Schofield, JA and S. Hahn. (2024) Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single cell RNA-seq. Cell Reports, Aug 27; 43:114593. doi: 10.1016/j.celrep.2024.114593

Mahendrawada, L., Warfield, L., Donczew, R., and S. Hahn. (2023). Surprising connections between DNA binding and function for the near-complete set of yeast transcription factors Biorxiv https://doi.org/10.1101/2023.07.25.550593.

Schofield, JA and S. Hahn (2023) Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity.  Cell Reports Apr 12;42(4):112387. doi: 10.1016/j.celrep.2023.112387

Warfield, L.*, Donczew, R*, Mahendrawada, L., and S. Hahn (2022) Yeast Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism.  Mol Cell, Nov 3;82(21):4033-4048.e7. doi: 10.1016/j.molcel.2022.09.016. Epub 2022 Oct 7.

Donczew, R and S. Hahn (2021). BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae.  Elife. 2021 Jun 17;10:e69619. doi: 10.7554/eLife.69619. Online ahead of print.PMID: 34137374

Tuttle, L., Pacheco, D., Warfield, L., Wilburn, D.B., Hahn, S., and R. Klevit (2021). Mediator subunit Med15 dictates the conserved “fuzzy” binding mechanism of yeast transcription activators Gal4 and Gcn4. Nat Commun. 2021 Apr 13;12(1):2220. doi: 10.1038/s41467-021-22441-4.

Donczew R., Lalou, A., Devys, D., Tora, L., and S. Hahn (2021). An improved ChEC-seq method accurately maps the genome-wide binding of transcription coactivators and sequence-specific transcription factors.  Bioxriv, doi: https://doi.org/10.1101/2021.02.12.430999

Tomko, E.J., Luyties, O., Rimel, JK, Chi-Lin Tsai, C-L, Fuss, J.O.,  Fishburn , J., Hahn, S., Tsutakawa, S.E., Taatjes D.J., and E.A. Galburt (2021). The role of XPB/Ssl2 dsDNA translocation processivity in transcription-start-site scanning. J. Mol Biol., Jan 13;166813.  doi: 10.1016/j.jmb.2021.166813. PMID: 33453189

Erijman, A. Kozlowski, L., Sohrabi-Jahromi, J., Fishburn, J., Warfield, L., Schreiber, J., Noble, WS, Söding, J., and S. Hahn (2020). A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning Mol Cell, May 12;S1097-2765(20)30262-8.doi: 10.1016/j.molcel.2020.04.020.

Donczew R*, Warfield L*, Pacheco D, Erijman A, S. Hahn S. (2020). Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA. Elife. 2020 Jan 8;9. pii: e50109. doi: 10.7554/eLife.50109. PMID: 31913117

Patel AB, Louder RK, Greber BJ, Grünberg S, Luo J, Fang J, Liu Y, Ranish J, Hahn S, E. Nogales (2018). Structure of human TFIID and mechanism of TBP loading onto promoter DNA.  Science, 362. pii: eaau8872. doi: 10.1126/science.aau8872. Epub 2018 Nov 15.

Hahn S. (2018). Phase Separation, Protein Disorder, and Enhancer Function. Cell 175:1723-1725. doi: 10.1016/j.cell.2018.11.034.

Pacheco, D*, Warfield L*, Brajcich M, Robbins H, Luo J, Ranish J, S. Hahn (2018). Transcription activation domains of the yeast factors Met4 and Ino2: tandem activation domains with properties similar to the yeast Gcn4 activator. Mol Cell Biol, doi: 10.1128/MCB.00038-18. [Epub ahead of print]

Tuttle LM, Pacheco D, Warfield L, Luo J, Ranish J, Hahn S, Klevit, R. (2018). Gcn4-Mediator specificity is mediated by a large and dynamic fuzzy protein-protein complex.  Cell Reports, 22:3251-3264.  https://doi.org/10.1016/j.celrep.2018.02.097

Donczew R and S. Hahn (2017).  Mechanistic differences in transcription initiation at TATA-less and TATA-containing promoters. Mol Cell Biol, Oct 16. pii: MCB.00448-17. doi: 10.1128/MCB.00448-17. [Epub ahead of print]  PMID: 29038161

