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Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells.

Overview

Authors: Parna Saha1,2,3,4, Shivali Patel5,4, Lucille H. Tsao6, Rafael CA. Tavares6,7, Hyeonseok Choi1,2,8, Rebecca E. Andersen1,2,9, Anna Marie Pyle6,10,11, Daniel A. Lim1,2,3,12
ORCID iDs: Rebecca E. Andersen
  1. Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
  2. Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
  3. San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA
  4. These authors contributed equally
  5. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
  6. Department of Chemistry, Yale University, New Haven, CT 06511, USA
  7. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
  8. Department of Molecular and Cell Biology Undergraduate Program, University of California, Berkeley, Berkeley, CA 94720, USA
  9. Division of Genetics and Genomics, Harvard Medical School, Boston Children’s Hospital, Boston, MA 02115, USA
  10. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
  11. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
  12. Lead contact
Institutions: San Francisco VA Medical Center (United States); University of California, San Francisco (United States); Yale University (United States); University of Cambridge (United Kingdom); Cancer Research UK (United Kingdom); University of California, Berkeley (United States); Boston Children's Hospital (United States); Howard Hughes Medical Institute (United States)
Journal: Cell reports, volume 45, issue 6, article 117451
Dates: published online 28 May 2026; in print 23 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.celrep.2026.117451 · PMID 42213787 · PMCID PMC13446462 · OpenAlex W7162663348
Open access: gold, a free copy (OpenAlex)
Status: code on request
Categories: genetics / omics (modality), mouse (organism)
Methods: Statistics, Connectivity
Keywords: Neuronal differentiation, Primary Neural Stem Cells, Shape-map, Cp: Molecular Biology, Cp: Stem Cell Research, Lncpnky, Lna-asos, Lncrna Structure-function Studies, Lncrna Pnky, Terbium Sequencing
MeSH: Neural Stem Cells*, Neurogenesis*, RNA, Long Noncoding*, Animals, Cell Differentiation, Mice, Nucleic Acid Conformation, Oligonucleotides (* major topic)
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: Howard Hughes Medical Institute; NINDS NIH HHS (R01 NS124881, R01 NS091544); Yale University; US Department of Veterans Affairs (5I01 BX000252); University of California, San Francisco; National Institute of Neurological Disorders and Stroke (1R01NS124881); BLRD VA (I01 BX000252); NIGMS NIH HHS (T32 GM007223); National Institutes of Health (T32GM007223-45)
Citations: not cited yet (Europe PMC); 77 references in the paper
Research resources: Anti Tubulin β3 (Tuj1) RRID:AB_2313773

Abstract

Long noncoding RNA (lncRNA) Pnky is a trans-acting regulator of neural stem cell (NSC) differentiation, but the molecular mechanisms by which Pnky regulates neurogenesis are unknown. A fundamental step toward mechanistic understanding is to determine whether lncRNA structure underlies biological function. Using chemical probing and high-throughput analysis, we determined the secondary structure of Pnky folded in vitro and in cellulo. In vitro-transcribed Pnky RNA adopts a compact, highly structured conformation with evidence of tertiary interactions. In cellulo, Pnky secondary structure is similar to the in vitro conformation. We used locked nucleic acid (LNA) oligonucleotides to interrogate the entire Pnky transcript for function in NSCs and identified regions that when targeted increase neurogenesis—phenocopying Pnky knockdown—without decreasing transcript abundance. Our findings implicate specific structured regions of Pnky in the regulation of neurogenesis and illustrate how structural maps combined with phenotypic data can advance our understanding of lncRNA function.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

The paper says that its authors' code is available on request: it was not published with the paper, so there is nothing to verify.

The paper's code and data availability statement is in the Data section.

Tracing map

A tracing map links a paper to the code its authors published: this paper has none (its code is available on request), so it has no map.

Data

No dataset and no data link were found in the paper.

Data and code availability

SHAPE-MaP and terbium-seq data have been deposited in the NCBI SRA database under the identifier BioProject ID: PRJNA1263515.

This paper does not report original code.

Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

  • Publisher: n/a → Cell Press

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 10 keywords, 8 MeSH terms, 9 funders, 77 references, 1 RRID.

Cite

This paper

Saha, P., Patel, S., Tsao, L. H., Tavares, R. C., Choi, H., Andersen, R. E., Pyle, A. M., & Lim, D. A. (2026). Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells. Cell reports, 45(6), 117451. https://doi.org/10.1016/j.celrep.2026.117451

BibTeX

@article{saha2026pnky,
author = {Saha, Parna and Patel, Shivali and Tsao, Lucille H. and Tavares, Rafael CA. and Choi, Hyeonseok and Andersen, Rebecca E. and Pyle, Anna Marie and Lim, Daniel A.},
title = {{Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells}},
journal = {Cell reports},
year = {2026},
month = may,
volume = {45},
number = {6},
pages = {117451},
publisher = {Cell Press},
issn = {2211-1247},
doi = {10.1016/j.celrep.2026.117451},
url = {https://doi.org/10.1016/j.celrep.2026.117451},
pmid = {42213787},
pmcid = {PMC13446462}
}

RIS

TY - JOUR
AU - Saha, Parna
AU - Patel, Shivali
AU - Tsao, Lucille H.
AU - Tavares, Rafael CA.
AU - Choi, Hyeonseok
AU - Andersen, Rebecca E.
AU - Pyle, Anna Marie
AU - Lim, Daniel A.
TI - Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells
T2 - Cell reports
J2 - Cell Rep
PY - 2026
DA - 2026/05/28
VL - 45
IS - 6
SP - 117451
SN - 2211-1247
PB - Cell Press
DO - 10.1016/j.celrep.2026.117451
UR - https://doi.org/10.1016/j.celrep.2026.117451
LA - en
ER -

CSL-JSON

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