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At the end of most cell signaling pathways lies a change in gene transcription or posttranscriptional regulation that affects the level or localization of protein expression. Characterization of the regulatory machinery is essential for understanding and potentially modulating biological responses encoded in genomic (and epigenomic) information. In the last decade, a new picture of gene regulatory machinery has emerged, in which transcription, RNA processing, RNA stabilization, RNA export, and even aspects of translational control, are closely coupled with one another.
Gene transcription is regulated by dynamic complexes of transcription factors, noncoding lincRNAs, coactivators and corepressors, histone acetylases, deacetylases, and other chromatin remodelers. Transcription factors are frequently the chief determinants of the composition and stability of these large transcription complexes, so it is important to develop robust assays to quantitate transcription factor activity.
Each transcription factor may have multiple DNA targets, but which particular gene is transcribed can be spatially and temporally regulated by transcription co-factors, chromatin structure, noncoding RNAs, epigenetic marks, or localization of the transcription factor itself. In this example, the transcription factor Oct 3/4 regulates SOX2, NANOG, NODAL, KLF4 and multiple other genes, thereby affecting diverse processes including differentiation, cell adhesion, insulin signaling, and apoptosis.