Research

CEGR research is aimed at understanding how eukaryotic genes are regulated at a molecular level. Our physical location within shared space maximizes interactions that promote innovative thinking. Each lab brings unique strengths that together achieve a level of synergy that is rarely matched in scientific research. This includes excellence in biochemical assembly mechanisms in chromatin and transcription. It includes methods X-ray crystallography, cryo-EM, and a variety of biophysical methods to elucidate the structure and mechanism by which proteins interact with nucleosomes. We aim to understand how the bizarre repetitive structure of RNA polymerase II C-terminal domain regulates the transcription cycle. As we all know, specificity in gene regulation boils down to proteins selectively recognizing specific features (sequence and shape) on DNA, as allowed by the chromatin landscape, then using these anchor points to coelsce transcription complex assembly. We have developed state-of-the-art concepts about how DNA binding proteins access DNA that is encased in chromatin. We are studying how this gives rise to cell-type specific gene expression, for example, in making motor neurons or red blood cells. Through our experiments on human and mouse model systems we develop concepts about transcriptional regulation goes awry in cancer, and how we might use this knowledge to develop rectifying therapeutic drugs.

Publications

2019

Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination
Marco Igor Valencia-Sánchez, Pablo De Ioannes, Miao Wang, Nikita Vasilyev, Ruoyu Chen, Evgeny Nudler, Jean-Paul Armache, and Karim-Jean Armache
Molecular Cell, 74:1010-1019, 2019
Molecular Cell, 74 (2019) 1010-1025. doi:10.1016/j.molcel.2019.03.029
Cryo-EM structures of remodeler- nucleosome intermediates suggest allosteric control through the nucleosome
Jean Paul Armache, Nathan Gamarra, Stephanie L Johnson, John D Leonard, Shenping Wu, Geeta J Narlikar and Yifan Cheng
eLife, 2019 Armache eLife, 2019
Dissociation rate compensation mechanism for budding yeast pioneer transcription factors
Benjamin T Donovan, Hengye Chen, Caroline Jipa, Lu Bai and Michael G Poirier
eLife, 8:e46057, 2019
Using time-lapse fluorescence microscopy to study gene regulation
Fan Zou and Lu Bai
Methods, 159-160:138-145
Methods, 159-160 (2019) 138-145. doi:10.1016/j.ymeth.2018.12.010
Genetic analysis of the RNA polymerase II CTD in Drosophila
Feiyue Lu and David S. Gilmour
Methods, 159-160:129-137, 2019
Methods, 159-160 (2019) 129-137. doi:10.1016/j.ymeth.2019.01.010
The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptad
Feiyue Lu, Bede Portz and David S. Gilmour
Molecular Cell, 73:1232-1242, 2019
Molecular Cell, 73 (2019) 1232-1246. doi:10.1016/j.molcel.2019.01.008
Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation
Caroline R. Bartman, Nicole Hamagami, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, Gerd A. Blobel and Arjun Raj
Molecular Cell, 73:519-532, 2019
Molecular Cell, 73 (2019) 519-536. doi:10.1016/j.molcel.2018.11.004
Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription
Vivek Behera, Aaron J. Stonestrom, Nicole Hamagami, Chris C. Hsiung, Cheryl A. Keller, Belinda Giardine, Simone Sidoli, Zuo-Fei Yuan, Natarajan V. Bhanu, Michael T. Werner, Hongxin Wang, Benjamin A. Garcia,
Ross C. Hardison and Gerd A. Blobel
Cell Reports, 27:400-415, 2019
CellReports, 27 (2019) 400-420. doi:10.1016/j.celrep.2019.03.057
Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes
Begüm Aydin, Akshay Kakumanu, Mary Rossillo, Mireia Moreno-Estellés, Görkem Garipler, Niels Ringstad, Nuria Flames, Shaun Mahony and Esteban O. Mazzoni
Nature Neuroscience, 22:897-908, 2019
Nature Neuroscience, doi:10.1038/s41593-019-0399-y
Biochemical methods to characterize RNA polymerase II elongation T complexes
J. Brooks Crickard and Joseph C. Reese
Methods, 159-160:70-81, 2019
Methods, 159-160 (2019) 70-81. doi:10.1016/j.ymeth.2019.01.011
Ccr4–Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII
Haoyang Jiang, Marley Wolgast, Laura M. Beebe and Joseph C. Reese
Genes & Development, 33:705-717, 2019
Solution Ensemble of the C‐Terminal Domain from the Transcription Factor Pdx1 Resembles an Excluded Volume Polymer
Erik C. Cook, Debashish Sahu, Monique Bastidas and Scott A. Showalter
J. Physical Chemistry B, 123:106-116, 2019
J. Phys. Chem. B 2019.123:106-116

