Evidence map›Paper›PMID 42213787›Full record

ArticleCell reports2026

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

Parna Saha, Shivali Patel, Lucille H Tsao, Rafael Ca Tavares, Hyeonseok Choi, Rebecca E Andersen, Anna Marie Pyle, Daniel A Lim

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Parna SahaDepartment of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
Shivali PatelDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
Lucille H TsaoDepartment of Chemistry, Yale University, New Haven, CT 06511, USA.
Rafael Ca TavaresDepartment of Chemistry, Yale University, New Haven, CT 06511, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Hyeonseok ChoiDepartment of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology Undergraduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.
Rebecca E AndersenDepartment of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Genetics and Genomics, Harvard Medical School, Boston Children's Hospital, Boston, MA 02115, USA.
Anna Marie PyleDepartment of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: anna.pyle@yale.edu.
Daniel A LimDepartment of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA. Electronic address: daniel.lim@ucsf.edu.

Funding

Skill Development for Diverse Scientific Careers: A New Course Predoctoral Program in Cellular and Molecular BiologyT32GM007223 · NIGMS · YALE UNIVERSITY · PI BASERGA, SUSAN J · 1985 to 2019
$31.0M
Functional long noncoding RNAs in neural developmentR01NS124881 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI DANIEL A LIM · 2022 to 2026
$3.0M
Long noncoding RNA regulation of neural stem cellsR01NS091544 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, DANIEL A · 2016 to 2020
$1.7M
BLRD VA I01 BX000252NIGMS NIH HHS T32 GM007223NINDS NIH HHS R01 NS091544NINDS NIH HHS R01 NS124881
6 · The paper itself

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.

Indexed as

Neural Stem CellsNeurogenesisRNA, Long NoncodingAnimalsCell DifferentiationMiceNucleic Acid ConformationOligonucleotidesOligonucleotidesRNA, Long NoncodingCP: molecular biologyCP: stem cell researchLNA-ASOsLncpnkylncRNA PnkylncRNA structure-function studiesneuronal differentiationprimary neural stem cellsSHAPE-MaPterbium sequencing

Identifiers

PMID42213787
PMCPMC13446462

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.