SERF2, an RNA G-quadruplex Binding Protein, promotes stress granule formation
Bikash R Sahoo, Xiexiong Deng, Ee Lin Wong, Nathan Clark, Harry Yang, Vivekanandan Subramanian, Bryan B Guzman, Sarah E Harris, Budheswar Dehury, EmiMiyashita, Hirohide Saito, Daniel Dominguez, James CA Bardwell
PREPRINT bioRxiv 2023 doi: https://doi.org/10.1101/2023.10.09.561572
SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells
Rachel E Cherney, Quinn E Eberhard, Gilbert Giri, Christine A Mills, Alessandro Porrello, Zhiyue Zhang, David White, Jackson B Trotman, Laura E Herring, Daniel Dominguez, J Mauro Calabrese. RNA 2023 DOI: 10.1261/rna.079569.122
Effects of protein G-quadruplex interactions on phase transitions and protein aggregation
Bikash Sahoo, Vojċ Kocman, Nathan Clark, Nikhil Myers, Xiexiong Deng, Ee L Wong, Harry J Yang, Anita Kotar, Bryan B Guzman, Daniel Dominguez, Janez Plavec, James CA Bardwell. PREPRINT bioRxiv, 2023 https://doi.org/10.1101/2023.09.21.558871
Emerging roles for G‐quadruplexes in proteostasis
BB Guzman, A Son, TJ Litberg, Z Huang, D Dominguez*, S Horowitz*
FEBS, 2022 DOI: doi.org/10.1111/febs.16608
Quantitative profiling of adaptation to cyclin E overproduction
Juanita C Limas, Amiee N Littlejohn, Amy M House, Katarzyna M Kedziora, Brandon L Mouery, Boyang Ma, Dalia Fleifel, Andrea Walens, Maria M Aleman, Daniel Dominguez, Jeanette Gowen Cook. Life Science Alliance, 2022 DOI: 10.26508/lsa.202201378
Alternative splicing regulation of membrane trafficking genes during myogenesis
Emma Hinkle, Hannah Wiedner, Eddie Torres, Micaela Jackson, Adam Black, Eric Blue, Sarah Harris, Bryan Guzman, Gabrielle
Gentile, Eunice Lee, Yi-Hsuan Tsai, Joel Parker, Daniel Dominguez, and Jimena Giudice RNA 2022, doi:10.1261/rna.078993.121
Multi-Omics Analysis of Multiple Glucose-Sensing Receptor Systems in Yeast
Li, Shuang, Yuanyuan Li, Blake R. Rushing, Sarah E. Harris, Susan L. McRitchie, Daniel Dominguez, Susan J. Sumner, and Henrik G. Dohlman. 2022. Biomolecules 12, no. 2: 175. https://doi.org/10.3390/biom12020175
LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy
Pavlos Missios, Edroaldo Lummertz da Rocha, Daniel S Pearson, Julia Philipp, Maria M Aleman, Mehdi Pirouz, Dorian Farache, Joseph W Franses, Caroline Kubaczka, Kaloyan M Tsanov, Deepak K Jha, Brian Pepe-Mooney, John T Powers, Richard I Gregory, Amy SY Lee, Daniel Dominguez, David T Ting, George Q Daley Journal of Clinical Investigation 131 (22), e145142 (2021)
Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1
Shuang Li, Yuanyuan Li, Blake R Rushing, Sarah E Harris, Susan L McRitchie, Janice C Jones, Daniel Dominguez, Susan J Sumner, Henrik G Dohlman PLoS genetics 17 (7), e1009640 (2021)
easyCLIP analysis of RNA-protein interactions incorporating absolute quantification
Douglas F. Porter, Weili Miao, Xue Yang, Grant A. Goda, Andrew L. Ji, Laura K. H. Donohue, Maria M. Aleman, Daniel Dominguez & Paul A. Khavari Nature Communications 12, Article number: 1569 (2021)
SRSF1 inhibits autophagy through regulating Bcl-x splicing and interacting with PIK3C3 in lung cancer
Yuesheng Lv, Wenjing Zhang, Jinyao Zhao, Bing Sun, Yangfan Qi, Haoyu Ji, Chaoqun Chen, Jinrui Zhang, Junxiu Sheng, Taishu Wang, Daniel Dominguez, Han Liu, Quentin Liu, Songshu Meng, Xiaoling Li & Yang Wang Signal Transduction and Targeted Therapy volume 6, Article number: 108 (2021)
A large-scale binding and functional map of human RNA-binding proteins
