All Publications

  • Chromatin potentiates transcription. Proceedings of the National Academy of Sciences of the United States of America Nagai, S., Davis, R. E., Mattei, P. J., Eagen, K. P., Kornberg, R. D. 2017; 114 (7): 1536-1541


    Chromatin isolated from the chromosomal locus of the PHO5 gene of yeast in a transcriptionally repressed state was transcribed with 12 pure proteins (80 polypeptides): RNA polymerase II, six general transcription factors, TFIIS, the Pho4 gene activator protein, and the SAGA, SWI/SNF, and Mediator complexes. Contrary to expectation, a nucleosome occluding the TATA box and transcription start sites did not impede transcription but rather, enhanced it: the level of chromatin transcription was at least sevenfold greater than that of naked DNA, and chromatin gave patterns of transcription start sites closely similar to those occurring in vivo, whereas naked DNA gave many aberrant transcripts. Both histone acetylation and trimethylation of H3K4 (H3K4me3) were important for chromatin transcription. The nucleosome, long known to serve as a general gene repressor, thus also performs an important positive role in transcription.

    View details for DOI 10.1073/pnas.1620312114

    View details for PubMedID 28137832

    View details for PubMedCentralID PMC5320956

  • Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell Robinson, P. J., Trnka, M. J., Bushnell, D. A., Davis, R. E., Mattei, P., Burlingame, A. L., Kornberg, R. D. 2016; 166 (6): 1411-1422 e16


    A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.

    View details for DOI 10.1016/j.cell.2016.08.050

    View details for PubMedID 27610567

  • Uncoupling Promoter Opening from Start-Site Scanning. Molecular cell Murakami, K., Mattei, P., Davis, R. E., Jin, H., Kaplan, C. D., Kornberg, R. D. 2015; 59 (1): 133-138


    Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp downstream of the TATA box in metazoans, TSSs are located 40-120 bp downstream in S. cerevisiae. Promoter melting begins about 12 bp downstream in all eukaryotes, so Pol II is presumed to "scan" further downstream before starting transcription in yeast. Here we report that removal of the kinase complex TFIIK from TFIIH shifts the TSS in a yeast system upstream to the location observed in metazoans. Conversely, moving the normal TSS to an upstream location enables a high level of TFIIK-independent transcription in the yeast system. We distinguish two stages of the transcription initiation process: bubble formation by TFIIH, which fills the Pol II active center with single-stranded DNA, and subsequent scanning downstream, also driven by TFIIH, which requires displacement of the initial bubble. Omission of TFIIK uncouples the two stages of the process.

    View details for DOI 10.1016/j.molcel.2015.05.021

    View details for PubMedID 26073544

    View details for PubMedCentralID PMC4490988