Publications

All Publications: PubMed Google Scholar

G.M. Otto, A. Green, J. Cabarrús, F.J. Miralles, P. Torres, L. DeLeon, J. Chea, D.M. Marciniak, M-C.G. Beltejar, Y.V. Kwon, S.-E. Ong, D.M. Shechner†, Y. Sancak† A Modular Platform for Purification of Organelle-associated Mitochondria Reveals Functional Specialization at Organelle Contact Sites BioRxiv 2026, Submitted

†–Co-corresponding authors

S.A. Schactler*, N.G. Skiados*, A.A. Gajendragadkar, L.E. DeLeon, D.M. Shechner. Mapping subcellular microenvironments using oligonucleotide-directed proximity labeling. Current Opinion in Chemical Biology 2026, 94:102743

*–Co-first authors

Y. Liu, C.D. McGann, C.P. Herlihy, M. Krebs, T.A. Perkins, R. Fields, C.K. Camplisson, D.Z. Nwizugbo, Q. Lin, N.J. Longhi, C. Hsu, S.C. Avanessian, A.F. Tsue, E.E. Kania, D.M. Shechner, B.J. Beliveau†, and D.K. Schweppe†. DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci eLife. 2026, 13:RP102489

†–Co-corresponding authors

F. Mardakheh† and D. M. Shechner†. A molecular cartographer’s toolkit for mapping RNA’s uncharted realms. Cell Reports 2025, 44(7):115877

†–Co-corresponding authors

J.B. Trotman, A. Porrello, S. A. Schactler, L. E. DeLeon, Q.E. Eberhard, S.P. Boyson, Z. Zhang, D.M. Lee, S.E. Kirik, N. Sultana, S.N. Nguyen, M.-C.G. Beltejar, M.K. Shinn, S.-E. Ong, M.P. Gonzalez-Perez, S.A. Shaffer, D. Dominguez, D.M. Shechner, and J.M. Calabrese. Xist Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing. BioRxiv 2025, in revision

S. Attar, V. E. Browning, M. Krebs, Y. Liu, E. K. Nichols, A. F. Tsue, D. M. Shechner, J. Shendure, J. A. Lieberman, D. K. Schweppe, S. Akilesh†, and B. J. Beliveau†. Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER Nature Methods 2025, 22(1):156-165

†–Co-corresponding authors

E. E. Kania*, S. Bianchi*, A. Fenix, D. M. Marciniak, S. Li, Q. Lin, M. Casini, B. Hristov, L. Truszkowski, N. G. Skiados, M. Mokhtaridoost, C. K. Camplisson, R. Fields, E. Wyart, S. Marchiano, B. J. Beliveau, P. G. Maass, D. Cacchiarelli, E. Balmas, D. K. Schweppe, W. S. Noble, S.-E. Ong, C.E. Murry†, A. Bertero†, and D. M. Shechner†. Nascent transcript O-MAP reveals the molecular architecture of an RBM20-regulated single-locus subnuclear compartment organized around the TTN RNA. BioRxiv 2024, in revision.

*–Co-first authors
†–Co-corresponding authors

A. F. Tsue*, E. E. Kania*, D. Q. Lei, R. Fields, C. D. McGann, D.M. Marciniak, E. A. Hershberg, X. Deng, M. Kihiu, S.-E. Ong, C. M. Disteche, S. Kugel, B. J. Beliveau, D. K. Schweppe, and D. M. Shechner Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping Nature Methods 2024, 21, 2058–2071

*–Co-first authors

T. M. Locke*, R. Fields*, H. Gizinski, G. M. Otto, M.J.S. MacEwen, D.-V. Rusnac, P. He, D.M. Shechner, C. D. McGann, M. D. Berg, J. Villen, Y. Sancak†, and D. K. Schweppe†. High-throughput identification of calcium-regulated proteins across diverse proteomes 2024, 43(11):114879

*–Co-first authors
†–Co-corresponding authors

D.M. Shechner Architecture of an RNA polymerase ribozyme illuminates the RNA World Trends in Genetics 2024, 40 (4): 291-292

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