Data , Mutagenesis, Site-Directed , NADH Dehydrogenase/chemistry , Sequence AlignmentABSTRACT
Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
