Publications

2017

Foley, S.W., Kramer, M.C., and Gregory, B.D. 2017. RNA structure, binding, and coordination in Arabidopsis. Wiley Interdiscip. Rev. RNA e1426.

Foley, S.W., Gosai, S.J., Wang, D., Selamoglu, N., Solitti, A.C., Koster, T., Steffen, A., Lyons, E., Daldal, F., Garcia, B.A., Staiger, D., Deal, R.B., and Gregory, B.D. 2017. A global view of RNA-protein interactions identifies post-transcriptional regulators of root hair cell fate. Dev. Cell 41: 204-220.

Developmental Cell Cover Article

Yu, X., Davenport, J.W., Urtishak, K.A., Carillo, M.L., Gosai, S.J., Kolaris, C.P., Byl, J.A.W., Rappaport, E.F., Osheroff, N., Gregory, B.D.*, and Felix, C.A.* 2017. Landscape of TOP2A-mediated DNA cleavage across the human genome. Genome Res. 27: 1238-1249. * denotes co-correspondents.

Vandivier, L.E. and Gregory, B.D. 2017. Reading the epitranscriptome: new techniques and perspectives. Enzymes 41: 269-298.

Kuksa, P.P., Leung, Y.Y., Vandivier, L.E., Anderson, Z., Gregory, B.D., and Wang, L.S. 2017. In silico identification of RNA modifications from high-throughput sequencing data using HAMR. Methods Mol. Biol. 1562: 211-229.

Slabodnick, M.M., Ruby, J.G., Reiff, S.B., Swart, E.C., Gosai, S., Prabakaran, S., Witkowska, E., Larue, G.E., Fisher, S., Freeman, R.M. Jr., Gunawardena, J., Chu, W., Stover, N.A., Gregory, B.D., Nowacki, M., Derisi, J., Roy, S.W., Marshall, W.F., Sood, P. 2017. The macronuclear genome of Stentor coeruleus reveals tiny introns in a giant cell. Curr. Biol. 27: 569-575.

2016

Yu, X., Willmann, M.R., Anderson, S.J., and Gregory, B.D. 2016. Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay. Plant Cell 28: 2385-2397.

Foley, S.W. and Gregory, B.D. 2016. Protein Interaction Profile Sequencing (PIP-seq). Curr. Protoc. Mol. Biol. 116: 27.5.1-27.5.15.

Anderson, S.J., Willmann, M.R., and Gregory, B.D. 2016. Protein interaction profile sequencing (PIP-seq) in plants. Curr. Protoc. Plant Biol. 1: 163-183.

Crowe, E.P., Tuzer, F., Gregory, B.D., Donahue, G., Gosai, S.J., Cohen, J., Leung, Y.Y., Yetkin, E., Nativio, R., Wang, L.S., Sell, C., Bonini, N.M., Berger, S.L., Johnson, F.B., and Torres, C. 2016. Changes in the transcriptome of human astrocytes accompanying oxidative stress-induced senescence. Front. Aging Neurosci. 8: 208.

Frederick, D.W., Loro, E., Liu, L., Davila, A. Jr., Chellappa, K., Silverman, I.M., Quinn, W.J. 3rd, Gosai, S.J., Tichy, E.D., Davis, J.G., Mourkioti, F., Gregory, B.D., Dellinger, R.W., Redpath, P., Migaud, M.E., Nakamaru-Ogiso, E., Rabinowitz, J.D., Khurana, T.S., and Baur, J.A. 2016. Loss of NAD homeostasis leads to progressive and reversible degeneration of skeletal muscle. Cell Metab. 24: 269-282.

Silverman I.M., Berkowitz, N.D., Gosai, S.J., and Gregory B.D. 2016. Genome-wide approaches for RNA structure probing. Adv. Exp. Med. Biol. 907: 29-59.

Berkowitz, N.D., Silverman, I.M., Childress, D.M., Wang, L.S., and Gregory, B.D. 2016. A comprehensive database of high-throughout sequencing-based RNA secondary structure probing data (Structure Surfer). BMC Bioinformatics 17: 215.

Pasoreck, E., Su, J., Silverman, I., Gosai, S., Gregory, B.D., Yuan, J., and Daniell, H. 2016.  Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signaling. Plant Biotechnol. J. 14: 1862-1875.

Vandivier, L.E., Anderson, S.J., Foley, S.W., and Gregory B.D. 2016. The conservation and function of RNAsecondary structure in plants. Annu. Rev. Plant Biol. 67: 463-488.