Tomko, E., Fishburn, J., Hahn, S., and E. Galburt (2017) TFIIH generates a six base-pair open complex during RNAP II transcription initiation and start-site scanning. Nat Struct Mol Biol, Nov 6. doi: 10.1038/nsmb.3500. [Epub ahead of print]  PMID: 29106413

Warfield, L.*, Ramachandran, S.*, Baptista, T., Tora, L., Devys, D., and S. Hahn (2017). Transcription of nearly all yeast RNA Polymerase II-transcribed genes is dependent on transcription factor TFIID. Mol Cell 68:118-129. PMID: 28918900

Baptista, T., Grünberg, S., Minoungou, N., Koster, M.J.E., Timmers, H.T.M., Hahn, S., Devys, D. and T., László (2017). SAGA is a general cofactor for RNA polymerase II transcription. Mol Cell, 68:130-143. PMID: 28918903

Grünberg, S, Henikoff, S., Hahn, S., and G. Zentner (2016). Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters.  EMBOJ, 35(22):2435-2446. Epub 2016 Oct 20. PMID: 27797823

Warfield L, Luo J, Ranish J, and Hahn S (2016).  Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH. Mol Cell Biol. 36:2464-75. doi: 10.1128/MCB.00182-16. Print 2016 Oct 1. PMID: 27381459.

Fishburn, J, Galburt, E, and Hahn, S. (2016)  Transcription start site scanning and the requirement for ATP during transcription initiation by RNA polymerase II, J Biol Chem, 291:13040-7. doi: 10.1074/jbc.M116.724583. Epub 2016 Apr 17.

Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. (2015) Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.  Mol Cell 59:794-806.

Fishburn, J., Tomko, E., Galburt, E. and S. Hahn S.  (2015). Double stranded DNA translocase activity of TFIIH and the mechanism of RNA Polymerase II Open Complex formation. Proc Natl Acad Sci USA., 112:3961-3966    

Hahn, S. (2014) Ellis Englesberg and the discovery of positive control in gene regulation.  Genetics, 198:455-460.

Han, Y., Luo, J., Ranish, J. and Hahn, S. (2014).  Architecture of the S. cerevisiae SAGA transcription coactivator complex.  EMBOJ,  pii: e201488638. [Epub ahead of print].

Knutson, B., Luo, J, Ranish, J., and Hahn, S. (2014) Architecture of the S. cerevisiae RNA polymerase I Core Factor complex. Nature Struct Mol Biol, 21:810-816.

Warfield, L, Tuttle, L., Pacheco, D., Klevit, R., and Hahn, S. (2014)  A sequence-specific transcription activator motif and powerful synthetic variants that bind Mediator using a "fuzzy" protein interface.  Proc Natl Acad Sci USA, 111(34):E3506-13.

Kamenova, I, Warfield, L., and Hahn, S. (2014) Mutations on the DNA binding surface of TBP discriminate between yeast TATA and TATA-less gene transcription.  Mol Cell Biol 39:2929-2943.

Grünberg, S. and Hahn, S. (2013) Structural insights into transcription initiation by RNA polymerase II.  Trends Biochem Sci 38: 603-611.

Knutson, B. and Hahn, S. (2013) TFIIB-related factors in RNA polymerae I transcription.  Biochem Biophys Acta 1829:265-73.

Grünberg, S., Warfield, L. and Hahn, S. (2012). Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nature Struct. Mol. Biol., 19:788-795.

Luo, J., Fishburn, J., Hahn, S. and Ranish, J. (2012). An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol Cell Proteomics, Feb;11(2):M111.008318. Epub 2011 Nov 7.

Fishburn, J. and Hahn, S. (2012). Architecture of the yeast RNA polymerase II open complex and regulation of activity by TFIIF. Mol Cell Biol, 32:12-25.

Brzovic, P.S., Heikaus, C.C., Kisselev, L., Vernon, R., Herbig, E., Pacheco, D., Warfield, L., Littlefield, P., Baker, D., Klevit, R. and Hahn, S. (2011). The acidic transcription activator Gcn4 binds the Mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Mol Cell 44:942-953.

Hahn, S. and Young, E.T. (2011). Transcriptional regulation in S. cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators.  (YeastBook) Genetics 189:705-736.

Knutson, B.A. and Hahn, S. (2011). Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors. Science, 333:1637-1640.

Knutson, B.A. and Hahn, S. (2011). Domains of Tra1 important for activator recruitment and transcription coactivator functions of SAGA and NuA4 complexes. Mol Cell Biol, 31:818-831.