Eric L. Van Nostrand, Peter Freese, Gabriel A. Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M. Blue, Jia-Yu Chen, Neal A. L. Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O. Duff, Keri E. Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J. Lambert, Hairi Li, Michael P. McGurk, Thai B. Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A. Yee, Bing Zhou, Ashley L. Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lécuyer, Christopher B. Burge, Brenton R. Graveley & Gene W. Yeo Nature volume 583, pages711–719 (2020)
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L. Van Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lécuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigó, Peggy J. Farnham, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos & Zhiping Weng Nature volume 583, pages699–710 (2020)
Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer
Luisa F. Escobar-Hoyos, Alex Penson, Ram Kannan, Hana Cho, Chun-Hao Pan, Rohit K. Singh, Lisa H. Apken, G. Aaron Hobbs, Renhe Luo, Nicolas Lecomte, Sruthi Babu, Fong Cheng Pan, Direna Alonso-Curbelo, John P. Morris IV, Gokce Askan, Olivera Grbovic-Huezo, Paul Ogrodowski, Jonathan Bermeo, Joseph Saglimbeni, Cristian D. Cruz, Yu-Jui Ho, Sharon A. Lawrence, Jerry P. Melchor, Grant A. Goda, Karen Bai, Alessandro Pastore, Simon J. Hogg, Srivatsan Raghavan, Peter Bailey, David K. Chang, Andrew Biankin, Kenneth R. Shroyer, Brian M. Wolpin, Andrew J. Aguirre, Andrea Ventura, Barry Taylor, Channing J. Der, Daniel Dominguez, Daniel Kümmel, Andrea Oeckinghaus, Scott W. Lowe, Robert K. Bradley, Omar Abdel-Wahab, Steven D. Leach
Cancer cell DOI:https://doi.org/10.1016/j.ccell.2020.05.010 (2020)
FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences. Raeann Goering, Laura I. Hudish, Bryan B. Guzman, Nisha Raj, Gary J. Bassell, Holger A. Russ, Daniel Dominguez, J. Matthew Taliaferro. eLife 2020;9:e52621 DOI: 10.7554/eLife.52621
Widespread accumulation of ribosome-isolated 3' UTRs in specific neuronal cell of the aging brain.
Sudmant PH, Lee H, Dominguez D, Goyal MS, Raichle ME, Heiman M, Burge CB. Cell reports 2018; 25, 2447–2456
Sequence, structure, and context preferences of human RNA binding proteins.
Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB. Molecular cell. 2018; 70(5):854-867.e9.
Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity.
Dronamraju R, Jha DK, Eser U, Adams AT, Dominguez D, Choudhury R, Chiang YC, Rathmell WK, Emanuele MJ, Churchman LS, Strahl BD. Nucleic acids research. 2018; 46(3):1331-1344.
MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress.
Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F. PNAS 2017; 114(29):7671-7676.
RNA sequence context effects measured In vitro predict In vivo protein binding and regulation.
Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB. Molecular cell. 2016; 64(2):294-306.
A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer.
Dominguez D, Tsai YH, Gomez N, Jha DK, Davis I, Wang Z. Cell research. 2016; 26(8):946-62.
An extensive program of periodic alternative splicing linked to cell cycle progression.
Dominguez D, Tsai YH, Weatheritt R, Wang Y, Blencowe BJ, Wang Z. eLife. 2016; 5.
Interactome analysis brings splicing into focus.
Dominguez D, Burge CB. Genome biology. 2015; 16:135.
Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors.
Tsai YS, Dominguez D, Gomez SM, Wang Z. Oncotarget. 2015; 6(9):6825-39.
The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression.
Wang Y, Chen D, Qian H, Tsai YS, Shao S, Liu Q, Dominguez D, Wang Z. Cancer cell. 2014; 26(3):374-389.
Engineering RNA endonucleases with customized sequence specificities.
Choudhury R, Tsai YS, Dominguez D, Wang Y, Wang Z. Nature communications. 2012; 3:1147.
Gα13 and Rho mediate endosomal trafficking of CXCR4 into Rab11+ vesicles upon stromal cell-derived factor-1 stimulation.
Kumar A, Kremer KN, Dominguez D, Tadi M, Hedin KE. Journal of immunology. 2011; 186(2):951-8.