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.

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Publications from 2018

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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

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Do Skeletal Dynamics Mediate Sugar Uptake and Transport in Human Erythrocytes, Robert J. Asaro, Qiang Zhu, Pedro Cabrales, and Anthony Carruthers

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Evaluation of a method to measure HHV-6B infection in vitro based on cell size, Aniuska Becerra, Tessa Santoro, and Lawrence J. Stern

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Ajulemic acid: potential treatment for chronic inflammation, Sumner Burstein

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Effects of Larval Density on Gene Regulation in Caenorhabditis elegans During Routine L1 Synchronization, Io Long Chan, Oliver J. Rando, and Colin C. Conine

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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

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Illuminating Biology with Membrane Penetrating Sulfonate Delivery Scaffolds and Near-Infrared Azasiline Fluorophores, Adam Choi

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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

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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

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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

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Nuclear Export Through Nuclear Envelope Remodeling in Saccharomyces cerevisiae, Baojin Ding, Anne M. Mirza, James A. Ashley, Vivian Budnik, and Mary Munson

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ETV4 transcription factor and MMP13 metalloprotease are interplaying actors of breast tumorigenesis, Mandy Dumortier, Franck Ladam, Isabelle Damour, Sophie Vacher, Ivan Bieche, Nathalie Marchand, Yvan de Launoit, David Tulasne, and Anne Chotteau-Lelievre

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Role of TRIP6 and Angiomotins in the Regulation of the Hippo Signaling Pathway, Shubham Dutta

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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

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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

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Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, and Zhiping Weng

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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

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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

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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

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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

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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

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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)

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Investigating the Gene Regulatory Network Underlying Caudal Hindbrain Specification in Embryonic Zebrafish, Priyanjali Ghosh

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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

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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)

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Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome, Kiran Girdhar, Gabriel E. Hoffman, Yan Jiang, Leanne Brown, Marija Kundakovic, Mads E. Hauberg, Nancy J. Francoeur, Ying-Chih Wang, Hardik Shah, David H. Kavanagh, Elizabeth Zharovsky, Rivka Jacobov, Jennifer R. Wiseman, Royce Park, Jessica S. Johnson, Bibi S. Kassim, Laura Sloofman, Eugenio Mattei, Zhiping Weng, Solveig K. Sieberts, Mette A. Peters, Brent T. Harris, Barbara K. Lipska, Pamela Sklar, Panos Roussos, and Schahram Akbarian

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Profiling of pluripotency factors in individual stem cells and early embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, and Thomas G. Fazzio

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Two-dimensional transition metal carbides and nitrides (MXenes) for biomedical applications, Kai Huang, Zhongjun Li, Jing Lin, Gang Han, and Peng Huang

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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

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Computer design of microfluidic mixers for protein/RNA folding studies, Venkatesh Inguva, Sagar V. Kathuria, Osman Bilsel, and Blair James Perot

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ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)

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ChIP-chip, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR), Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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ChIP-seq, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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Formaldehyde Cross-Linking, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)

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Generation of 3C Libraries from Cross-Linked Cells, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)

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Generation of ChIP-Loop Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)

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Generation of Control Ligation Product Libraries for 3C Analyses, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)

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Preparation of Cross-Linked Chromatin for ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)

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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

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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

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Understanding Human Erythrocyte Glucose Transporter (GLUT1) Mediated Glucose Transport Phenomena Through Structural Analysis, Kenneth P. Lloyd

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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

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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

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Targeting Drug Resistance In HCV NS3/4A Protease: Mechanisms And Inhibitor Design Strategies, Ashley N. Matthew

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A parental requirement for dual-specificity phosphatase 6 in zebrafish, Jennifer M. Maurer and Charles G. Sagerstrom

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Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance, David Mavor, Daniel N. Bolon, Martin Kampmann, and James S. Fraser

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RNA binding proteins co-localize with small tau inclusions in tauopathy, Brandon F. Maziuk, Daniel J. Apicco, Anna Lourdes Cruz, Lulu Jiang, Peter E. A. Ash, Edroaldo Lummertz. da Rocha, Cheng Zhang, Wai Haung Yu, John D. Leszyk, Jose F. Abisambra, Hu Li, and Benjamin Wolozin

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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

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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

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Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing, Aamir Mir, Julia F. Alterman, Matthew R. Hassler, Alexandre J. Debacker, Edward Hudgens, Dimas Echeverria, Michael H. Brodsky, Anastasia Khvorova, Jonathan K. Watts, and Erik J. Sontheimer

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Photochemical Control of Protein Arginine Deiminase (PAD) Activity, Santanu Mondal, Sangram S. Parelkar, Mitesh Nagar, and Paul R. Thompson

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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

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Donated chemical probes for open science, Susanne Muller, Paul R. Thompson, and Anke Mueller-Fahrnow

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The N-terminal region of photocleavable peptides that bind HLA-DR1 determines the kinetics of fragment release, Maria P. Negroni and Lawrence J. Stern

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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

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Citrullination Inactivates Nicotinamide-N-methyltransferase, Venkatesh V. Nemmara, Ronak Tilvawala, Ari J. Salinger, Lacey Miller, Son Hong Nguyen, Eranthie Weerapana, and Paul R. Thompson

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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

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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)

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Effects of larval density on gene regulation in C. elegans during routine L1 synchronization, Oliver J. Rando, Io Long Chan, and Colin C. Conine

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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

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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

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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

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Investigating the Structural Basis for Human Disease: APOBEC3A and Profilin, Tania V. Silvas

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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

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Watching Sugar Transport in Real Time in Single Cells and Cell Populations, Andrew H. Simon

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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

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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

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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

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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

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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

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pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans, Wei-Sheng Wu, Wei-Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, and Heng-Chi Lee

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Efficient Blue to Red Afterglow Tuning in a Binary Nanocomposite Plastic Film, Yan Xia, Huase Ou, Wanbin Li, Gang Han, and Zhanjun Li

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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

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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

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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

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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

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The temporal landscape of recursive splicing during Pol II transcription elongation in human cells, Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, and Zhiping Weng

Publications from 2017

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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

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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

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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)

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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

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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

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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

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Adapting the EMPIRIC Approach to Investigate Evolutionary Constraints in Influenza A Virus Surface Proteins, Aneth S. Canale

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Synovial fibroblast-neutrophil interactions promote pathogenic adaptive immunity in rheumatoid arthritis, Carmelo Carmona-Rivera, Paul R. Thompson, and Mariana J. Kaplan

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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

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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

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The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins, Yvonne H. Chan

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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

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Transcriptome-Wide Analysis of Roles for Transfer RNA Modifications in Translational Regulation, Hsin-Jung Chou

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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

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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)

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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

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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

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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

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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

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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

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Temporal regulation of chromatin during myoblast differentiation, Akihito Harada, Yasuyuki Ohkawa, and Anthony N. Imbalzano