MORE BIOLOGICAL CONTRBUTIONS FROM ROGER KORNBERG

Further contributions from Kornberg’s study of transcription give insight into the area of understanding how the regions of the DNA actually become available to be transcribed by the polymerase. Histones, nucleosome occupancy and chromatin association are additional areas that have been affected from the enlightened understanding of transcription. Looking at how these factors affect regulation will aide in understanding the significance of the contributions. 

 Sequence motifs that are potentially recognized by DNA-binding proteins occur far more often in genomic DNA than do observed in vivo protein-DNA interactions. Liu et al. (15)in an up coming December 16, 2006 issue of nature gives insight into determination of how chromatin influences particular DNA-binding sites. Comparing the in vivo genome-wide binding location of the yeast transcription factor Leu3 to the binding location observed on the same genomic DNA in the absence of any protein cofactors is the process that they used. They found that the DNA-sequence motifs recognized by Leu3 in vitro and in vivo were functionally indistinguishable, but Leu3 bound to a different genomic location under the two of the experimental conditions. To over come some of the problems they accounted for nucleosome occupancy. In addition, DNA-sequence motifs significantly improved the prediction of the protein-DNA interactions in vivo, but not the prediction of sites bound by purified Leu3 in vitro. The results permit them to state that the influence chromatin exerts on DNA binding-site selection provides evidence for an instructive, functionally important role of nucleosome occupancy in determining patterns of regulatory factor targeting through out the entire genome.

 Eukaryotic genomes are generally thought to be entirely chromatin-associated; the activated PHO5 promoter in yeast lacks the relative amount of nucleosomes. Bernstein et al. in 2004 (14) evaluated the nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal DNA and quantified it using a microarray. They found that nucleosome depletion is observed in promoters that regulate active genes and/or contain multiple conserved motifs that recruit transcription factors. The Rap1 consensus was the only binding motif identified in a search of nucleosome-depleted promoters. Nucleosome occupancy in these regions was increased by the small molecule rapamycin or, in the case of the RPS11B promoter, by the removal of the Rap1 consensus sites. The presence of transcription factor-binding motifs is an important determinant of nucleosome depletion. Most motifs are associated with marked depletion only when they appear in combination, consistent with a model in which transcription factors act collaboratively to exclude nucleosomes and gain access to target sites in the DNA. In contrast, Rap1-binding sites caused depletion under steady-state conditions. From their finding they speculate that nucleosome depletion enables Rap1 to define chromatin domains and alter them in response to environmental cues.

 Functional understanding of such forms of regulation has gained more respect now that the transcription process can be visualized and essentially understood at a molecular level. Gene’s cannot be transcribed by the polymerase unless the area of template DNA can be accessed and free of any transcriptional inhibitory products. Turning DNA into RNA and translating in into proteins is just the part that we understand quite well. The processes that control and regulate transcription are just being studied due to the furthered understanding of the process in which these factors regulate, although somewhat backwards, that is just how it works sometimes, you have to seen and understand the end before you can look at the beginning.