This collection showcases the books, journal articles, book reviews, and other publications and presentations written by faculty and researchers of the Department of Biochemistry and Molecular Pharmacology.
Publications from 2018
NmeCas9 is an intrinsically high-fidelity genome editing platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer
Do Skeletal Dynamics Mediate Sugar Uptake and Transport in Human Erythrocytes, Robert J. Asaro, Qiang Zhu, Pedro Cabrales, and Anthony Carruthers
Evaluation of a method to measure HHV-6B infection in vitro based on cell size, Aniuska Becerra, Tessa Santoro, and Lawrence J. Stern
Ajulemic acid: potential treatment for chronic inflammation, Sumner Burstein
Effects of Larval Density on Gene Regulation in Caenorhabditis elegans During Routine L1 Synchronization, Io Long Chan, Oliver J. Rando, and Colin C. Conine
Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling, Weijun Chen, Jill E. Moore, Hakan Ozadam, Hennady P. Shulha, Nicholas Rhind, Zhiping Weng, and Melissa J. Moore
Small RNAs gained during epididymal transit of sperm are essential for embryonic development in mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, and Oliver J. Rando
Immunocontraceptive target repertoire defined by systematic identification of sperm membrane alloantigens in a single species, Nathaly Cormier, John J. McGlone, John D. Leszyk, and Daniel M. Hardy
Nuclear Export Through Nuclear Envelope Remodeling in Saccharomyces cerevisiae, Baojin Ding, Anne M. Mirza, James A. Ashley, Vivian Budnik, and Mary Munson
Role of TRIP6 and Angiomotins in the Regulation of the Hippo Signaling Pathway, Shubham Dutta
Heterochromatin drives organization of conventional and inverted nuclei, Martin Falk; Yana Feodorova; Natasha Naumova; Massachusetts Institute of Technology; Illumina Incorporated; Heinrich Leonhardt; Ludwig Maximilians Universitat, Munchen; Job Dekker; University of California, San Francisco; Ludwig Maximilians Universitat, Munchen; and Massachusetts Institute of Technology
Intranuclear and higher-order chromatin organization of the major histone gene cluster in breast cancer, Andrew J. Fritz, Deli Hong, A. Rasim Barutcu, Anthony N. Imbalzano, and Gary S. Stein
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, and Zhiping Weng
The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, and Phillip D. Zamore
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2, Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomas Rodriguez, Yue-He Ding, John D. Leszyk, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer (Nature methods, 2018-05-07)
C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2, Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomas Rodriguez, Yue-He Ding, John D. Leszyk, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer
Investigating the Gene Regulatory Network Underlying Caudal Hindbrain Specification in Embryonic Zebrafish, Priyanjali Ghosh
Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish, Priyanjali Ghosh, Jennifer M. Maurer, and Charles G. Sagerstrom
A pathway for mitotic chromosome formation, Johan H. Gibcus, Kumiko Samejima, Anton Goloborodko, Itaru Samejima, Natalia Naumova, Johannes Nuebler, Masato T. Kanemaki, Linfeng Xie, James R. Paulson, William C. Earnshaw, Leonid A. Mirny, and Job Dekker (Science (New York, N.Y.), 2018-02-09)
Profiling of pluripotency factors in individual stem cells and early embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, and Thomas G. Fazzio
Two-dimensional transition metal carbides and nitrides (MXenes) for biomedical applications, Kai Huang, Zhongjun Li, Jing Lin, Gang Han, and Peng Huang
Oligonucleotides targeting TCF4 triplet repeat expansion inhibit RNA foci and mis-splicing in Fuchs' dystrophy, Jiaxin Hu, Ziye Rong, Xin Gong, Zhengyang Zhou, Vivek K. Sharma, Chao Xing, Jonathan K. Watts, David R. Corey, and V. Vinod Mootha
Computer design of microfluidic mixers for protein/RNA folding studies, Venkatesh Inguva, Sagar V. Kathuria, Osman Bilsel, and Blair James Perot
ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)
ChIP-chip, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR), Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