Lorenzi, H., Khan, A., Behnke, M.S., Namasivayam, S., Swapna, L.S., Hadjithomas, M., Karamycheva, S., Pinney, D., Brunk, B.P., Ajioka, J.W., Ajzenberg, D., Boothroyd, J.C., Boyle, J.P., Dardé, M.L., Diaz-Miranda, M.A., Dubey, J.P., Fritz, H.M., Gennari, S.M., Gregory, B.D., Kim, K., Saeij, J.P., Su, C., White, M.W., Zhu, X.Q., Howe, D.K., Rosenthal, B.M., Grigg, M.E., Parkinson, J., Liu, L., Kissinger, J.C., Roos, D.S., and Sibley, D.L. 2016. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaicToxoplasma gondii genomes. Nat. Commun. 7: 10147.

Zhao, X., Bergland, A.O., Behrman, E.L., Gregory, B.D., Petrov, D.A., and Schmidt, P.S. 2016. Global transcriptional profiling of diapause and climatic adaptation in Drosophila melanogaster. Mol. Biol. Evol. 33: 707-720.

Kini, H.K., Silverman, I.M., Ji, X., Gregory, B.D., and Liebhaber, S.A. 2015. Cytoplasmic poly(A) bidning protein-1 binds to genomically encoded sequences within mammalian mRNAs. RNA 22: 61-74.

Leung, Y.Y., Kuksa, P.P., Amlie-Wolf, A., Valladares, O., Ungar, L.H., Kannan, S.K., Gregory, B.D.*, and Wang, L.S.* 2016. DASHR: Database of small human noncoding RNAs. Nucleic Acids Res. 44: D216-D222. *denotes co-correspondents.

2015

Vandivier, L.E., Campos, R., Kuksa, P.P., Silverman, I.M., Wang, L.S., and Gregory B.D. 2015. Chemical modifications mark alternatively spliced and uncapped messenger RNAs in Arabidopsis. Plant Cell 27: 3024-3037.

Yu, Z., Li, N., Parada, K., Li, F., Naqvi, A.S., Wang, S., Nakauka-Ddamba, A., Rao, S., Valvezan, A., Shankar, S., Deering, R.P., Klein, P.S., Kharas, M.G., Gregory, B.D., and Lengner, C.J. 2015. The Msi family of RNA binding proteins function redundantly as intestinal oncoproteins. Cell Rep. 13: 2440-2455.

Amlie-Wolf, A., Ryvkin, P., Tong, R., Dragomir, I., Suh, E., Xu, Y., Van Deerlin, V.M., Gregory, B.D., Kwong, L.K., Trojanowski, J.Q., Lee, V.M., Wang, L.S., and Lee, E.B. 2015. Transcriptomic changes due to cytoplasmic TDP-43 expression reveal dysregulation of histone transcripts and nuclear chromatin. PLoS ONE 10: e0141836.

Lin, J.J., Zhang, X., Xue, C., Zhang, H., Shashaty, M.G., Gosai, S., Grazioli, A., Hinkle, C., Caughey, J., Li., W., Susztak, K., Gregory, B.D., Li, M., and Reilly, M.P. 2015 The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury. Am. J. Physiol. Renal Physiol. 309: F901-F913.

Foley, S.W., Vandivier, L.E., Kuksa, P.P., and Gregory, B.D. 2015. Transcriptome-wide measurement of plant RNA secondary structure. Curr. Opin. Plant Biol. 27: 36-43.

Payel, S., Dang, W., Donahue, G., Dai, J., Dorsey, J., Cao, X., Liu, W., Cao, K., Perry, R., Lee, J.Y., Wasko, B.M., Carr, D.T., He, C., Robison, B., Wagner, J., Gregory, B.D., Kaeberlein, M., Kennedy, B.K., Boeke, J.D., and Berger, S.L. 2015. H3K36 methylation promotes longevity by enhancing transcriptional fidelity. Genes Dev. 29: 1362-1376.

Zhang, H., Xue, C., Shah, R., Bermingham, K., Hinkle, C.C., Li, W., Rodrigues, A., Tabita-Martinez, J., Millar, J.S., Cuchel, M., Pashos, E.E., Liu, Y., Yan, R., Yang, W., Gosai, S.J., VanDorn, D., Chou, S.T., Gregory, B.D., Morrisey, E.E., Li, M., Rader, D.J., and Reilly, M.P. Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling mendelian disease. Circ. Res. 117: 17-28.

