The paper introduces ORCA, a method to isolate mitochondria associated with specific organelles, revealing distinct proteomes and functional roles at organelle contact sites.

bioRxiv · Aug 4, 2026 · PreprintCell Biology

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

Yuzhen Liu, Christopher D. McGann, Conor P. Herlihy, Mary Krebs, Thomas A. Perkins, Rose Fields, Conor K. Camplisson, David Z Nwizugbo, Qiaoyi Lin, Nicolas J. Longhi, Chris Hsu, Shayan C. Avanessian, Ashley F. Tsue, Evan E. Kania, David M Shechner, , Devin K. Schweppe

DNA O-MAP identifies molecular neighborhoods around specific genomic loci using programmable probes and proteomics.

eLife · Apr 7, 2026Peer-reviewedSystems Biology

Xist Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing

Jackson B. Trotman, Alessandro Porrello, Scott A. Schactler, Lorenzo E. DeLeon, Quinn E. Eberhard, Samuel P. Boyson, Zhiyue Zhang, Shuang Li, David M. Lee, Sarah E. Kirik, Nadia Sultana, Son N. Nguyen, Michael-Claude G. Beltejar, Min Kyung Shinn, Shao-En Ong, , J. Mauro Calabrese

The paper identifies how Xist Repeat A recruits SPEN via SR proteins to induce gene silencing, revealing a role for splicing factors in this process.

bioRxiv · May 21, 2025 · PreprintGenetics

Nascent transcript O-MAP reveals the molecular architecture of an RBM20-regulated single-locus subnuclear compartment organized around the TTN RNA

Evan E. Kania, Sara Bianchi, Aidan M. Fenix, Daphnée M. Marciniak, Shuai Li, Qiaoyi Lin, Marilu Casini, Borislav Hrisimirov Hristov, Lukasz Truszkowski, Nicholas G. Skiados, Milad Mokhtaridoost, Conor K. Camplisson, Elisabeth Wyart, Silvia Marchianò, Rose Fields, , David M Shechner

The paper uses O-MAP to study a cardiac-specific RNA factory around TTN RNA, revealing its chromatin interactions, RNA composition, and role of RBM20 in gene regulation.

bioRxiv · Nov 5, 2024 · PreprintGenomics

Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER

Sahar Attar, Valentino E. Browning, Yuzhen Liu, Eva K. Nichols, Ashley F. Tsue, David M Shechner, Jay Shendure, Joshua A. Lieberman, Shreeram Akilesh, Brian J. Beliveau

The paper introduces pSABER, a method for amplifying in situ hybridization signals in cellular and histopathological samples, achieving 25-fold amplification over conventional methods.

bioRxiv · Jan 30, 2023 · PreprintGenomics

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.

Ashley F. Tsue, Evan E. Kania, Diana Q. Lei, Rose Fields, Christopher D. McGann, Elliot A. Hershberg, Xinxian Deng, Maryanne Kihiu, Shao‐En Ong, Christine M. Distèche, Sita Kugel, Brian J. Beliveau, Devin K. Schweppe, David M Shechner

The paper introduces O-MAP, a method for discovering RNA-interacting proteins, transcripts, and genomic loci in situ with high precision and without genetic manipulation.

bioRxiv · Jan 19, 2023 · PreprintMolecular Biology

High-throughput identification of RNA nuclear enrichment sequences

Chinmay J. Shukla, Alexandra L. McCorkindale, Chiara Gerhardinger, Keegan D. Korthauer, Moran N. Cabili, David M Shechner, Rafael A. Irizarry, Philipp G. Maass, John L. Rinn

The paper identifies RNA sequences responsible for nuclear enrichment in lncRNAs using a modified MPRA approach and validates findings with smRNA-FISH.

The EMBO Journal · Jan 15, 2018Peer-reviewedGenomics

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

Marta Melé, Kaia Mattioli, William Mallard, David M Shechner, Chiara Gerhardinger, John L. Rinn

The paper identifies differences in chromatin environment, transcriptional regulation, and splicing between lincRNAs and mRNAs in human cell lines.

Genome Research · Jan 1, 2017Peer-reviewedGenomics