2018

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast
Chao Yan, Hengye Chen and Lu Bai
Molecular Cell, 71:294-305, 2018
Molecular Cell, 71 (2018) 294-309. doi:10.1016/j.molcel.2018.06.017
GFZF, a Glutathione S-Transferase Protein Implicated in Cell Cycle Regulation and Hybrid Inviability, Is a Transcriptional Coactivator
Douglas G. Baumann, Mu-Shui Dai, Hua Lu and David S. Gilmour
Mol. Cell. Biol., 38:e00476-17, 2018
Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility
Vivek Behera, Perry Evans, Carolyne J. Face, Nicole Hamagami, Laavanya Sankaranarayanan, Cheryl A. Keller, Belinda Giardine, Kai Tan, Ross C. Hardison, Junwei Shi & Gerd A. Blobe
Nature Communications, 9:782, 2018
Nature Communications, doi:10.1038/s41467-018-03082-6
Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells
Jeremy D. Grevet, Xianjiang Lan, Nicole Hamagami, Christopher R. Edwards, Laavanya Sankaranarayanan, Xinjun Ji, Saurabh K. Bhardwaj, Carolyne J. Face, David F. Posocco, Osheiza Abdulmalik, Cheryl A. Keller, Belinda Giardine, Simone Sidoli, Ben A. Garcia, Stella T. Chou, Stephen A. Liebhaber,
Ross C. Hardison, Junwei Shi and Gerd A. Blobel
Science, 361:285-290, 2018
Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points
Elisabeth F. Heuston, Cheryl A. Keller, Jens Lichtenberg, Belinda Giardine, Stacie M. Anderson, NIH Intramural Sequencing Center, Ross C. Hardison and David M. Bodine
Epigenetics & Chromatin, 11:22, 2018
Epigenetics & Chromatin, https://doi.org/10.1186/s13072-018-0195-z
Open-source discovery of chemical leads for next-generation chemoprotective antimalarials
Yevgeniya Antonova-Koch et al
Science, 362:1129, 2018
Specific Inhibition of the Bifunctional Farnesyl/ Geranylgeranyl Diphosphate Synthase in Malaria Parasites via a New Small-Molecule Binding Site
Jolyn E. Gisselberg, Zachary Herrera, Lindsey M. Orchard, Manuel Llinás and Ellen Yeh
Cell Chemical Biology, 25:185-193, 2018
Cell Chemical Biology, 25 (2018) 185-198. doi:10.1016/j.chembiol.2017.11.010
Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development
Heather J. Painter, Neo Christopher Chung, Aswathy Sebastian, Istvan Albert, John D. Storey, & Manuel Llinás
Nature Communications, 9:2656, 2018
Nature Communications, doi:10.1038/s41467-018-04966-3
Characterizing protein–DNA binding event subtypes in ChIP-exo data
Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh and Shaun Mahony
Bioinformatics, 35:903-913, 2018
Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh
Genome Research, 28:497-508, 2018
Simplified ChIP-exo assays
Matthew J. Rossi, William K.M. Lai & B. Franklin Pugh
Nature Communications, 9:2842, 2018
Nature Communications, doi:10.1038/s41467-018-05265-7
Widespread and precise reprogramming of yeast protein–genome interactions in response to heat shock
Vinesh Vinayachandran, Rohit Reja, Matthew J. Rossi, Bongsoo Park, Lila Rieber, Chitvan Mittal, Shaun Mahony and B. Franklin Pugh
Genome Research, 28:357=366, 2018
Genome-Wide Mapping of Decay Factor–mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4
Jason E. Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B. Franklin Pugh and Joseph C. Reese
G3, 8:315-330, 2018
The Use of 13C Direct-Detect NMR to Characterize Flexible and Disordered Proteins
Erik C. Cook, Grace A. Usher and Scott A. Showalter
Methods in Enzymology, 611:81-100, 2018
Intrinsically Disordered Proteins, 1, (2018) 81-100. doi:10.1016/bs.mie.2018.08.025
Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2
Jian Sun, Marcin Paduch, Sang-Ah Kim, Ryan M. Kramer, Adam F. Barrios, Vincent Lu, Judy Luke, Svitlana Usatyuk, Anthony A. Kossiakoff and Song Tan
PNAS, 115:10010-10015, 2018

