Publications

Here are the latest publications from the lab:

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Selected Publications

100. Krietenstein, N., Wal, M., Watanabe, S., Park, B., Peterson, C.L., Pugh*, B.F., and Korber*, P. (2016). Genomic nucleosome organization reconstituted with pure proteins. Cell 167, 709-721. *co-corresponding author. This work was performed equally between the two labs, and reports on the genome-wide reconstitution of promoter nucleosome organization with purified proteins. This represents the first-ever biochemical reconstitution of an entire epigenome (chromatin on a genomic scale) using only pure components: histones, DNA, six remodelers, and two sequence-specific DNA binding proteins. From this, a four-stage genome-wide assembly mechanism was deduced, that now paves the way for detailed mechanistic understanding of chromatin regulation through a blend of redundancy and specialization.

89.  Rhee, H-S., Bataille, A. R., Zhang, L., and Pugh, B.F. (2014) Subnucleosomal Structures and Nucleosome Asymmetry Across a Genome. Cell 159, 1377-1388. This work reports on the widespread subnucleosomal structures in dynamic chromatin, including novel half-nucleosomes, regulated interactions of H3 tails with linker DNA and asymmetric placement of histone variants and modifications on nucleosomes in relation to the direction of transcription.

81.  Yen, K., Vinayachandran, V., Batta, K., Koerber, R.T., and Pugh, B.F. (2012). Genome­wide nucleosome specificity and directionality of chromatin remodelers. Cell. 149, 1461-1473. How chromatin remodelers organize nucleosomes on chromosomes was unknown. High-resolution mapping was used to show that remodelers use a “division-of-labor” approach to bind specific nucleosome positions on genes and slide them into an organized state.

76.  Rhee, H-S., and Pugh, B.F. (2012) Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 483, 295-301. Here, the ChIP-exo assay was applied to define the first structure of transcription pre-initation complexes located at core promoters across a genome.

75.  Rhee, H-S., and Pugh, B.F. (2011) Comprehensive genome-wide protein-DNA interactions detected at single nucleotide resolution. Cell. 147, 1408-19. Technologies for determining where proteins bind along a genome had been rather low resolution, thereby limiting our understanding of chromosome regulation. This paper reports the development of the ChIP-exo assay. Its single-nucleotide resolution allows the structural organization of protein-DNA interactions to be defined on a genome scale.

71.  Zhang, Z., Wippo, C.J., Wal, M. Ward, E., Korber, P., Pugh, B.F. (2011) A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome. Science. 332, 977-980. How nucleosomes become organized on genes was unclear. This manuscript reports the astonishing feat of biochemical reconstitution of proper nucleosome organization on a genomic scale using pure DNA, pure histones, ATP and a cell-free extract. It revealed the chromatin remodelers are responsible for organizing nucleosomes on a genomic scale. This opens the door to creating synthetic chromosomes that can be studied in vitro as enzymological substrates (see pub. 100).

54.  Mavrich, T.N., Jiang, C., Ioshikhes, I.P., Li, X., Venters, B.J., Zanton, S.J., Tomsho, L.P., Qi, J., Glaser, R., Schuster, S.C., Gilmour, D.S., Albert, I., and Pugh, B.F. (2008). Nucleosome organization in the Drosophila genome. Nature. 453, 358-362. It was not known whether higher eukaryotes packaged their chromosomes as in yeast.  This paper describes the first genome-wide map of individual nucleosome positions in flies. It also revealed the organization of the transcription machinery and DNA regulatory elements around nucleosomes on a genomic scale.

48.  Albert, I., Mavrich, T. N., Tomsho, L. P, Qi, J., Zanton, S. J., Schuster, S. C., and Pugh, B.F. (2007) Translational and rotational settings of H2A.Z nucleosomes across the S. cerevisiae genome. Nature 446, 572-576. Whether the nucleosomes that package eukaryotic chromosomes are randomly distributed across a genome or organized into specific patterns was unknown.  This paper reports the first-ever ChIP-seq experiment, a technology that now dominates the field of functional genomics. Equally important, it demonstrated that every eukaryotic gene is packaged into an array of nucleosomes, all essentially organized in the same way (except for the TATA-class).

38.  Basehoar, A. D., Zanton, S. J., and Pugh, B.F. (2004). Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709. The TATA box DNA element resides at the core of eukaryotic gene regulation, but it was unknown which genes contained a TATA box.  This paper describes the first assignment of TATA boxes to genes on a genomic scale. This identification also precipitated the discovery of a deep dichotomy in the regulatory mechanism of eukaryotic genes. It defined stress-induced genes as having a distinct core transcription initiation complex and distinct mechanism of regulation compared to “housekeeping” genes. This discovery allowed scientists to infer how any gene of interest was likely to be regulated.

23.  Taggart, A. K., and Pugh, B.F. (1996). Dimerization of TFIID when not bound to DNA. Science 272, 1331-3. TFIID promotes gene transcription by assembling the transcription machinery via stable interactions with promoters. This paper describes the mechanism by which human TFIID auto-regulates its own assembly, and suggests a novel mechanism by which genes are kept quiescent.

11.  Pugh, B.F., and Tjian, R. (1990). Mechanism of transcriptional activation by Sp1: evidence for coactivators. Cell 61, 1187-97. This paper reports the initial discovery of a class of human proteins, termed “coactivators”, that connect transcriptional activators to the transcription machinery, thereby biochemically-defining gene regulatory circuit.