ChIP-seq, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
Formaldehyde Cross-Linking, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)
Preparation of Cross-Linked Chromatin for ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)
TALE factors use two distinct functional modes to control an essential zebrafish gene expression program, Franck Ladam, William Stanney, Ian J. Donaldson, Ozge Yildiz, Nicoletta Bobola, and Charles G. Sagerstrom
BB-Cl-Amidine as a novel therapeutic for canine and feline mammary cancer via activation of the endoplasmic reticulum stress pathway, Melissa M. Ledet, Robyn Anderson, Rebecca Harman, Aaron Muth, Paul R. Thompson, Scott A. Coonrod, and Gerlinde R. Van de Walle
Understanding Human Erythrocyte Glucose Transporter (GLUT1) Mediated Glucose Transport Phenomena Through Structural Analysis, Kenneth P. Lloyd
Optogenetic Control of Voltage-Gated Calcium Channels, Guolin Ma, Jindou Liu, Yuepeng Ke, Xin Liu, Minyong Li, Fen Wang, Gang Han, Yun Huang, Youjun Wang, and Yubin Zhou
Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA, Atanu Maiti, Wazo Myint, Tapan Kanai, Krista Delviks-Frankenberry, Christina Sierra Rodriguez, Vinay K. Pathak, Celia A. Schiffer, and Hiroshi Matsuo
Targeting Drug Resistance In HCV NS3/4A Protease: Mechanisms And Inhibitor Design Strategies, Ashley N. Matthew
A parental requirement for dual-specificity phosphatase 6 in zebrafish, Jennifer M. Maurer and Charles G. Sagerstrom
Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines, Sean M. McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, and Jeremy Luban
Higher-Order Organization Principles of Pre-translational mRNPs, Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, and Melissa J. Moore
Photochemical Control of Protein Arginine Deiminase (PAD) Activity, Santanu Mondal, Sangram S. Parelkar, Mitesh Nagar, and Paul R. Thompson
The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5alpha, Damien Morger, Franziska Zosel, Martin Buhlmann, Sara Zuger, Maximilian Mittelviefhaus, Benjamin Schuler, Jeremy Luban, and Markus G. Grutter
Donated chemical probes for open science, Susanne Muller, Paul R. Thompson, and Anke Mueller-Fahrnow
The Development of Benzimidazole-Based Clickable Probes for the Efficient Labeling of Cellular Protein Arginine Deiminases (PADs), Venkatesh V. Nemmara, Venkataraman Subramanian, Aaron Muth, Santanu Mondal, Ari J. Salinger, Aaron J. Maurais, Ronak Tilvawala, Eranthie Weerapana, and Paul R. Thompson
Citrullination Inactivates Nicotinamide-N-methyltransferase, Venkatesh V. Nemmara, Ronak Tilvawala, Ari J. Salinger, Lacey Miller, Son Hong Nguyen, Eranthie Weerapana, and Paul R. Thompson
Ras hyperactivation versus overexpression: Lessons from Ras dynamics in Candida albicans, Vavilala A. Pratyusha, Guiliana Soraya Victoria, Mohammad Firoz Khan, Dominic T. Haokip, Bhawna Yadav, Nibedita Pal, Subhash Chandra Sethi, Priyanka Jain, Sneh Lata Singh, Sobhan Sen, and Sneha Sudha Komath
CBFbeta-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia, John A. Pulikkan, Mahesh Hegde, Hafiz Mohd Ahmad, Houda Belaghzal, Anuradha Illendula, Jun Yu, Kelsey O'Hagan, Jianhong Ou, Carsten Muller-Tidow, Scot A. Wolfe, Lihua J. Zhu, Job Dekker, John Hackett Bushweller, and Lucio H. Castilla (Cell, 2018-06-28)
Effects of larval density on gene regulation in C. elegans during routine L1 synchronization, Oliver J. Rando, Io Long Chan, and Colin C. Conine
Posttranslational modification of a histone-like protein regulates phenotypic resistance to isoniazid in mycobacteria, Alexandra Sakatos, Gregory H. Babunovic, Michael R. Chase, Alexander Dills, John D. Leszyk, Tracy Rosebrock, Bryan Bryson, and Sarah M. Fortune
Regulation of ATM and ATR by SMARCAL1 and BRG1, Ramesh Sethy, Radhakrishnan Rakesh, Ketki Patne, Vijendra Arya, Tapan Sharma, Dominic T. Haokip, Reshma Kumari, and Rohini Muthuswami
Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline, En-Zhi Shen, Hao Chen, Ahmet R. Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, and Craig C. Mello
Investigating the Structural Basis for Human Disease: APOBEC3A and Profilin, Tania V. Silvas
Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions, Tania V. Silvas, Shurong Hou, Wazo Myint, Ellen A. Nalivaika, Mohan Somasundaran, Brian A. Kelch, Hiroshi Matsuo, Nese Kurt Yilmaz, and Celia A. Schiffer
Watching Sugar Transport in Real Time in Single Cells and Cell Populations, Andrew H. Simon
Pervasive contingency and entrenchment in a billion years of Hsp90 evolution, Tyler N. Starr, Julia Flynn, Parul Mishra, Daniel N. Bolon, and Joseph W. Thornton
A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans, Wen Tang, Meetu Seth, Shikui Tu, En-Zhi Shen, Qian Li, Masaki Shirayama, Zhiping Weng, and Craig C. Mello
Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking, Thom Vreven, Devin K. Schweppe, Juan D. Chavez, Chad R. Weisbrod, Sayaka Shibata, Chunxiang Zheng, James E. Bruce, and Zhiping Weng
HIV-1 unmasks the plasticity of innate lymphoid cells, Yetao Wang, Kyle Gellatly, Alan G. Derr, Smita Jaiswal, Alper Kucukural, Patrick McDonel, Thomas C. Greenough, JeanMarie Houghton, Manuel Garber, and Jeremy Luban
Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection, Eric R. Weiss, Susanna L. Lamers, Jennifer L. Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Chad Nusbaum, and Katherine Luzuriaga
Efficient Blue to Red Afterglow Tuning in a Binary Nanocomposite Plastic Film, Yan Xia, Huase Ou, Wanbin Li, Gang Han, and Zhanjun Li
Partial DNA-guided Cas9 enables genome editing with reduced off-target activity, Hao Yin, Chun-Qing Song, Sneha Suresh, Suet-Yan Kwan, Qiongqiong Wu, Stephen Walsh, Junmei Ding, Roman L. Bogorad, Lihua Julie Zhu, Scot A. Wolfe, Victor Koteliansky, Wen Xue, Robert Langer, and Daniel G. Anderson
Primate immunodeficiency virus Vpx and Vpr counteract transcriptional repression of proviruses by the HUSH complex, Leonid Yurkovetskiy, Mehmet Hakan Guney, Kyusik Kim, Shih Lin Goh, Sean M. McCauley, Ann Dauphin, William E. Diehl, and Jeremy Luban
Nuclear organization mediates cancer-compromised genetic and epigenetic control, Sayyed K. Zaidi, Andrew J. Fritz, Kirsten M. Tracy, Jonathan A. Gordon, Coralee E. Tye, Joseph Boyd, Andre J. Van Wijnen, Jeffrey A. Nickerson, Anthony N. Imbalzano, Jane B. Lian, Janet L. Stein, and Gary S. Stein
The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes, Donglei Zhang, Shikui Tu, Michael Stubna, Wei-Sheng Wu, Wei-Che Huang, Zhiping Weng, and Heng-Chi Lee
Publications from 2017
Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry, Bandar Alghanem, Frederic Nikitin, Thomas Stricker, Eva Duchoslav, Jeremy Luban, Caterina Strambio-De-Castilla, Markus Muller, Frederique Lisacek, Emmanuel Varesio, and Gerard Hopfgartner
Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope, Yuval Avnir, Kristina L. Prachanronarong, Shurong Hou, Brendan J. Hilbert, Markus-Frederik Bohn, Timothy F. Kowalik, Robert W. Finberg, Jennifer P. Wang, Nese Kurt Yilmaz, Celia A. Schiffer, and Wayne A. Marasco
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation, Houda Belaghzal, Job Dekker, and Johan H. Gibcus (Methods (San Diego, Calif.), 2017-07-01)
The Trypanosome Exocyst: A Conserved Structure Revealing a New Role in Endocytosis, Cordula M. Boehm, Samson Obado, Catarina Gadelha, Alexandra Kaupisch, Paul T. Manna, Gwyn W. Gould, Mary Munson, Brian T. Chait, Michael P. Rout, and Mark C. Field
ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes, Tyler M. Borrman, Jennifer M. Cimons, Michael Cosiano, Michael Purcaro, Brian G. Pierce, Brian M. Baker, and Zhiping Weng
A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes, Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, and Giovanni Bosco
Adapting the EMPIRIC Approach to Investigate Evolutionary Constraints in Influenza A Virus Surface Proteins, Aneth S. Canale
Synovial fibroblast-neutrophil interactions promote pathogenic adaptive immunity in rheumatoid arthritis, Carmelo Carmona-Rivera, Paul R. Thompson, and Mariana J. Kaplan
Lowering relative humidity level increases epidermal protein deimination and drives human filaggrin breakdown, Laura Cau, Valerie Pendaries, Emeline Lhuillier, Paul R. Thompson, Guy Serre, Hidenari Takahara, Marie-Claire Mechin, and Michel Simon