2017

Three distinct mechanisms of long-distance modulation of gene expression in yeast
Manyu Du,, Qian Zhang and Lu Bai
PLOS Genetics, 13:e1006736, 2017
A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes
Douglas G. Baumann and David S. Gilmour
Nucleic Acids Research, 45:10481-10491, 2017
Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain
Bede Portz, Feiyue Lu,, Eric B. Gibbs, Joshua E. Mayfield, M. Rachel Mehaffey, Yan Jessie Zhang, Jennifer S. Brodbelt, Scott A. Showalter & David S. Gilmour
Nature Communications, 8:15231, 2017
Nature Communications 8, (2017). doi:10.1038/ncomms15231
Identification of Regions in the Spt5 Subunit of DRB Sensitivity-inducing Factor (DSIF) That Are Involved in Promoter-proximal Pausing
Yijun Qiu and David S. Gilmour
J. Biol. Chem., 292:5555-5570, 2017
Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element
Peng Huang, Cheryl A. Keller, Belinda Giardine, Jeremy D. Grevet, James O.J. Davies, Jim R. Hughes, Ryo Kurita, Yukio Nakamura, Ross C. Hardison and Gerd A. Blobel
Genes & Development, 31:1704-1713, 2017
Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation
Yu Zhang and Ross C. Hardison
Nucleic Acids Research, 45:9823-9836, 2017
Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
Heather J. Painter, Manuela Carrasquilla and Manuel Llinás
Genome Research, 27:1074-1086, 2017
Red Blood Cell Invasion by the Malaria Parasite Is Coordinated by the PfAP2-I Transcription Factor
Joana Mendonca Santos, Gabrielle Josling, Philipp Ross, Preeti Joshi, Lindsey Orchard, Tracey Campbell, Ariel Schieler, Ileana M. Cristea, and Manuel Llinás
Cell Host & Microbe, 731-741.e10, 2017
Cell Host and Microbe, 21 (2017) 731-751. doi:10.1016/j.chom.2017.05.006
Deconvolving sequence features that discriminate between overlapping regulatory annotations
Akshay Kakumanu, Silvia Velasco, Esteban Mazzoni, Shaun Mahony
PLOS Computational Biology, 13:e1005795, 2017
miniMDS: 3D structural inference from high-resolution Hi-C data
Lila Rieber and Shaun Mahony
Bioinformatics, 33:i261–i266, 2017
A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells
Silvia Velasco, Mahmoud M. Ibrahim, Akshay Kakumanu, Görkem Garipler, Begu€m Aydin, Mohamed Ahmed Al-Sayegh, Antje Hirsekorn, Farah Abdul-Rahman, Rahul Satija, Uwe Ohler, Shaun Mahony and Esteban O. Mazzoni
Cell Stem Cell, 20:205-217, 2017
Cell Stem Cell, 20 (2017) 205-217.e8. doi:10.1016/j.stem.2016.11.006
The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome
John B. Crickard, Jaehyoun Lee, Tae-Hee Lee and Joseph C. Reese
Nucleic Acids Research, 45:6362-6374, 2017
Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain
Eric B. Gibbs, Feiyue Lu, Bede Portz, Michael J. Fisher, Brenda P. Medellin, Tatiana N. Laremore, Yan Jessie Zhang, David S. Gilmour & Scott A. Showalter
Nature Communications, 8:15233, 2017
Nature Communications 8, (2017). doi:10.1038/ncomms15233
Substrate Specificity of the Kinase P-TEFb towards the RNA Polymerase II C-Terminal Domain
Eric B. Gibbs, Tatiana N. Laremore, Grace A. Usher, Bede Portz, Erik C. Cook and Scott A. Showalter
Biophysical Journal, 113:1909-1911, 2017
Biophysj, 113 (2017) 1909-1911. doi:10.1016/j.bpj.2017.09.011
Engineering double-stranded RNA binding activity into the Drosha double-stranded RNA binding domain results in a loss of microRNA processing function
Joshua C. Kranick, Durga M. Chadalavada, Debashish Sahu and Scott A. Showalter
PLOS One, 12:e0182445, 2017
The pPSU Plasmids for Generating DNA Molecular Weight Markers
Ryan C. Henrici, Turner J. Pecen, James L. Johnston & Song Tan
Scientific Reports, 7:2438, 2017