Wang, S., Li, N., Yousefi, M., Nakauka-Ddamba, A., Li, F., Parada, K., Rao, S., Minuesa, G., Katz, Y., Gregory, B.D., Kharas, M.G., Yu, Z., and Lengner, C.J. 2015. Transformation of the intestinal epithelium by the MSI2 RNA binding protein. Nat. Commun. 6: 6517.

Vandivier, L.E., Li, F., and Gregory B.D. 2015. High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes. Methods Mol. Biol. 1284: 41-70.

Stein, P., Rozhkov, N.V., Li, F., Cardenas, F.L., Davydenko, O., Vandivier, L.E., Gregory, B.D., Hannon, G.J., and Schultz, R.M. 2015. Essential role for endogenous siRNAs during meiosis in mouse oocytes. PLoS Genet. 11: e1005013.

Gosai, S.J., Foley, S.W., Wang, D., Silverman, I.M., Selamoglu, N., Nelson, A.D.L., Beilstein, M.A., Daldal, F., Deal, R.B., and Gregory, B.D. 2015. Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Mol. Cell 57: 376-388.

Hwang, Y.C., Lin, C.F., Valladares, O., Malamon, J., Kuksa, P., Zheng, Q., Gregory, B.D.*, and Wang, L.S.* 2015. HIPPIE: A high-throughput identification pipeline for promoter-interacting enhancer elements.Bioinformatics 31: 1290-1292. * denotes co-correspondents.

Silverman, I.M. and Gregory, B.D. 2015. Transcriptome-wide ribonuclease-mediated protein footprinting to identify RNA-protein interaction sites. Methods 72: 76-85.

Li, S., Vandivier, L.E., Tu, B., Gao, L., Won, S.Y., Li, S., Zheng, B., Gregory, B.D., and Chen, X. 2015. Detection of PolIV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Res. 25: 235-245.

2014

Liu, X., Zheng, Q., Vrettos, N., Maragkakis, M., Alexiou, P., Gregory, B.D., and Mourelatos, Z. 2014. A microRNA surveillance system in quality control of microRNA synthesis. Mol. Cell 55: 868-879.

Dang, W., Sutphin, G.L., Dorsey, J.A., Otte G.L., Cao, K., Perry, R.M., Wanat, J.J., Saviolaki, D., Murakami, C.J., Tsuchiyama, S., Robison, B., Gregory, B.D., Vermeulen, M., Shiekhattar, R., Johnson, F.B., Kennedy, B.K., Kaeberlein, M., and Berger, S.L. 2014. Repression of yeast Isw2 chromatin remodeling mimics the longevity effect of calorie restriction by potentiating genotoxic stress response. Cell Metab. 19: 952-966.

Ihara, M., Meyer-Ficca, M.L., Leu, N.A., Rao, S., Li, F., Gregory, B.D., Zalenskaya, I.A., Schultz R.M., and Meyer, R.G. 2014. Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression. PLoS Genet. 10: e1004317.

Gregory, B.D.* and Meyers, B.C.* 2014. Genomic approaches for transcriptional and post-transcriptional processes. Methods 67: 1-2. * denotes co-correspondents.

Willmann, M.R., Berkowitz, N.D., and Gregory, B.D. Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes-GMUCT2.0. Methods 67: 64-73.

Ryvkin, P., Leung, Y,Y., Ungar, L., Gregory, B.D.*, and Wang, L.S.* 2014. Using machine learning and high-throughput RNA sequencing to characterize small non-coding RNAs. Methods 67: 28-35. * denotes co-correspondents.

Liu, Y., Ferguson, J.F., Xue, C., Ballantyne, R., Silverman, I.M., Gosai, S.J., Serfecz, J., Morley, M.P., Gregory, B.D., Li, M., and Reilly, M.P. 2014. Tissue-specific RNA-seq in human evoked inflammation identifies blood and adipose lincRNA signatures of cardio-metabolic diseases. Arterioscler. Thromb. Vasc. Biol. 34: 902-912.

Silverman, I.M., Li, F., Alexander, A., Goff, L., Trapnell, C., Rinn, J.L., and Gregory, B.D. 2014. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.Genome Biol. 15: R3.

2013

Ryvkin, P., Leung, Y,Y., Silverman, I., Childress, M., Valladares, O., Dragomir, I., Gregory, B.D.*, and Wang, L.S.* 2013. HAMR: High throughput Annotation of Modified Ribonucleotides. RNA 19: 1684-1692. * denotes co-correspondents.

Elliot, R., Li, F., Dragomir, I., Chua, M.M.W., Gregory, B.D., and Weiss, S.R. Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice. PLoS ONE 8: e75346.

