Publications
Check out the latest publications powered by Eclipsebio technologies!
2023
- Serine 970 of RNA helicase MOV10 is phosphorylated and controls unfolding activity and fate of mRNAs targeted for AGO2-mediated silencing. Aatiqa Nawaz, Phillip J. Kenny, Temirlan Shilikbay, Matt Reed, Olga Stuchlik, Jan Pohl, Stephanie Ceman. Journal of Biological Chemistry - RBP-eCLIP
- The 5’UTR of HCoV-OC43 Adopts a Topologically Constrained Structure to Intrinsically Repress Translation. Matthew Mackeown, Yu-An Kung, Jesse Davila-Calderon, William P. Ford, Le Luo, Barrington Henry, Mei-Ling Li, Gary Brewer, Shin-Ru Shih, Blanton S. Tolbert. Journal of Biological Chemistry - eSHAPE
- Discovery of novel microRNA regulators of ribosome biogenesis. Carson J. Bryant, Mason A. McCool, Gabriela T. Rosado-González, Laura Abriola, Yulia V. Surovtseva, Susan J. Baserga. bioRxiv - miR-eCLIP
2022
- Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. Daniel A. Lorenz, Hsuan-Lin Her, Kylie A. Shen, Katie Rothamel, Kasey R. Hutt, Allan C. Nojadera, Stephanie C. Bruns, Sergei A. Manakov, Brian A. Yee, Karen B. Chapman & Gene W. Yeo. Nature Methods. - Antibody Bardcode CLIP (ABC)
- Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia. Eric Wang, Jose Mario Bello Pineda, Won Jun Kim, Sisi Chen, Jessie Bourcier, Maximilian Stahl, Simon J. Hogg, Jan Phillipp Bewersdorf, Cuijuan Han, Michael E. Singer, Daniel Cui, Caroline E. Erickson, Steven M. Tittley, Alexander V. Penson, Katherine Knorr, Robert F. Stanley, Jahan Rahman, Gnana Krishnamoorthy, James A. Fagin, Emily Creger, Elizabeth McMillan, Chi-Ching Mak, Matthew Jarvis, Carine Bossard, Darrin M. Beaupre, Robert K. Bradley, Omar Abdel-Wahab. Science Direct. - RBP-eCLIP
- The PNUTS-PP1 complex acts as an intrinsic barrier to herpesvirus KSHV gene expression and replication. Anne M. Devlin, Ashutosh Shukla, Julio C. Ruiz, Spencer D. Barnes, Ashwin Govindan, Olga V. Hunter, Anna M. Scarborough, Iván D’Orso, Nicholas K. Conrad. Nature Communications. - RBP-eCLIP
- The APE2 nuclease is essential for DNA double strand break repair by microhomology-mediated end-joining. Hubert Fleury, Myles K. MacEachern, Clara M. Stiefel, Roopesh Anand, Colin Sempeck, Benjamin Nebenfuehr, Benjamin Dodd, Erin Taylor, Djelika Dansoko, Raquel Ortega, Justin W. Leung, Simon J. Boulton, Nausica Arnoult. BioRxiv. - FLI-Seq
- NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Matthew T. Witkowski, Soobeom Lee, Eric Wang, Anna K. Lee, Alexis Talbot, Chao Ma, Nikolaos Tsopoulidis, Justin Brumbaugh, Yaqi Zhao, Kathryn G. Roberts, Simon J. Hogg, Sofia Nomikou, Yohana E. Ghebrechristos, Palaniraja Thandapani, Charles G. Mullighan, Konrad Hochedlinger, Weiqiang Chen, Omar Abdel-Wahab, Justin Eyquem & Iannis Aifantis. Nature Communications. - RBP-eCLIP
- Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Thomas Hollin, Steven Abel, Alejandra Falla, Charisse Flerida A. Pasaje, Anil Bhatia, Manhoi Hur, Jay S. Kirkwood, Anita Saraf, Jacques Prudhomme, Amancio De Souza, Laurence Florens, Jacquin C. Niles & Karine G. Le Roch. Nature Communications. - RBP-eCLIP
- Genomewide m6A mapping uncovers dynamic changes in the m6A epitranscriptome of cisplatin-treated apoptotic HeLa cells. Azime Akçaöz, Özge Tüncel, Ayşe Bengisu Gelmez, Buket Sağlam, İpek Erdoğan Vatansever, Bünyamin Akgül. BioRxiv. - m6A-eCLIP
- Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP. Sergei A Manakov, Alexander A Shishkin, Brian A Yee, Kylie A Shen, Diana C Cox, Samuel S Park, Heather M Foster, Karen B Chapman, Gene W Yeo, Eric L Van Nostrand. BioRxiv. - miR-eCLIP
- Neurotransmitter Activation Sequesters Specific mRNAs Into Stress Granules. Lela Jackson, Allison Poussaint, Suzanne Scarlata. Research Square. - RBP-eCLIP
- Tobramycin-induced secretion of P. aeruginosa 5′ tRNA-fMet halves suppresses lung inflammation via AGO2 gene silencing. Zhongyou Li, Katja Koeppen, Alix Ashare, Deborah A. Hogan, Scott A. Gerber, Bruce A. Stanton. BioRxiv. - RBP-eCLIP
- Efficacy of longevity interventions in C. elegans is determined by early life activity of RNA splicing factors. Sneha Dutta, Caroline Heintz, Maria C. Perez-Matos, Ayse Sena Mutlu, Mary E. Piper, Meeta Mistry, Arpit Sharma, Hannah J. Smith, Porsha Howell, Rohan Sehgal, Anne Lanjuin, Meng C. Wang, William B. Mair. bioRxiv. - RBP-eCLIP
- Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition. Inoue et al. Nature Genetics. - RBP-eCLIP
- Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation. Wang E, Zhou H, Nadorp B, Cayanan G, Chen X, Yeaton AH, Nomikou S, Witkowski MT, Narang S, Kloetgen A, Thandapani P, Ravn-Boess N, Tsirigos A, Aifantis I. Cell Stem Cell. - RBP-eCLIP
- The Musashi proteins are post-transcriptional activators of protein expression and alternative exon splicing in vertebrate photoreceptors. Fatimah Matalkah, Bohye Jeong, Macie Sheridan, Eric Horstick, Visvanathan Ramamurthy, Peter Stoilov. BioRxiv. - RBP-eCLIP
- The m6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay. Daniel Macveigh-Fierro, Angelina Cicerchia, Ashley Cadorette, Vasudha Sharma, Mandy Muller. PNAS. - m6A-eCLIP
- miR-486 is essential for muscle function and suppresses a dystrophic transcriptome. Adrienne Samani, Rylie M Hightower, Andrea L Reid, Katherine G English, Michael A Lopez, J Scott Doyle, Michael J Conklin, David A Schneider, Marcas M Bamman, Jeffrey J Widrick, David K Crossman, Min Xie, David Jee, Eric C Lai, Matthew S Alexander. Life Science Alliance. - miR-eCLIP
- A functional screen of RNA binding proteins identifies genes that promote or limit the accumulation of CD138+ plasma cells. David J Turner, Alexander Saveliev, Fiamma Salerno, Louise S Matheson, Michael Screen, Hannah Lawson, David Wotherspoon, Kamil R Kranc, Martin Turner. eLife. - m6A-eCLIP
2021
- The RNA-binding protein IGF2BP3 is critical for MLL-AF4-mediated leukemogenesis. Tran TM, Philipp J, Bassi JS, Nibber N, Draper JM, Lin TL, Palanichamy JK, Jaiswal AK, Silva O, Paing M, King J, Katzman S, Sanford JR and Rao DS. Nature Leukemia.– RBP-eCLIP
- The RNA m6A binding protein YTHDF2 promotes the B cell to plasma cell transition. Turner DJ, Saveliev A, Salerno F, Matheson LS, Screen M, Lawson H, Wotherspoon D, Kranc KR, Turner M. bioRxiv – m6A-eCLIP
- Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes. Powell NR, Zhao H, Ipe J, Liu Y, Skaar TC. Clin Pharmacol Ther. – miR-eCLIP
- miR-486 is an epigenetic modulator of Duchenne muscular dystrophy pathologies. Hightower RM, Samani A, Reid AL, English KG, Lopez MA, Doyle JS, Conklin MJ, Schneider DA, Bamman MM, Widrick JJ, Crossman DK, Xie M, Jee D, Lai EC, Alexander MS. BioRxiv. – miR-eCLIP
- Activation of Gαq sequesters specific transcripts into Ago2 particles. Lela Jackson, Alison Poussaint, Suzanne Scarlata. Research Square. – RBP-eCLIP
- G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities. Xiaomei He, Jun Yuan, Yinsheng Wang. Nucleic Acids Research. – RBP-eCLIP
- SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Jess Floro, Anqi Dai, Abigail Metzger, Alexandra Mora-Martin, Neil J Ganem, Daniel Cifuentes, Ching-Shyi Wu, Jasbir Dalal, Shawn M Lyons, Adam Labadorf, Rachel L Flynn. Nucleic Acids Research. – RBP-eCLIP
- The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Nitin Raj, Mengxiong Wang, Jose A. Seoane, Nancie A. Moonie, Janos Demeter, Alyssa M. Kaiser, Anthony M. Boutelle, Abigail S. Mulligan, Clare Moffatt, Christina Curtis, Howard Y. Chang, Peter. K. Jackson, Laura D. Attardi. BioRxiv. – m6A-eCLIP
2020
- Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program. Bieging-Rolett KT, Kaiser AM, Morgens DW, Boutelle AM, Seoane JA, Van Nostrand EL, Zhu C, Houlihan SL, Mello SS, Yee BA, McClendon J, Pierce SE, Winters IP, Wang M, Connolly AJ, Lowe SW, Curtis C, Yeo GW, Winslow MM, Bassik MC, Attardi LD. Mol Cell. - RBP-eCLIP
- The FMRP-MOV10 complex: a translational regulatory switch modulated by G-Quadruplexes. Kenny PJ, Kim M, Skariah G, Nielsen J, Lannom MC, Ceman S. Nucleic Acids Res. - RBP-eCLIP
- Adaptation of enhanced crosslinking and immunoprecipitation (eCLIP) for the high-throughput, high-resolution mapping of N6-methyladenosine modifications. Rabano I, Shishkin AA, Shen K, Foster HM, Chu P, Van Nostrand EL, Yeo GW. FASEB - m6A-eCLIP
- Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen. Eric L. Van Nostrand, Sarah A. Barnhill, Alexander A. Shishkin, David A. Nelles, Eric Byeon, Thai Nguyen, Yiu Chueng Eric Wong, Nathan C. Gianneschi, Gene W. Yeo. bioRxiv - FLI-Seq
- Footprinting SHAPE-eCLIP Reveals Transcriptome- wide Hydrogen Bonds at RNA-Protein Interfaces. Meredith Corley, Ryan A. Flynn, Byron Lee, Steven M. Blue, Howard Y. Chang, Gene W. Yeo. Molecular Cell - SHAPE db-K562
2019
- Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D, Ki M, Cho H, Bitner L, Kloetgen A, Lin KT, Uehara T, Owa T, Tibes R, Krainer AR, Abdel-Wahab O, Aifantis I. Cancer Cell. - RBP-eCLIP
- The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification. Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM. PLoS One. - RBP-eCLIP