TY - JOUR AU - Vo Ngoc, L. AU - Wang, Y. L. AU - Kassavetis, G. A. AU - Kadonaga, J. T. PY - 2017 DA - 2017// TI - The punctilious RNA polymerase II core promoter JO - Genes Dev VL - 31 UR - https://doi.org/10.1101/gad.303149.117 DO - 10.1101/gad.303149.117 ID - Vo Ngoc2017 ER - TY - JOUR AU - Kadonaga, J. T. PY - 2012 DA - 2012// TI - Perspectives on the RNA polymerase II core promoter JO - Wiley Interdiscip Rev Dev Biol VL - 1 UR - https://doi.org/10.1002/wdev.21 DO - 10.1002/wdev.21 ID - Kadonaga2012 ER - TY - JOUR AU - Juven-Gershon, T. AU - Kadonaga, J. T. PY - 2010 DA - 2010// TI - Regulation of gene expression via the core promoter and the basal transcriptional machinery JO - Dev Biol VL - 339 UR - https://doi.org/10.1016/j.ydbio.2009.08.009 DO - 10.1016/j.ydbio.2009.08.009 ID - Juven-Gershon2010 ER - TY - JOUR AU - Juven-Gershon, T. AU - Hsu, J. Y. AU - Kadonaga, J. T. PY - 2006 DA - 2006// TI - Perspectives on the RNA polymerase II core promoter JO - Biochem Soc Trans VL - 34 UR - https://doi.org/10.1042/BST0341047 DO - 10.1042/BST0341047 ID - Juven-Gershon2006 ER - TY - JOUR AU - Smale, S. T. AU - Kadonaga, J. T. PY - 2003 DA - 2003// TI - The RNA polymerase II core promoter JO - Annu Rev Biochem VL - 72 UR - https://doi.org/10.1146/annurev.biochem.72.121801.161520 DO - 10.1146/annurev.biochem.72.121801.161520 ID - Smale2003 ER - TY - JOUR AU - Butler, J. E. AU - Kadonaga, J. T. PY - 2002 DA - 2002// TI - The RNA polymerase II core promoter: a key component in the regulation of gene expression JO - Genes Dev VL - 16 UR - https://doi.org/10.1101/gad.1026202 DO - 10.1101/gad.1026202 ID - Butler2002 ER - TY - JOUR AU - Danino, Y. M. AU - Even, D. AU - Ideses, D. AU - Juven-Gershon, T. PY - 2015 DA - 2015// TI - The core promoter: at the heart of gene expression JO - Biochim Biophys Acta VL - 1849 UR - https://doi.org/10.1016/j.bbagrm.2015.04.003 DO - 10.1016/j.bbagrm.2015.04.003 ID - Danino2015 ER - TY - JOUR AU - Juven-Gershon, T. AU - Hsu, J. Y. AU - Theisen, J. W. AU - Kadonaga, J. T. PY - 2008 DA - 2008// TI - The RNA polymerase II core promoter - the gateway to transcription JO - Curr Opin Cell Biol VL - 20 UR - https://doi.org/10.1016/j.ceb.2008.03.003 DO - 10.1016/j.ceb.2008.03.003 ID - Juven-Gershon2008 ER - TY - JOUR AU - Haberle, V. AU - Stark, A. PY - 2018 DA - 2018// TI - Eukaryotic core promoters and the functional basis of transcription initiation JO - Nat Rev Mol Cell Biol VL - 19 UR - https://doi.org/10.1038/s41580-018-0028-8 DO - 10.1038/s41580-018-0028-8 ID - Haberle2018 ER - TY - JOUR AU - Roy, A. L. AU - Singer, D. S. PY - 2015 DA - 2015// TI - Core promoters in transcription: old problem, new insights JO - Trends Biochem Sci VL - 40 UR - https://doi.org/10.1016/j.tibs.2015.01.007 DO - 10.1016/j.tibs.2015.01.007 ID - Roy2015 ER - TY - JOUR AU - Sainsbury, S. AU - Bernecky, C. AU - Cramer, P. PY - 2015 DA - 2015// TI - Structural basis of transcription initiation by RNA polymerase II JO - Nat Rev Mol Cell Biol VL - 16 UR - https://doi.org/10.1038/nrm3952 DO - 10.1038/nrm3952 ID - Sainsbury2015 ER - TY - JOUR AU - Patel, A. B. AU - Greber, B. J. AU - Nogales, E. PY - 2019 DA - 2019// TI - Recent insights into the structure of TFIID, its assembly, and its binding to core promoter JO - Curr Opin Struct Biol VL - 61 UR - https://doi.org/10.1016/j.sbi.2019.10.001 DO - 10.1016/j.sbi.2019.10.001 ID - Patel2019 ER - TY - JOUR AU - Nogales, E. AU - Patel, A. B. AU - Louder, R. K. PY - 2017 DA - 2017// TI - Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID JO - Curr Opin Struct Biol VL - 47 UR - https://doi.org/10.1016/j.sbi.2017.05.015 DO - 10.1016/j.sbi.2017.05.015 ID - Nogales2017 ER - TY - JOUR AU - Rhee, H. S. AU - Pugh, B. F. PY - 2012 DA - 2012// TI - Genome-wide structure and organization of eukaryotic pre-initiation complexes JO - Nature VL - 483 UR - https://doi.org/10.1038/nature10799 DO - 10.1038/nature10799 ID - Rhee2012 ER - TY - JOUR AU - Weiner, A. AU - Hughes, A. AU - Yassour, M. AU - Rando, O. J. AU - Friedman, N. PY - 2010 DA - 2010// TI - High-resolution nucleosome mapping reveals transcription-dependent promoter packaging JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.098509.109 DO - 10.1101/gr.098509.109 ID - Weiner2010 ER - TY - JOUR AU - Tirosh, I. AU - Barkai, N. AU - Verstrepen, K. J. PY - 2009 DA - 2009// TI - Promoter architecture and the evolvability of gene expression JO - J Biol VL - 8 UR - https://doi.org/10.1186/jbiol204 DO - 10.1186/jbiol204 ID - Tirosh2009 ER - TY - JOUR AU - Jiang, C. AU - Pugh, B. F. PY - 2009 DA - 2009// TI - A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-10-r109 DO - 10.1186/gb-2009-10-10-r109 ID - Jiang2009 ER - TY - JOUR AU - Tirosh, I. AU - Barkai, N. PY - 2008 DA - 2008// TI - Two strategies for gene regulation by promoter nucleosomes JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.076059.108 DO - 10.1101/gr.076059.108 ID - Tirosh2008 ER - TY - JOUR AU - Mavrich, T. N. AU - Jiang, C. AU - Ioshikhes, I. P. AU - Li, X. AU - Venters, B. J. AU - Zanton, S. J. AU - Tomsho, L. P. AU - Qi, J. AU - Glaser, R. L. AU - Schuster, S. C. PY - 2008 DA - 2008// TI - Nucleosome organization in the Drosophila genome JO - Nature VL - 453 UR - https://doi.org/10.1038/nature06929 DO - 10.1038/nature06929 ID - Mavrich2008 ER - TY - JOUR AU - Xu, Z. AU - Wei, W. AU - Gagneur, J. AU - Perocchi, F. AU - Clauder-Munster, S. AU - Camblong, J. AU - Guffanti, E. AU - Stutz, F. AU - Huber, W. AU - Steinmetz, L. M. PY - 2009 DA - 2009// TI - Bidirectional promoters generate pervasive transcription in yeast JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07728 DO - 10.1038/nature07728 ID - Xu2009 ER - TY - JOUR AU - Neil, H. AU - Malabat, C. AU - d’Aubenton-Carafa, Y. AU - Xu, Z. AU - Steinmetz, L. M. AU - Jacquier, A. PY - 2009 DA - 2009// TI - Widespread bidirectional promoters are the major source of cryptic transcripts in yeast JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07747 DO - 10.1038/nature07747 ID - Neil2009 ER - TY - JOUR AU - Preker, P. AU - Nielsen, J. AU - Kammler, S. AU - Lykke-Andersen, S. AU - Christensen, M. S. AU - Mapendano, C. K. AU - Schierup, M. H. AU - Jensen, T. H. PY - 2008 DA - 2008// TI - RNA exosome depletion reveals transcription upstream of active human promoters JO - Science VL - 322 UR - https://doi.org/10.1126/science.1164096 DO - 10.1126/science.1164096 ID - Preker2008 ER - TY - JOUR AU - Core, L. J. AU - Lis, J. T. PY - 2008 DA - 2008// TI - Transcription regulation through promoter-proximal pausing of RNA polymerase II JO - Science VL - 319 UR - https://doi.org/10.1126/science.1150843 DO - 10.1126/science.1150843 ID - Core2008 ER - TY - JOUR AU - Seila, A. C. AU - Calabrese, J. M. AU - Levine, S. S. AU - Yeo, G. W. AU - Rahl, P. B. AU - Flynn, R. A. AU - Young, R. A. AU - Sharp, P. A. PY - 2008 DA - 2008// TI - Divergent transcription from active promoters JO - Science VL - 322 UR - https://doi.org/10.1126/science.1162253 DO - 10.1126/science.1162253 ID - Seila2008 ER - TY - JOUR AU - Jin, Y. AU - Eser, U. AU - Struhl, K. AU - Churchman, L. S. PY - 2017 DA - 2017// TI - The ground state and evolution of promoter region directionality JO - Cell VL - 170 UR - https://doi.org/10.1016/j.cell.2017.07.006 DO - 10.1016/j.cell.2017.07.006 ID - Jin2017 ER - TY - JOUR AU - Andersson, R. AU - Chen, Y. AU - Core, L. AU - Lis, J. T. AU - Sandelin, A. AU - Jensen, T. H. PY - 2015 DA - 2015// TI - Human gene promoters are intrinsically bidirectional JO - Mol Cell VL - 60 UR - https://doi.org/10.1016/j.molcel.2015.10.015 DO - 10.1016/j.molcel.2015.10.015 ID - Andersson2015 ER - TY - JOUR AU - Duttke, S. H. AU - Lacadie, S. A. AU - Ibrahim, M. M. AU - Glass, C. K. AU - Corcoran, D. L. AU - Benner, C. AU - Heinz, S. AU - Kadonaga, J. T. AU - Ohler, U. PY - 2015 DA - 2015// TI - Human promoters are intrinsically directional JO - Mol Cell VL - 57 UR - https://doi.org/10.1016/j.molcel.2014.12.029 DO - 10.1016/j.molcel.2014.12.029 ID - Duttke2015 ER - TY - JOUR AU - Duttke, S. H. AU - Lacadie, S. A. AU - Ibrahim, M. M. AU - Glass, C. K. AU - Corcoran, D. L. AU - Benner, C. AU - Heinz, S. AU - Kadonaga, J. T. AU - Ohler, U. PY - 2015 DA - 2015// TI - Perspectives on unidirectional versus divergent transcription JO - Mol Cell VL - 60 UR - https://doi.org/10.1016/j.molcel.2015.10.014 DO - 10.1016/j.molcel.2015.10.014 ID - Duttke2015 ER - TY - JOUR AU - Lee, W. AU - Tillo, D. AU - Bray, N. AU - Morse, R. H. AU - Davis, R. W. AU - Hughes, T. R. AU - Nislow, C. PY - 2007 DA - 2007// TI - A high-resolution atlas of nucleosome occupancy in yeast JO - Nat Genet VL - 39 UR - https://doi.org/10.1038/ng2117 DO - 10.1038/ng2117 ID - Lee2007 ER - TY - JOUR AU - Lu, Z. AU - Lin, Z. PY - 2019 DA - 2019// TI - Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae JO - Genome Res VL - 29 UR - https://doi.org/10.1101/gr.245456.118 DO - 10.1101/gr.245456.118 ID - Lu2019 ER - TY - STD TI - Donczew R, Warfield L, Pacheco D, Erijman A, Hahn S. Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA. eLife 2020;9:e50109. https://doi.org/10.7554/eLife.50109. ID - ref31 ER - TY - JOUR AU - Huisinga, K. L. AU - Pugh, B. F. PY - 2004 DA - 2004// TI - A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae JO - Mol Cell VL - 13 UR - https://doi.org/10.1016/S1097-2765(04)00087-5 DO - 10.1016/S1097-2765(04)00087-5 ID - Huisinga2004 ER - TY - JOUR AU - Basehoar, A. D. AU - Zanton, S. J. AU - Pugh, B. F. PY - 2004 DA - 2004// TI - Identification and distinct regulation of yeast TATA box-containing genes JO - Cell VL - 116 UR - https://doi.org/10.1016/S0092-8674(04)00205-3 DO - 10.1016/S0092-8674(04)00205-3 ID - Basehoar2004 ER - TY - JOUR AU - Kuras, L. AU - Kosa, P. AU - Mencia, M. AU - Struhl, K. PY - 2000 DA - 2000// TI - TAF-containing and TAF-independent forms of transcriptionally active TBP in vivo JO - Science VL - 288 UR - https://doi.org/10.1126/science.288.5469.1244 DO - 10.1126/science.288.5469.1244 ID - Kuras2000 ER - TY - JOUR AU - Li, X. Y. AU - Bhaumik, S. R. AU - Green, M. R. PY - 2000 DA - 2000// TI - Distinct classes of yeast promoters revealed by differential TAF recruitment JO - Science VL - 288 UR - https://doi.org/10.1126/science.288.5469.1242 DO - 10.1126/science.288.5469.1242 ID - Li2000 ER - TY - JOUR AU - Wu, R. AU - Li, H. PY - 2010 DA - 2010// TI - Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.103226.109 DO - 10.1101/gr.103226.109 ID - Wu2010 ER - TY - JOUR AU - Seizl, M. AU - Hartmann, H. AU - Hoeg, F. AU - Kurth, F. AU - Martin, D. E. AU - Soding, J. AU - Cramer, P. PY - 2011 DA - 2011// TI - A conserved GA element in TATA-less RNA polymerase II promoters JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0027595 DO - 10.1371/journal.pone.0027595 ID - Seizl2011 ER - TY - JOUR AU - Vo Ngoc, L. AU - Kassavetis, G. A. AU - Kadonaga, J. T. PY - 2019 DA - 2019// TI - The RNA polymerase II Core promoter in Drosophila JO - Genetics VL - 212 UR - https://doi.org/10.1534/genetics.119.302021 DO - 10.1534/genetics.119.302021 ID - Vo Ngoc2019 ER - TY - JOUR AU - Warfield, L. AU - Ramachandran, S. AU - Baptista, T. AU - Devys, D. AU - Tora, L. AU - Hahn, S. PY - 2017 DA - 2017// TI - Transcription of nearly all yeast RNA polymerase II-transcribed genes is dependent on transcription factor TFIID JO - Mol Cell VL - 68 UR - https://doi.org/10.1016/j.molcel.2017.08.014 DO - 10.1016/j.molcel.2017.08.014 ID - Warfield2017 ER - TY - JOUR AU - Baptista, T. AU - Grunberg, S. AU - Minoungou, N. AU - Koster, M. J. E. AU - Timmers, H. T. M. AU - Hahn, S. AU - Devys, D. AU - Tora, L. PY - 2017 DA - 2017// TI - SAGA is a general cofactor for RNA polymerase II transcription JO - Mol Cell VL - 68 UR - https://doi.org/10.1016/j.molcel.2017.08.016 DO - 10.1016/j.molcel.2017.08.016 ID - Baptista2017 ER - TY - JOUR AU - Hampsey, M. PY - 2006 DA - 2006// TI - The Pol II initiation complex: finding a place to start JO - Nat Struct Mol Biol VL - 13 UR - https://doi.org/10.1038/nsmb0706-564 DO - 10.1038/nsmb0706-564 ID - Hampsey2006 ER - TY - JOUR AU - Corden, J. L. PY - 2008 DA - 2008// TI - Yeast Pol II start-site selection: the long and the short of it JO - EMBO Rep VL - 9 UR - https://doi.org/10.1038/embor.2008.192 DO - 10.1038/embor.2008.192 ID - Corden2008 ER - TY - JOUR AU - Zhang, Z. AU - Dietrich, F. S. PY - 2005 DA - 2005// TI - Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki583 DO - 10.1093/nar/gki583 ID - Zhang2005 ER - TY - JOUR AU - Park, D. AU - Morris, A. R. AU - Battenhouse, A. AU - Iyer, V. R. PY - 2014 DA - 2014// TI - Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1366 DO - 10.1093/nar/gkt1366 ID - Park2014 ER - TY - JOUR AU - Pelechano, V. AU - Wei, W. AU - Steinmetz, L. M. PY - 2013 DA - 2013// TI - Extensive transcriptional heterogeneity revealed by isoform profiling JO - Nature VL - 497 UR - https://doi.org/10.1038/nature12121 DO - 10.1038/nature12121 ID - Pelechano2013 ER - TY - JOUR AU - Chen, R. A. AU - Down, T. A. AU - Stempor, P. AU - Chen, Q. B. AU - Egelhofer, T. A. AU - Hillier, L. W. AU - Jeffers, T. E. AU - Ahringer, J. PY - 2013 DA - 2013// TI - The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.153668.112 DO - 10.1101/gr.153668.112 ID - Chen2013 ER - TY - JOUR AU - Yamashita, R. AU - Sathira, N. P. AU - Kanai, A. AU - Tanimoto, K. AU - Arauchi, T. AU - Tanaka, Y. AU - Hashimoto, S. AU - Sugano, S. AU - Nakai, K. AU - Suzuki, Y. PY - 2011 DA - 2011// TI - Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.110254.110 DO - 10.1101/gr.110254.110 ID - Yamashita2011 ER - TY - JOUR AU - Hoskins, R. A. AU - Landolin, J. M. AU - Brown, J. B. AU - Sandler, J. E. AU - Takahashi, H. AU - Lassmann, T. AU - Yu, C. AU - Booth, B. W. AU - Zhang, D. AU - Wan, K. H. PY - 2011 DA - 2011// TI - Genome-wide analysis of promoter architecture in Drosophila melanogaster JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.112466.110 DO - 10.1101/gr.112466.110 ID - Hoskins2011 ER - TY - STD TI - Consortium F, the RP, Clst, Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, et al: A promoter-level mammalian expression atlas. Nature 2014, 507:462–470. ID - ref49 ER - TY - JOUR AU - Nepal, C. AU - Hadzhiev, Y. AU - Previti, C. AU - Haberle, V. AU - Li, N. AU - Takahashi, H. AU - Suzuki, A. M. AU - Sheng, Y. AU - Abdelhamid, R. F. AU - Anand, S. PY - 2013 DA - 2013// TI - Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.153692.112 DO - 10.1101/gr.153692.112 ID - Nepal2013 