Shah, P.P., Donahue, G., Otte, G.L., Capell, B.C., Nelson, D.M., Cao, K., Aggarwala, V., Cruickshanks, H.A., Rai, T.S., McBryan, T., Gregory, B.D., Adams, P.D., and Berger, S.L. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev. 27: 1787-1799.

Liu, Y., Ferguson, J.F., Xue, C., Silverman, I.M., Gregory, B., Reilly, M.P., and Li, M. 2013. Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. PLoS ONE 8: e66883.

Leung, Y,Y., Ryvkin, P., Ungar, L., Gregory, B.D.*, and Wang, L.S.* 2013. CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res. 41: e137. * denotes co-correspondents.

Vandivier, L.E., Li, F., Zheng, Q., Willmann, M.R., Chen, Y., and Gregory, B.D. 2013. Arabidopsis mRNA secondary structure correlates with protein function and domains. Plant Signal. Behav. 8: e24301.

Hwang, Y-C., Zheng, Q., Gregory, B.D.*, and Wang, L.S.* 2013. High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res. 41: 4835-4846. * denotes co-correspondents.

Sabin, L.R., Zheng, Q., Thekkat, P., Yang, J., Hannon, G.J., Gregory, B.D.*, Tudor, M.*, and Cherry, S.* 2013. Dicer-2 processes diverse viral RNAs. PLoS ONE 8: e55458. * denotes co-correspondents.

Silverman, I.M., Li, F., and Gregory, B.D. 2013. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Sci. 205-206: 55-62.

Zheng, Q., Rowley, M.J., Bohmdorfer, G., Sandhu, D., Gregory, B.D.*, and Wierzbicki, A.T.* 2013. RNA Polymerase V targets transcriptional silencing components to promoters of protein-coding genes. Plant J. 73: 179-189.§
* denotes co-correspondents.
§. Plant J. cover article.

 

2012

Li, F., Zheng, Q., Vandivier, L.E., Willmann, M.R., Chen, Y., and Gregory, B.D. 2012. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 24: 4346-4359.

Wierzbicki, A.T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M.J., Gregory, B.D., Ecker, J.R., Tang, H., and Pikaard, C.S. 2012. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 26: 1825-1836.

Vourekas, A., Zheng, Q., Alexiou, P., Maragkakis, M., Kirino, Y., Gregory, B.D., and Mourelatos, Z. 2012. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 19: 773-781.

Li, F., Ryvkin, P., Childress, D.M., Valladares, O., Gregory, B.D.*, and Wang, L.S.* 2012. SAVoR: a server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res. 40: W59-W64. * denotes co-correspondents.

Li, F., Zheng, Q., Ryvkin, P., Dragomir, I., Desai, Y., Aiyer, S., Valladares, O., Yang, J., Bambina, S., Sabin, L.R., Murray, J.I., Lamitina, T., Raj, A., Cherry, S., Wang, L.S., and Gregory, B.D. 2012. Global analysis of RNA secondary structure in two metazoans. Cell Rep. 1: 69-82.

2011

Willmann, M.R., Endres, M.W., Cook R.T., and Gregory, B.D. 2011. The functions of RNA-dependent RNA Polymerases in Arabidopsis. The Arabidopsis Book 9: e0146.

Endres, M.W., Cook R.T., and Gregory, B.D. 2011. A High-Throughput Sequencing-Based Methodology to Identify All Uncapped and Cleaved RNA Molecules in Eukaryotic Genomes. Methods Mol. Biol. 732: 209-223.

2010

Zheng, Q., Ryvkin, P., Li, F., Dragomir, I., Valladares, O., Yang, J., Cao, K., Wang, L.S., and Gregory, B.D.2010. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. 6: e1001141.

Earley, K., Smith, M., Weber, R., Gregory, B.D., and Poethig, R. 2010. An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana. Silence 1: 15.

Selected Postdoctoral Publications

Gregory, B.D., O’ Malley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H., and Ecker, J.R. 2008. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell 14: 854-866.

Lister, R., O’ Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H., and Ecker, J.R. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.

Chekanova, J.A.*, Gregory, B.D.*, Reverdatto, S.V., Chen, H., Kumar, R., Hooker, T., Yazaki, J., Li, P., Skiba, N., Peng, Q., Alonso, J., Brukhin, V., Grossniklaus, U., Ecker, J.R., and Belostotsky, D.A. 2007. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell131: 1340-1353. *These authors contributed equally to this work.