2. Academic Validation
  3. Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme

Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme

  • Commun Biol. 2026 Mar 23;9(1):649. doi: 10.1038/s42003-026-09819-0.
Ankush Singhal # 1,  Tyler Mrozowich # 2 3 4,  Carlos Rivera # 2 3,  Susmit Narayan Chaudhury 1,  Lilei Xu 2 3,  Rodrigo Aguilar 2 3,  Maulik Badmalia 4,  Jeannie T Lee 2 3,  Trushar R Patel 4 5 6,  Karissa Y Sanbonmatsu 7 8
Affiliations

Affiliations

  • 1 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
  • 2 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
  • 3 Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
  • 4 Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada.
  • 5 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.
  • 6 Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
  • 7 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA. [email protected].
  • 8 New Mexico Consortium, Los Alamos, NM, USA. [email protected].
  • # Contributed equally.
PMID: 41872304 DOI: 10.1038/s42003-026-09819-0
Abstract

The SINE-encoded B2 retrotransposon is an RNA Polymerase III (POL-III)-derived transcript whose expression is substantially upregulated during various cellular stress responses. Beyond retrotransposition, the B2 non-coding RNA can directly bind and repress the activity of RNA Polymerase II (POL-II), leading to a significant downregulation of transcripts during stress. Notably, our recent findings have shown that B2 is a self-cleaving ribozyme whose activity can be induced by interactions with chromatin-modifying factors through non-canonical epigenetic mechanisms that co-regulate its function across distinct chromatin-binding target loci. Here, by integrating RNA chemical probing, small-angle X-ray scattering, and 3D motif modeling, we determine structural ensemble-to-function relations for the B2 SINE ribozyme RNA. Genetic perturbations of the RNA suggest that the B2 SINE ribozyme has a well-defined secondary and dynamic tertiary structure that depends on the integrity of the critical region, which confers ribozymatic activity and repressive extent by POL-II. Using an RNA engineering approach, we examine the effects of point mutations, deletions of the main cleavage site, and deletions of the cleavage domain on the structural ensemble of the RNA. Combining this approach with in vitro and in vivo functional perturbation methods highlights the relationships between structural ensembles and various biologically relevant functional outcomes.

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