ER - TY - JOUR AU - Gleghorn, M. L. AU - Davydova, E. K. AU - Basu, R. AU - Rothman-Denes, L. B. AU - Murakami, K. S. PY - 2011 DA - 2011// TI - X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1016691108 DO - 10.1073/pnas.1016691108 ID - Gleghorn2011 ER - TY - JOUR AU - Smale, S. T. AU - Baltimore, D. PY - 1989 DA - 1989// TI - The “initiator” as a transcription control element JO - Cell VL - 57 UR - https://doi.org/10.1016/0092-8674(89)90176-1 DO - 10.1016/0092-8674(89)90176-1 ID - Smale1989 ER - TY - JOUR AU - Vo Ngoc, L. AU - Cassidy, C. J. AU - Huang, C. Y. AU - Duttke, S. H. AU - Kadonaga, J. T. PY - 2017 DA - 2017// TI - The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters JO - Genes Dev VL - 31 UR - https://doi.org/10.1101/gad.293837.116 DO - 10.1101/gad.293837.116 ID - Vo Ngoc2017 ER - TY - JOUR AU - Sainsbury, S. AU - Niesser, J. AU - Cramer, P. PY - 2013 DA - 2013// TI - Structure and function of the initially transcribing RNA polymerase II-TFIIB complex JO - Nature VL - 493 UR - https://doi.org/10.1038/nature11715 DO - 10.1038/nature11715 ID - Sainsbury2013 ER - TY - JOUR AU - Struhl, K. PY - 1987 DA - 1987// TI - Promoters, activator proteins, and the mechanism of transcriptional initiation in yeast JO - Cell VL - 49 UR - https://doi.org/10.1016/0092-8674(87)90277-7 DO - 10.1016/0092-8674(87)90277-7 ID - Struhl1987 ER - TY - STD TI - Lu Z, Lin Z: The origin and evolution of a distinct mechanism of transcription initiation in yeasts. bioRxiv 2020.04.04.025502. https://doi.org/10.1101/2020.04.04.025502. ID - ref56 ER - TY - JOUR AU - Breathnach, R. AU - Chambon, P. PY - 1981 DA - 1981// TI - Organization and expression of eucaryotic split genes coding for proteins JO - Annu Rev Biochem VL - 50 UR - https://doi.org/10.1146/annurev.bi.50.070181.002025 DO - 10.1146/annurev.bi.50.070181.002025 ID - Breathnach1981 ER - TY - JOUR AU - Giardina, C. AU - Lis, J. T. PY - 1993 DA - 1993// TI - DNA melting on yeast RNA polymerase II promoters JO - Science VL - 261 UR - https://doi.org/10.1126/science.8342041 DO - 10.1126/science.8342041 ID - Giardina1993 ER - TY - JOUR AU - Yang, C. AU - Ponticelli, A. S. PY - 2012 DA - 2012// TI - Evidence that RNA polymerase II and not TFIIB is responsible for the difference in transcription initiation patterns between Saccharomyces cerevisiae and Schizosaccharomyces pombe JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks323 DO - 10.1093/nar/gks323 ID - Yang2012 ER - TY - JOUR AU - Goel, S. AU - Krishnamurthy, S. AU - Hampsey, M. PY - 2012 DA - 2012// TI - Mechanism of start site selection by RNA polymerase II: interplay between TFIIB and Ssl2/XPB helicase subunit of TFIIH JO - J Biol Chem VL - 287 UR - https://doi.org/10.1074/jbc.M111.281576 DO - 10.1074/jbc.M111.281576 ID - Goel2012 ER - TY - JOUR AU - Khaperskyy, D. A. AU - Ammerman, M. L. AU - Majovski, R. C. AU - Ponticelli, A. S. PY - 2008 DA - 2008// TI - Functions of Saccharomyces cerevisiae TFIIF during transcription start site utilization JO - Mol Cell Biol VL - 28 UR - https://doi.org/10.1128/MCB.02272-07 DO - 10.1128/MCB.02272-07 ID - Khaperskyy2008 ER - TY - JOUR AU - Kuehner, J. N. AU - Brow, D. A. PY - 2006 DA - 2006// TI - Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M601937200 DO - 10.1074/jbc.M601937200 ID - Kuehner2006 ER - TY - JOUR AU - Pal, M. AU - Ponticelli, A. S. AU - Luse, D. S. PY - 2005 DA - 2005// TI - The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II JO - Mol Cell VL - 19 UR - https://doi.org/10.1016/j.molcel.2005.05.024 DO - 10.1016/j.molcel.2005.05.024 ID - Pal2005 ER - TY - JOUR AU - Majovski, R. C. AU - Khaperskyy, D. A. AU - Ghazy, M. A. AU - Ponticelli, A. S. PY - 2005 DA - 2005// TI - A functional role for the switch 2 region of yeast RNA polymerase II in transcription start site utilization and abortive initiation JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M502932200 DO - 10.1074/jbc.M502932200 ID - Majovski2005 ER - TY - JOUR AU - Freire-Picos, M. A. AU - Krishnamurthy, S. AU - Sun, Z. W. AU - Hampsey, M. PY - 2005 DA - 2005// TI - Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki825 DO - 10.1093/nar/gki825 ID - Freire-Picos2005 ER - TY - JOUR AU - Ghazy, M. A. AU - Brodie, S. A. AU - Ammerman, M. L. AU - Ziegler, L. M. AU - Ponticelli, A. S. PY - 2004 DA - 2004// TI - Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II JO - Mol Cell Biol VL - 24 UR - https://doi.org/10.1128/MCB.24.24.10975-10985.2004 DO - 10.1128/MCB.24.24.10975-10985.2004 ID - Ghazy2004 ER - TY - JOUR AU - Chen, B. S. AU - Hampsey, M. PY - 2004 DA - 2004// TI - Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation JO - Mol Cell Biol VL - 24 UR - https://doi.org/10.1128/MCB.24.9.3983-3991.2004 DO - 10.1128/MCB.24.9.3983-3991.2004 ID - Chen2004 ER - TY - JOUR AU - Faitar, S. L. AU - Brodie, S. A. AU - Ponticelli, A. S. PY - 2001 DA - 2001// TI - Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites JO - Mol Cell Biol VL - 21 UR - https://doi.org/10.1128/MCB.21.14.4427-4440.2001 DO - 10.1128/MCB.21.14.4427-4440.2001 ID - Faitar2001 ER - TY - JOUR AU - Pappas, D. L. AU - Hampsey, M. PY - 2000 DA - 2000// TI - Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae JO - Mol Cell Biol VL - 20 UR - https://doi.org/10.1128/MCB.20.22.8343-8351.2000 DO - 10.1128/MCB.20.22.8343-8351.2000 ID - Pappas2000 ER - TY - JOUR AU - Wu, W. H. AU - Pinto, I. AU - Chen, B. S. AU - Hampsey, M. PY - 1999 DA - 1999// TI - Mutational analysis of yeast TFIIB. A functional relationship between Ssu72 and Sub1/Tsp1 defined by allele-specific interactions with TFIIB JO - Genetics VL - 153 ID - Wu1999 ER - TY - JOUR AU - Bangur, C. S. AU - Faitar, S. L. AU - Folster, J. P. AU - Ponticelli, A. S. PY - 1999 DA - 1999// TI - An interaction between the N-terminal region and the core domain of yeast TFIIB promotes the formation of TATA-binding protein-TFIIB-DNA complexes JO - J Biol Chem VL - 274 UR - https://doi.org/10.1074/jbc.274.33.23203 DO - 10.1074/jbc.274.33.23203 ID - Bangur1999 ER - TY - JOUR AU - Pardee, T. S. AU - Bangur, C. S. AU - Ponticelli, A. S. PY - 1998 DA - 1998// TI - The N-terminal region of yeast TFIIB contains two adjacent functional domains involved in stable RNA polymerase II binding and transcription start site selection JO - J Biol Chem VL - 273 UR - https://doi.org/10.1074/jbc.273.28.17859 DO - 10.1074/jbc.273.28.17859 ID - Pardee1998 ER - TY - JOUR AU - Sun, Z. W. AU - Tessmer, A. AU - Hampsey, M. PY - 1996 DA - 1996// TI - Functional interaction between TFIIB and the Rpb9 (Ssu73) subunit of RNA polymerase II in Saccharomyces cerevisiae JO - Nucleic Acids Res VL - 24 UR - https://doi.org/10.1093/nar/24.13.2560 DO - 10.1093/nar/24.13.2560 ID - Sun1996 ER - TY - JOUR AU - Sun, Z. W. AU - Hampsey, M. PY - 1995 DA - 1995// TI - Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae JO - Proc Natl Acad Sci U S A VL - 92 UR - https://doi.org/10.1073/pnas.92.8.3127 DO - 10.1073/pnas.92.8.3127 ID - Sun1995 ER - TY - JOUR AU - Pinto, I. AU - Wu, W. H. AU - Na, J. G. AU - Hampsey, M. PY - 1994 DA - 1994// TI - Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast JO - J Biol Chem VL - 269 ID - Pinto1994 ER - TY - JOUR AU - Berroteran, R. W. AU - Ware, D. E. AU - Hampsey, M. PY - 1994 DA - 1994// TI - The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations JO - Mol Cell Biol VL - 14 UR - https://doi.org/10.1128/MCB.14.1.226 DO - 10.1128/MCB.14.1.226 ID - Berroteran1994 ER - TY - JOUR AU - Pinto, I. AU - Ware, D. E. AU - Hampsey, M. PY - 1992 DA - 1992// TI - The yeast SUA7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo JO - Cell VL - 68 UR - https://doi.org/10.1016/0092-8674(92)90040-J DO - 10.1016/0092-8674(92)90040-J ID - Pinto1992 ER - TY - JOUR AU - Hampsey, M. AU - Na, J. G. AU - Pinto, I. AU - Ware, D. E. AU - Berroteran, R. W. PY - 1991 DA - 1991// TI - Extragenic suppressors of a translation initiation defect in the cyc1 gene of Saccharomyces cerevisiae JO - Biochimie VL - 73 UR - https://doi.org/10.1016/0300-9084(91)90177-3 DO - 10.1016/0300-9084(91)90177-3 ID - Hampsey1991 ER - TY - JOUR AU - Knaus, R. AU - Pollock, R. AU - Guarente, L. PY - 1996 DA - 1996// TI - Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co-activator PC4 JO - EMBO J VL - 15 UR - https://doi.org/10.1002/j.1460-2075.1996.tb00544.x DO - 10.1002/j.1460-2075.1996.tb00544.x ID - Knaus1996 ER - TY - JOUR AU - Jin, H. AU - Kaplan, C. D. PY - 2014 DA - 2014// TI - Relationships of RNA polymerase II genetic interactors to transcription start site usage defects and growth in Saccharomyces cerevisiae JO - G3 (Bethesda) VL - 5 UR - https://doi.org/10.1534/g3.114.015180 DO - 10.1534/g3.114.015180 ID - Jin2014 ER - TY - JOUR AU - Braberg, H. AU - Jin, H. AU - Moehle, E. A. AU - Chan, Y. A. AU - Wang, S. AU - Shales, M. AU - Benschop, J. J. AU - Morris, J. H. AU - Qiu, C. AU - Hu, F. PY - 2013 DA - 2013// TI - From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II JO - Cell VL - 154 UR - https://doi.org/10.1016/j.cell.2013.07.033 DO - 10.1016/j.cell.2013.07.033 ID - Braberg2013 ER - TY - JOUR AU - Kaplan, C. D. AU - Jin, H. AU - Zhang, I. L. AU - Belyanin, A. PY - 2012 DA - 2012// TI - Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1002627 DO - 10.1371/journal.pgen.1002627 ID - Kaplan2012 ER - TY - JOUR AU - Eichner, J. AU - Chen, H. T. AU - Warfield, L. AU - Hahn, S. PY - 2010 DA - 2010// TI - Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex JO - EMBO J VL - 29 UR - https://doi.org/10.1038/emboj.2009.386 DO - 10.1038/emboj.2009.386 ID - Eichner2010 ER - TY - JOUR AU - Kaplan, C. D. AU - Larsson, K. M. AU - Kornberg, R. D. PY - 2008 DA - 2008// TI - The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin JO - Mol Cell VL - 30 UR - https://doi.org/10.1016/j.molcel.2008.04.023 DO - 10.1016/j.molcel.2008.04.023 ID - Kaplan2008 ER - TY - JOUR AU - Kireeva, M. L. AU - Nedialkov, Y. A. AU - Cremona, G. H. AU - Purtov, Y. A. AU - Lubkowska, L. AU - Malagon, F. AU - Burton, Z. F. AU - Strathern, J. N. AU - Kashlev, M. PY - 2008 DA - 2008// TI - Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation JO - Mol Cell VL - 30 UR - https://doi.org/10.1016/j.molcel.2008.04.017 DO - 10.1016/j.molcel.2008.04.017 ID - Kireeva2008 ER - TY - JOUR AU - Malagon, F. AU - Kireeva, M. L. AU - Shafer, B. K. AU - Lubkowska, L. AU - Kashlev, M. AU - Strathern, J. N. PY - 2006 DA - 2006// TI - Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil JO - Genetics VL - 172 UR - https://doi.org/10.1534/genetics.105.052415 DO - 10.1534/genetics.105.052415 ID - Malagon2006 ER - TY - JOUR AU - Qiu, C. AU - Erinne, O. C. AU - Dave, J. M. AU - Cui, P. AU - Jin, H. AU - Muthukrishnan, N. AU - Tang, L. K. AU - Babu, S. G. AU - Lam, K. C. AU - Vandeventer, P. J. PY - 2016 DA - 2016// TI - High-resolution phenotypic landscape of the RNA polymerase II trigger loop JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006321 DO - 10.1371/journal.pgen.1006321 ID - Qiu2016 ER - TY - JOUR AU - Xu, C. AU - Park, J. K. AU - Zhang, J. PY - 2019 DA - 2019// TI - Evidence that alternative transcriptional initiation is largely nonadaptive JO - PLoS Biol VL - 17 UR - https://doi.org/10.1371/journal.pbio.3000197 DO - 10.1371/journal.pbio.3000197 ID - Xu2019 ER - TY - STD TI - Borlin CS, Cvetesic N, Holland P, Bergenholm D, Siewers V, Lenhard B, Nielsen J. Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. FEMS Yeast Res. 2019;19(2):128. https://doi.org/10.1093/femsyr/foy128. ID - ref89 ER - TY - JOUR AU - Lubliner, S. AU - Keren, L. AU - Segal, E. PY - 2013 DA - 2013// TI - Sequence features of yeast and human core promoters that are predictive of maximal promoter activity JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt256 DO - 10.1093/nar/gkt256 ID - Lubliner2013 ER - TY - JOUR AU - Lubliner, S. AU - Regev, I. AU - Lotan-Pompan, M. AU - Edelheit, S. AU - Weinberger, A. AU - Segal, E. PY - 2015 DA - 2015// TI - Core promoter sequence in yeast is a major determinant of expression level JO - Genome Res VL - 25 UR - https://doi.org/10.1101/gr.188193.114 DO - 10.1101/gr.188193.114 ID - Lubliner2015 ER - TY - JOUR AU - Kamenova, I. AU - Warfield, L. AU - Hahn, S. PY - 2014 DA - 2014// TI - Mutations on the DNA binding surface of TBP discriminate between yeast TATA and TATA-less gene transcription JO - Mol Cell Biol VL - 34 UR - https://doi.org/10.1128/MCB.01685-13 DO - 10.1128/MCB.01685-13 ID - Kamenova2014 ER - TY - STD TI - Donczew R, Hahn S. Mechanistic differences in transcription initiation at TATA-less and TATA-containing promoters. Mol Cell Biol. 2017;38(1):e00448-17. https://doi.org/10.1128/MCB.00448-17. ID - ref93 ER - TY - JOUR AU - Lorch, Y. AU - Maier-Davis, B. AU - Kornberg, R. D. PY - 2014 DA - 2014// TI - Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions JO - Genes Dev VL - 28 UR - https://doi.org/10.1101/gad.250704.114 DO - 10.1101/gad.250704.114 ID - Lorch2014 ER - TY - JOUR AU - Krietenstein, N. AU - Wal, M. AU - Watanabe, S. AU - Park, B. AU - Peterson, C. L. AU - Pugh, B. F. AU - Korber, P. PY - 2016 DA - 2016// TI - Genomic nucleosome organization reconstituted with pure proteins JO - Cell VL - 167 UR - https://doi.org/10.1016/j.cell.2016.09.045 DO - 10.1016/j.cell.2016.09.045 ID - Krietenstein2016 ER - TY - JOUR AU - Rossi, M. J. AU - Lai, W. K. M. AU - Pugh, B. F. PY - 2018 DA - 2018// TI - Simplified ChIP-exo assays JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-05265-7 DO - 10.1038/s41467-018-05265-7 ID - Rossi2018 ER - TY - JOUR AU - Rossi, M. J. AU - Lai, W. K. M. AU - Pugh, B. F. PY - 2018 DA - 2018// TI - Genome-wide determinants of sequence-specific DNA binding of general regulatory factors JO - Genome Res VL - 28 UR - https://doi.org/10.1101/gr.229518.117 DO - 10.1101/gr.229518.117 ID - Rossi2018 ER - TY - JOUR AU - Fazal, F. M. AU - Meng, C. A. AU - Murakami, K. AU - Kornberg, R. D. AU - Block, S. M. PY - 2015 DA - 2015// TI - Real-time observation of the initiation of RNA polymerase II transcription JO - Nature VL - 525 UR - https://doi.org/10.1038/nature14882 DO - 10.1038/nature14882 ID - Fazal2015 ER - TY - JOUR AU - Tomko, E. J. AU - Fishburn, J. AU - Hahn, S. AU - Galburt, E. A. PY - 2017 DA - 2017// TI - TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning JO - Nat Struct Mol Biol VL - 24 UR - https://doi.org/10.1038/nsmb.3500 DO - 10.1038/nsmb.3500 ID - Tomko2017 ER - TY - STD TI - Bhuiyan T, Timmers HTM. Promoter recognition: putting TFIID on the spot. Trends Cell Biol. 2019;29(9):752-73. ID - ref100 ER - TY - STD TI - Tramantano M, Sun L, Au C, Labuz D, Liu Z, Chou M, Shen C, Luk E: Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. eLife 2016;5:e14243. https://doi.org/10.7554/eLife.14243. ID - ref101 ER - TY - STD TI - Zhou X, Blocker AW, Airoldi EM, O'Shea EK. A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution. eLife 2016;5:e16970. https://doi.org/10.7554/eLife.16970. ID - ref102 ER - TY - JOUR AU - Struhl, K. PY - 1989 DA - 1989// TI - Molecular mechanisms of transcriptional regulation in yeast JO - Annu Rev Biochem VL - 58 UR - https://doi.org/10.1146/annurev.bi.58.070189.005155 DO - 10.1146/annurev.bi.58.070189.005155 ID - Struhl1989 ER - TY - JOUR AU - Li, H. AU - Hou, J. AU - Bai, L. AU - Hu, C. AU - Tong, P. AU - Kang, Y. AU - Zhao, X. AU - Shao, Z. PY - 2015 DA - 2015// TI - Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE JO - RNA Biol VL - 12 UR - https://doi.org/10.1080/15476286.2015.1022704 DO - 10.1080/15476286.2015.1022704 ID - Li2015 ER - TY - JOUR AU - Kaplan, C. D. PY - 1829 DA - 1829// TI - Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae JO - Biochim Biophys Acta VL - 2013 ID - Kaplan1829 ER - TY - JOUR AU - Fishburn, J. AU - Galburt, E. AU - Hahn, S. PY - 2016 DA - 2016// TI - Transcription start site scanning and the requirement for ATP during transcription initiation by RNA polymerase II JO - J Biol Chem VL - 291 UR - https://doi.org/10.1074/jbc.M116.724583 DO - 10.1074/jbc.M116.724583 ID - Fishburn2016 ER - TY - JOUR AU - Haberle, V. AU - Li, N. AU - Hadzhiev, Y. AU - Plessy, C. AU - Previti, C. AU - Nepal, C. AU - Gehrig, J. AU - Dong, X. AU - Akalin, A. AU - Suzuki, A. M. PY - 2014 DA - 2014// TI - Two independent transcription initiation codes overlap on vertebrate core promoters JO - Nature VL - 507 UR - https://doi.org/10.1038/nature12974 DO - 10.1038/nature12974 ID - Haberle2014 ER - TY - JOUR AU - Lai, W. K. AU - Pugh, B. F. PY - 2017 DA - 2017// TI - Genome-wide uniformity of human ‘open’ pre-initiation complexes JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.210955.116 DO - 10.1101/gr.210955.116 ID - Lai2017 ER - TY - JOUR AU - Shao, W. AU - Zeitlinger, J. PY - 2017 DA - 2017// TI - Paused RNA polymerase II inhibits new transcriptional initiation JO - Nat Genet VL - 49 UR - https://doi.org/10.1038/ng.3867 DO - 10.1038/ng.3867 ID - Shao2017 ER - TY - JOUR AU - Scruggs, B. S. AU - Gilchrist, D. A. AU - Nechaev, S. AU - Muse, G. W. AU - Burkholder, A. AU - Fargo, D. C. AU - Adelman, K. PY - 2015 DA - 2015// TI - Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin JO - Mol Cell VL - 58 UR - https://doi.org/10.1016/j.molcel.2015.04.006 DO - 10.1016/j.molcel.2015.04.006 ID - Scruggs2015 ER - TY - JOUR AU - Kaplan, C. D. PY - 2016 DA - 2016// TI - Pairs of promoter pairs in a web of transcription JO - Nat Genet VL - 48 UR - https://doi.org/10.1038/ng.3649 DO - 10.1038/ng.3649 ID - Kaplan2016 ER - TY - JOUR AU - Core, L. J. AU - Waterfall, J. J. AU - Lis, J. T. PY - 2008 DA - 2008// TI - Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters JO - Science VL - 322 UR - https://doi.org/10.1126/science.1162228 DO - 10.1126/science.1162228 ID - Core2008 ER - TY - JOUR AU - Murakami, K. AU - Mattei, P. J. AU - Davis, R. E. AU - Jin, H. AU - Kaplan, C. D. AU - Kornberg, R. D. PY - 2015 DA - 2015// TI - Uncoupling promoter opening from start-site scanning JO - Mol Cell VL - 59 UR - https://doi.org/10.1016/j.molcel.2015.05.021 DO - 10.1016/j.molcel.2015.05.021 ID - Murakami2015 ER - TY - JOUR AU - Singh, A. AU - Compe, E. AU - May, N. AU - Egly, J. M. PY - 2015 DA - 2015// TI - TFIIH subunit alterations causing xeroderma pigmentosum and trichothiodystrophy specifically disturb several steps during transcription JO - Am J Hum Genet VL - 96 UR - https://doi.org/10.1016/j.ajhg.2014.12.012 DO - 10.1016/j.ajhg.2014.12.012 ID - Singh2015 ER - TY - JOUR AU - Egly, J. M. AU - Coin, F. PY - 2011 DA - 2011// TI - A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor JO - DNA Repair (Amst) VL - 10 UR - https://doi.org/10.1016/j.dnarep.2011.04.021 DO - 10.1016/j.dnarep.2011.04.021 ID - Egly2011 ER - TY - JOUR AU - Compe, E. AU - Egly, J. M. PY - 2012 DA - 2012// TI - TFIIH: when transcription met DNA repair JO - Nat Rev Mol Cell Biol VL - 13 UR - https://doi.org/10.1038/nrm3350 DO - 10.1038/nrm3350 ID - Compe2012 ER - TY - JOUR AU - Clapier, C. R. AU - Iwasa, J. AU - Cairns, B. R. AU - Peterson, C. L. PY - 2017 DA - 2017// TI - Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes JO - Nat Rev Mol Cell Biol VL - 18 UR - https://doi.org/10.1038/nrm.2017.26 DO - 10.1038/nrm.2017.26 ID - Clapier2017 ER - TY - JOUR AU - Puig, O. AU - Caspary, F. AU - Rigaut, G. AU - Rutz, B. AU - Bouveret, E. AU - Bragado-Nilsson, E. AU - Wilm, M. AU - Seraphin, B. PY - 2001 DA - 2001// TI - The tandem affinity purification (TAP) method: a general procedure of protein complex purification JO - Methods VL - 24 UR - https://doi.org/10.1006/meth.2001.1183 DO - 10.1006/meth.2001.1183 ID - Puig2001 ER - TY - JOUR AU - Ghaemmaghami, S. AU - Huh, W. K. AU - Bower, K. AU - Howson, R. W. AU - Belle, A. AU - Dephoure, N. AU - O'Shea, E. K. AU - Weissman, J. S. PY - 2003 DA - 2003// TI - Global analysis of protein expression in yeast JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02046 DO - 10.1038/nature02046 ID - Ghaemmaghami2003 ER - TY - JOUR AU - Winston, F. AU - Dollard, C. AU - Ricupero-Hovasse, S. L. PY - 1995 DA - 1995// TI - Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C JO - Yeast VL - 11 UR - https://doi.org/10.1002/yea.320110107 DO - 10.1002/yea.320110107 ID - Winston1995 ER - TY - JOUR AU - Boeke, J. D. AU - Trueheart, J. AU - Natsoulis, G. AU - Fink, G. R. PY - 1987 DA - 1987// TI - 5-Fluoroorotic acid as a selective agent in yeast molecular genetics JO - Methods Enzymol VL - 154 UR - https://doi.org/10.1016/0076-6879(87)54076-9 DO - 10.1016/0076-6879(87)54076-9 ID - Boeke1987 ER - TY - JOUR AU - Xia, Y. AU - Chu, W. AU - Qi, Q. AU - Xun, L. PY - 2015 DA - 2015// TI - New insights into the QuikChange process guide the use of Phusion DNA polymerase for site-directed mutagenesis JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1189 DO - 10.1093/nar/gku1189 ID - Xia2015 ER - TY - JOUR AU - Schmitt, M. E. AU - Brown, T. A. AU - Trumpower, B. L. PY - 1990 DA - 1990// TI - A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae JO - Nucleic Acids Res VL - 18 UR - https://doi.org/10.1093/nar/18.10.3091 DO - 10.1093/nar/18.10.3091 ID - Schmitt1990 ER - TY - JOUR AU - Goldman, S. R. AU - Sharp, J. S. AU - Vvedenskaya, I. O. AU - Livny, J. AU - Dove, S. L. AU - Nickels, B. E. PY - 2011 DA - 2011// TI - NanoRNAs prime transcription initiation in vivo JO - Mol Cell VL - 42 UR - https://doi.org/10.1016/j.molcel.2011.06.005 DO - 10.1016/j.molcel.2011.06.005 ID - Goldman2011 ER - TY - JOUR AU - Vvedenskaya, I. O. AU - Goldman, S. R. AU - Nickels, B. E. PY - 2015 DA - 2015// TI - Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5′ ends JO - Methods Mol Biol VL - 1276 UR - https://doi.org/10.1007/978-1-4939-2392-2_12 DO - 10.1007/978-1-4939-2392-2_12 ID - Vvedenskaya2015 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - JOUR AU - Saldanha, A. J. PY - 2004 DA - 2004// TI - Java Treeview--extensible visualization of microarray data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth349 DO - 10.1093/bioinformatics/bth349 ID - Saldanha2004 ER - TY - JOUR AU - Hoon, M. J. AU - Imoto, S. AU - Nolan, J. AU - Miyano, S. PY - 2004 DA - 2004// TI - Open source clustering software JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth078 DO - 10.1093/bioinformatics/bth078 ID - Hoon2004 ER - TY - JOUR AU - Ramirez, F. AU - Dundar, F. AU - Diehl, S. AU - Gruning, B. A. AU - Manke, T. PY - 2014 DA - 2014// TI - deepTools: a flexible platform for exploring deep-sequencing data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku365 DO - 10.1093/nar/gku365 ID - Ramirez2014 ER - TY - JOUR AU - Kawaji, H. AU - Frith, M. C. AU - Katayama, S. AU - Sandelin, A. AU - Kai, C. AU - Kawai, J. AU - Carninci, P. AU - Hayashizaki, Y. PY - 2006 DA - 2006// TI - Dynamic usage of transcription start sites within core promoters JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-12-r118 DO - 10.1186/gb-2006-7-12-r118 ID - Kawaji2006 ER - TY - JOUR AU - Malik, I. AU - Qiu, C. AU - Snavely, T. AU - Kaplan, C. D. PY - 2017 DA - 2017// TI - Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo JO - Nucleic Acids Res VL - 45 ID - Malik2017 ER - TY - JOUR AU - Kuras, L. AU - Struhl, K. PY - 1999 DA - 1999// TI - Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme JO - Nature VL - 399 UR - https://doi.org/10.1038/21239 DO - 10.1038/21239 ID - Kuras1999 ER - TY - STD TI - Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013, 1303.3997. ID - ref134 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Bakel, H. AU - Tsui, K. AU - Gebbia, M. AU - Mnaimneh, S. AU - Hughes, T. R. AU - Nislow, C. PY - 2013 DA - 2013// TI - A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003479 DO - 10.1371/journal.pgen.1003479 ID - Bakel2013 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - STD TI - Abante J: NucSeq v1.0. v1.0 edition: Zenodo; 2016. ID - ref138 ER - TY - STD TI - Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Schwartz SL, Cui P, Čabart P, Han KH, et al: Datasets. BioProject https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522619 Sequence Read Archive; 2020. UR - https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522619 ID - ref139 ER -