A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification, Can Cenik, Hon Nian Chua, Guramrit Singh, Abdalla Akef, Michael P. Snyder, Alexander F. Palazzo, Melissa J. Moore, and Frederick P. Roth
The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins, Yvonne H. Chan
Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints, Yvonne H. Chan, Sergey V. Venev, Konstantin B. Zeldovich, and C. Robert Matthews
Transcriptome-Wide Analysis of Roles for Transfer RNA Modifications in Translational Regulation, Hsin-Jung Chou
Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation, Hsin-Jung Chou, Elisa Donnard, H. Tobias Gustafsson, Manuel Garber, and Oliver J. Rando
The 4D nucleome project, Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh C. O'Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay Shendure, Sheng Zhong, and 4D Nucleome Network (Nature, 2017-09-13)
The 4D Nucleome Project, Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh C. O'Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay Shendure, and Sheng Zong
Structure of RNA polymerase bound to ribosomal 30S subunit, Gabriel Demo, Aviram Rasouly, Nikita Vasilyev, Vladimir Svetlov, Anna B. Loveland, Ruben Diaz-Avalos, Nikolaus Grigorieff, Evgeny Nudler, and Andrei A. Korostelev
Mechanism of ribosome rescue by ArfA and RF2, Gabriel Demo, Egor Svidritskiy, Rohini Madireddy, Ruben Diaz-Avalos, Timothy Grant, Nikolaus Grigorieff, Duncan Sousa, and Andrei A. Korostelev
Heterogeneity and Intrinsic Variation in Spatial Genome Organization, Elizabeth Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, and Tom Misteli
Exploring the Role of Large Clusters of Branched Aliphatic Residues on the Folding Free Energy Landscape of (βα)8 TIM Barrel Proteins, Kevin T. Halloran
Temporal regulation of chromatin during myoblast differentiation, Akihito Harada, Yasuyuki Ohkawa, and Anthony N. Imbalzano
PGBD5 promotes site-specific oncogenic mutations in human tumors, Anton G. Henssen, Jiali Zhuang, Zhiping Weng, and Alex Kentsis
The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain, Brendan J. Hilbert, Janelle A. Hayes, Nicholas P. Stone, Rui-Gang Xu, and Brian A. Kelch
Role of peptidylarginine deiminase 2 (PAD2) in mammary carcinoma cell migration, Sachi Horibata, Katherine E. Rogers, David Sadegh, Lynne J. Anguish, John L. McElwee, Pragya Shah, Paul R. Thompson, and Scott A. Coonrod
Three-dimensional Folding of Eukaryotic Genomes, Tsung-Han S. Hsieh
Discovering cis-Regulatory Motifs, Jui-Hung Hung and Zhiping Weng
Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding), Jui-Hung Hung and Zhiping Weng
Mapping Short Sequence Reads to a Reference Genome, Jui-Hung Hung and Zhiping Weng
Motif Finding, Jui-Hung Hung and Zhiping Weng
Global increase in replication fork speed during a p57KIP2-regulated erythroid cell fate switch, Yung Hwang, Melinda Futran, Daniel Hidalgo, Ramona Pop, Divya Ramalingam Iyer, Ralph Scully, Nicholas R. Rhind, and Merav Socolovsky
A synthetic biology approach to probing nucleosome symmetry, Yuichi Ichikawa, Yuanyuan Chen, Vineeta Bajaj, Caitlin M. Connolly, Hsin-Jung Chou, Upasna Sharma, Hsiuyi V. Chen, Daniel N. Bolon, Oliver J. Rando, and Paul D. Kaufman
A synthetic biology approach to probing nucleosome symmetry, Yuichi Ichikawa, Caitlin M. Connolly, Hsin-Jung Chou, Yuanyuan Chen, Upasna Sharma, Hsuiyi V. Chen, Vineeta Bajaj, Daniel Na. Bolon, Oliver J. Rando, and Paul D. Kaufman
Single-Molecule Studies of Replication Kinetics in Response to DNA Damage, Divya Ramalingam Iyer
Replication fork slowing and stalling are distinct, checkpoint-independent consequences of replicating damaged DNA, Divya Ramalingam Iyer and Nicholas R. Rhind
The Intra-S Checkpoint Responses to DNA Damage, Divya Ramalingam Iyer and Nicholas R. Rhind
LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo, Joanna W. Jachowicz, Xin Y. Bing, Julien Pontabry, Ana Boskovic, Oliver J. Rando, and Maria-Elena Torres-Padilla
Size-Dependent Expression of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast, Daniel L. Keifenheim, Xi-Ming Sun, Edridge D'Souza, Makoto J. Ohira, Mira Magner, Lawrence Livermore National Laboratory, Samuel Marguerat, and Nicholas R. Rhind