Publications

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A.F. Tsue†, E.E. Kania†, D.Q. Lei, R. Fields, C.D. McGann, E. Hershberg, X. Deng, M. Kihiu, S.-E. Ong, C. Disteche, S. Kugel, B.J. Beliveau, D.K. Schweppe, and D.M. Shechner Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ. BioRxiv. 2023. In review

† – Co-First authors

S. Attar, V.E. Browning, Y. Liu, E.K. Nichols, A.F. Tsue, D.M.Shechner, J. Shendure, J.A. Lieberman, S. Akilesh†, B.J. Beliveau† Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER. BioRxiv. 2023. In review

†– Co-Corresponding authors

D.M. Shechner. Targeting Noncoding RNA Domains to Genomic Loci with CRISPR-Display: Guidelines for Designing, Building, and Testing sgRNA–ncRNA Expression Constructs. In: Fulga T.A., Knapp D.J.H.F., Ferry Q.R.V. (eds) CRISPR Guide RNA Design. Methods in Molecular Biology. 2021, 2162: 115-152

Y. Han, T.C. Branon, J.D. Martell, D. Boassa, D. M. Shechner, M.H. Ellisman, and A.Y. Ting, Directed evolution of split APEX2 peroxidase. ACS Chemical Biology, 2019, 14(4): 619–635

P. Maass, R. Barutucu, D.M. Shechner, C.L. Weiner, M. Melé, and J.L. Rinn. Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nature Structural and Molecular Biology, 2018, 25(2): 176–84

C.J. Shukla, C. Gerhardinger, K.D. Korthauer, A. McCorkindale, M. N. Cabili, D.M. Shechner, R.A. Irizarry, P.G. Maas, and J.L. Rinn. High-throughput identification of RNA nuclear enrichment sequences. EMBO Journal, 2018, pii: e98452.

P. Kaewsapsak†, D.M. Shechner†, W. Mallard, J.L. Rinn, and A. Y. Ting. Live cell mapping of organelle-associated RNAs by proximity biotinylation and protein-RNA crosslinking. eLife, 2017, 6:e29224

†–Co first-authors.

M. Melé, K. Mattioli, W. Mallard, D.M. Shechner, C. Gerhardinger, and J.L. Rinn. Chromatin environment, transcriptional regulation and splicing distinguishes lncRNAs and mRNAs. Genome Research, 2017, 27(1):27-37

D.M. Shechner, E. Hacisuleyman, S.T. Younger, and J.L. Rinn. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nature Methods, 2015, 12(7): 664–70.

D.M. Shechner and D.P. Bartel. The structural basis of RNA-catalyzed RNA polymerization. Nature Structural and Molecular Biology, 2011, 18(9): 1036–42

Y. Koldobskaya, E.M. Duguid, D.M. Shechner, N.B. Suslov, J. Ye, S.S. Sidhu, D.P. Bartel, S. Koide, A.A. Kossiakoff, and J.A. Piccirilli. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nature Structural and Molecular Biology, 2011, 18(1): 100–6

S.C. Bagby†, N.H. Bergman†, D.M. Shechner, C.C. Yen, and D.P. Bartel. A class I ligase ribozyme with reduced Mg2+ dependence: selection, sequence analysis, and tertiary-structure mapping. RNA, 2009, 15(12): 2129–46

†—Co-first authors

D.M. Shechner, R.A. Grant, S.C. Bagby, Y. Koldobskaya, J.A. Piccirilli, and D.P. Bartel. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science, 2009, 326(5957): 1271–5

S. F. Marino, D. Shechner, and Regan L. ‘Morphs’ (MRFs): Metal-Reversible Folding Domains for Differential IgG Binding. Chemisty and Biology, 2001, 8(12): 1221–9