Worthwhile items from the peer-reviewed literature:
If you want to get up to speed on the literature of transcription at the single cell level, a field where you find some of the most interesting outstanding questions in biology at the molecular, cellular level, you can’t do better than starting with this review by Li and Xie, and then working systematically through the references:
Central dogma at the single-molecule level in living cells, Nature 2011 Jul 20;475(7356):308-15
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Yeah, we really don’t understand why sequence-specific DNA binding factors don’t get lost in the huge search space of the genome. But this paper shows that nucleosomes are a big part of the picture.
Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection, Xiao Liu, Cheol-Koo Lee, Joshua A. Granek, Neil D. Clarke, and Jason D. Lieb, Genome Research 2006. 16:1517-1528
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. To determine how chromatin influences the utilization of particular DNA-binding sites, we compared 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. We found that the DNA-sequence motif recognized by Leu3 in vitro and in vivo was functionally indistinguishable, but Leu3 bound different genomic locations under the two conditions.
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Clinical assessment incorporating a personal genome, The Lancet, Volume 375, Issue 9725, Pages 1525 – 1535, 1 May 2010. A first pass at trying to incorporate information from a completely sequenced genome into a patient work-up.
The Finch and Pea 