Herbig, E., Warfield, L., Fish, L., Fishburn, J., Kutson, B.A., Moorefield, B., Pacheco, D. and Hahn, S. (2010). Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains.  Mol Cell Biol, 30:2376-2390.

Knutson, B.A. (2010). Insights into the domain and repeat architecture of target of rapamycin. Journal of Structural Biology, 170:354-63.

Eichner, J., Chen, H-T., Warfield, L., and Hahn, S. (2010). Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex.  EMBOJ 17: 706-716.

Hahn, S. (2009). New beginnings for transcription. (News and Views) Nature 462:292-293.

Liu, Y, Warfield, L., Zhang, C., Luo, J., Allen, J., Lang, W.H., Ranish, J, Shokat, K.M. and Hahn, S. (2009). Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol 29:4852-4863.

Mohibullah, N and Hahn, S. (2008). Site-specific crosslinking of TBP in vivo and in vitro reveals a direct functional interaction with the SAGA subunit Spt3. Genes Dev, 22:2994-3006.

Hahn, S. (2008) Transcriptional Regulation (Meeting Review) EMBO Reports 9:612-619.

Lariviere, L., Seizl, M., van Wageningen, S., Rother, S., van de Pasch, L., Feldmann, H., Strasser, K, Hahn, S., Holstege, F.C.P. and Cramer, P. (2008). Structure-system correlation identifies a gene regulatory Mediator Submodule. Genes Dev 22:872-877.

Kim, B. Nesvizhskii, A.I., Rani, P.G., Hahn, S., Aebersold, R. and Ranish, J.A. (2007). The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci USA 104:16068-16073.

Chen H-T., Warfield, L. and Hahn, S. (2007). The positions of TFIIF and TFIIE in the RNA Polymerase II transcription Preinitiation Complex. Nat Struct Mol Biol. 14:696-703.

Kanin, E.I, Kipp, R.T., Kung, C., Slattery, M., Viale, A., Hahn, S., Shokat, K.M. and Ansari, A.Z. (2007). Chemical inhibition of the TFIIH associated kinase Cdk7/Kin28 does not impair global gene expression. Proc Acad Sci USA 104:5812-5817.

Miller, G. and Hahn, S. (2006). A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex. Nat. Struct. Mol. Biol., 13:603-610.

Reeves, W. M. and Hahn, S. Targets of the Gal4 transcription activator in functional transcription complexes. (2005) Mol Cell Biol., 25:9092-9102.

Fishburn, J., Mohibullah, N. and Hahn, S. (2005) Function of a eukaryotic transcription activator during the transcription cycle. Mol. Cell., 18:369-378.

Chen, H-T. and Hahn, S. (2004) Mapping the location of TFIIB within the RNA Polymerase II Transcription Preinitiation Complex: A model for the Structure of the PIC Cell 119:169-180.

Ranish, J.A., Hahn, S., Lu, Y, Yi, E.C., Li, X-j, Eng, J. and Aebersold, R. (2004). Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nature Genetics 36:1-7.

Warfield, L, Ranish, J.A. and Hahn, S. (2004). Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. Genes Dev. 18:1022-1034.

Hahn, S. (2004). Structure and Mechanism of the RNA Polymerase II transcription machinery (Review). Nat Struct Mol Biol. 11:394-403.

Liu, Y, Kung, C., Fishburn, J., Ansari, A.Z., Shokat, K.M. and Hahn, S. (2004). Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the Scaffold Complex. Mol Cell Biol. 24:1721-1735.

Rani, G., Ranish, J.A. and Hahn, S. (2004). The Pol II-TFIIF and Pol II-Mediator complexes: the major stable RNA Polymerase II complexes and their activity in transcription initiaiton and reinitiation. Mol Cell Biol 24:1709-1720.

Chen, H-T. and Hahn, S. (2003). Binding of TFIIB to RNA Polymerase II: Mapping the Binding Site for the TFIIB Zinc Ribbon Domain within the Preinitiation Complex. Mol Cell12:437-448.

Reeves, W.M. and Hahn, S. (2003). Activator-Independent functions of the yeast mediator Sin4 complex in Preinitiation Complex Formation and Transcription Reinitiation. Mol Cell Biol. 23:349-358.