2016

Regulation of cell-to-cell variability in divergent gene expression
Chao Yan,, Shuyang Wu, Christopher Pocetti & Lu Bai
Nature Communications, 7:11099, 2016
Nature Communications 7, (2016). doi:10.1038/ncomms11099
Interallelic interaction and gene regulation in budding yeast
Daoyong Zhang and Lu Bai
PNAS, 113:4428-4433, 2016
A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition
Chris C.-S. Hsiung, Caroline R. Bartman, Peng Huang, Paul Ginart, Aaron J. Stonestrom, Cheryl A. Keller, Carolyne Face, Kristen S. Jahn, Perry Evans, Laavanya Sankaranarayanan, Belinda Giardine, Ross C. Hardison, Arjun Raj, and Gerd A. Blobel
Genes & Development, 30:1423-14439, 2016
Unlinking an lncRNA from Its Associated cis Element
Vikram R. Paralkar, Cristian C. Taborda, Peng Huang, Yu Yao, Andrew V. Kossenkov, Rishi Prasad, Jing Luan, James O.J. Davies, Jim R. Hughes, Ross C. Hardison, Gerd A. Blobel, and Mitchell J. Weiss
Molecular Cell, 62:104-110, 2016
Molecular Cell, 62 (2016) 104-110. doi:10.1016/j.molcel.2016.02.029
Jointly characterizing epigenetic dynamics across multiple human cell types
Yu Zhang, Lin An, Feng Yue and Ross C. Hardison
Nucleic Acids Research, 44:6721-6731, 2016
Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite
Simon A. Cobbold, Joana M. Santos, Alejandro Ochoa, David H. Perlman & Manuel Llinás
Scientific Reports, 6:19722, 2016
srep , (2015). doi:10.1038/srep19722
The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation
Makiko Iwafuchi-Doi, Greg Donahue, Akshay Kakumanu, Jason A. Watts, Shaun Mahony, B. Franklin Pugh, Dolim Lee, Klaus H. Kaestner and Kenneth S. Zaret
Molecular Cell, 62:79-91, 2016
Molecular Cell, 62 (2016) 79-91. doi:10.1016/j.molcel.2016.03.001
Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution
G. Celine Han, Vinesh Vinayachandran, Alain R. Bataille, Bongsoo Park, Ka Yim Chan-Salis, Cheryl A. Keller, Maria Long, Shaun Mahony, Ross C. Hardison, B. Franklin Pugh
Mol Cell Biol, 36:157-172, 2016
Genomic Nucleosome Organization Reconstituted with Pure Proteins
Nils Krietenstein, Megha Wal, Shinya Watanabe, Bongsoo Park, Craig L. Peterson, B. Franklin Pugh, and Philipp Korber
Cell, 167:709-721, 2016
Biochemical Analysis of Yeast Suppressor of Ty 4/5 (Spt4/5) Reveals the Importance of Nucleic Acid Interactions in the Prevention of RNA Polymerase II Arrest
J. Brooks Crickard, Jianhua Fu, and Joseph C. Reese
J. Biol. Chem., 291:9853-9870, 2016
Quantification of Compactness and Local Order in the Ensemble of the Intrinsically Disordered Protein FCP1
Eric B. Gibbs and Scott A. Showalter
J. Physical Chemistry B, 120:8960-8689, 2016
J. Phys. Chem. B 2016.120:8960-8969
Elimination of truncated recombinant protein expressed in Escherichia coli by removing cryptic translation initiation site
Matthew J. Jennings, Adam F. Barrios and Song Tan
Prot. Expr. and Purif., 12:17-21, 2016
Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate
Taverekere S. Girish, Robert K. McGinty and Song Tan
J. Mol. Biol, 428:1531-1543, 2016
Preparation, Crystallization, and Structure Determination of Chromatin Enzyme/Nucleosome Complexes
R.K. McGinty, R.D. Makde, S. Tan
Methods in Enzymology, 573:43-65, 2016

2015

Decoupling of divergent gene regulation by sequence-specific DNA binding factors
Chao Yan, Daoyong Zhang, Juan Antonio Raygoza Garay, Michael M. Mwangi and Lu Bai
Nucleic Acids Research, 43:7292-7305, 2015
Molecular mechanisms of ribosomal protein gene coregulation
Rohit Reja, Vinesh Vinayachandran, Sujana Ghosh, and B. Franklin Pugh
Genes & Development, 29:1942-1954, 2015
Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II
Arnob Dutta, Vinod Babbarwal, Jianhua Fu, Deborah Brunke-Reese, Diane M. Libert, Jonathan Willis and Joseph C. Reese
Mol Cell Biol, 35:1915-1925, 2015
Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex
Sang-Ah Kim, Nilanjana Chatterjee, Matthew J. Jennings, Blaine Bartholomew and Song Tan
Nucleic Acids Research, 43:4868-4880, 2015

2014

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
PLOS Computational Biology, 10:1-14, 2014
Subnucleosomal Structures and Nucleosome Asymmetry across a Genome
Ho Sung Rhee, Alain R. Bataille, Liye Zhang and B. Franklin Pugh
Cell, 159:1377-1388, 2014
Cell, 159 (2014) 1377-1388. doi:10.1016/j.cell.2014.10.054
Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome
Robert K. McGinty, Ryan C. Henrici & Song Tan
Nature, 514:591-596, 2014