Sources and characteristics of binding factors

The processes controlling gene transcription have been defined in substantial detail and generally involve the activity of a broad collection of proteins, many of which function through direct interaction with DNA (11). There are many DNA binding factors which are constitutively active and are involved either in the regulation of constitutively transcribed genes or are part of general transcription machinery of the cell. With regard to inducible gene expression, however, many transcription factors are inactive in unstimulated cells and are the substrates of signalling pathways initiated by exposure of cells to exogenous stimuli. Active DNA binding factors are almost always localized in the nucleus. Inactive forms are often maintained in the cytosol and undergo nuclear translocation as part of the activation process. There are many distinct mechanisms involved in regulation of DNA binding activities. Though not a property of all transcription factors, many function in the form of dimers, being composed of either two homologous proteins or two distinct proteins. The dimerization principle provides opportunity for combinatorial complexity both within one transcription factor family as well as between structurally distinct gene families. As understanding of transcriptional mechanisms increases in complexity, many additional layers of protein-protein interaction are likely to emerge which will provide additional specificity to the overall process. Thus protein-nucleic acid interactions provide nucleotide sequence recognition specificity as well as specificity for interaction with other protein components of larger functional complexes.

As is the case with transcriptional control, post-transcriptional control mechanisms involving protein-RNA interactions are impressively broad in functional scope. Perhaps the best studied examples involve the complex processes of trans-lational initiation, elongation, and termination. Less detailed information is available regarding the nature of primary transcript processing, nuclear-cytosolic transport, and mRNA decay. Unlike most DNA binding factors, RNA binding proteins can be found in both nuclear and cytosolic locations and often exhibit shuttling characteristics based upon the physiologic status of the cell.

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