Liu, Y., Ranish, J.A., Aebersold, R. and Hahn, S. (2001). Yeast nuclear extract contains two major forms of RNA polymerase II Mediator complexes. (2001). J. Biol. Chem 276:7169-7175.

Yudkovsky, N., Ranish, J.A. and Hahn, S. (2000). A transcription reinitiation intermediate that is stabilized by activator. Nature 408:225-229.

Hahn, S. and Roberts, S. (2000) The zinc ribbon domains of the general transcription factors TFIIB and Brf: Conserved functional surfaces but different roles in transcription initiation. Genes and Dev. 14:719-730.

Yudkovsky, N., Logie, C., Hahn, S. and Peterson, C.L. (1999). Recruitment of theSWI/SNF chromatin remodeling complex by transcriptional activators. Genes and Dev. 13:2369-2374.

Ranish, J.A., Yudkovsky, N. and Hahn, S. (1999). Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB Genes and Dev. 13:49-63.

Hahn, S. (1998). Activation and the role of reinitiation in the control of transcription by RNA Polymerase II. Cold Spring Harbor Symp. Quant. Biol. 63:181-188.

Hahn, S. (1998). The role of TAFs in RNA Polymerase II Transcription. Cell 95:579-582.

Colbert, T., Lee, S., Schimmack, G. and Hahn, S. (1998). Architecture of protein and DNA contacts within the TFIIIB-DNA complex. Mol. Cell. Biol. 18:1682-1691.

Auble, D.T., Wang, D., Post, K.W. and Hahn, S. (1997). Molecular analysis of the SNF2/SWI2 protein family member MAOT1, an ATP-driven enzyme that dissociates TATA-binding protein from DNA. Mol Cell Biol. 8:4842-51.

Geiger, J.H., Hahn, S., Lee, S. and Sigler, P.B. (1996). The crystal structure of the yeast TFIIA/TBP/DNA complex. Science, 272:830-836.

Roberts, S., Miller, S., Lane W.S., Lee, S. and Hahn, S. (1996). Cloning and functional characterization of the gene encoding the TFIIIB90 subunit of RNA polymerase III transcription factor TFIIIB. J. Biol Chem 271:14903-14909.

Lee, S. and Hahn, S. (1995). Model for binding of transcription factor TFIIB to the TBP-DNA complex. Nature, 376:609-612.

Kang, J.J., Auble, D.T., Ranish, J.A. and Hahn, S. (1995). Analysis of the yeast transcription factor TFIIA: distinct functional regions and a polymerase II-specific role in basal and activated transcription. Mol Cell Biol. 15:1234-1243.

Roberts, S., Colbert, T. and Hahn, S. (1995). TFIIIC determines RNA polymerase III specificity at the TATA-containing yeast U6 promoter.  Genes Dev 9:832-842.

Auble, D.T., Hansen, K.E., Mueller, C.G.F., Lane, W.S., Thorner, J. and Hahn, S. (1994). Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes and Development 8:1920-1934.

Kim, Y., Geiger, J.H., Hahn, S. and Sigler, P.B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature 365: 512-520.

Auble, D., and Hahn, S. (1993). An ATP-dependent inhibitor of TATA binding protein to DNA.  Genes Dev 7:844-856.

Colbert, T. and Hahn, S. (1992). A yeast TFIIB related factor involved in RNA polymerase III transcription. Genes and Dev. 6: 1940-1949.

M.C. Schultz, R.H. Reeder, and Hahn, S. (1992). Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II, and III promoters. Cell: 69, 697-702.

Ranish, J., Lane, W.S. and Hahn, S. (1992). Isolation of two genes that encode subunits of the yeast transcription factor IIA. Science 255: 1127-1128.

Ranish, J. and Hahn, S. (1991). The yeast general transcription factor TFIIA is composed to two polypeptide subunits.  J. Biol Chem 266:19320-19327.

Hahn, S., Buratowski, S., Sharp, P.A. and Guarente, L. (1989). Isolation of the gene encoding the yeast TATA binding protein TFIID: a gene identical to the SPT15 suppressor of Ty element insertions. Cell 58:1173-1181

Hahn, S., Buratowski, S., Sharp, P.A. and Guarente, L. (1989). Identification of a yeast protein homologous in function to the mammalian general transcription factor, TFIIA. EMBO J. 8:3379-3382.