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Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis

Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

Ivana Borovská
Chundan Zhang
Danny Incarnato
ResearchOpen Access25 Jul 2025
Nature Biotechnology

P: 1-13
Author Correction: CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells

Liang-Zhong Yang
Yi-Hui Min
Ling-Ling Chen
Amendments and Corrections02 Aug 2024
Nature Methods

Volume: 21, P: 1958
SHAPE-guided RNA structure homology search and motif discovery

SHAPEwarp is a method that allows identifying structurally-similar RNAs by direct comparison of reactivity profiles derived from chemical probing experiments. Its application to viral genomes identified conserved RNA structure elements.

Edoardo Morandi
Martijn J. van Hemert
Danny Incarnato
ResearchOpen Access31 Mar 2022
Nature Communications

Volume: 13, P: 1-7
Probing the dynamic RNA structurome and its functions

In this Review, Spitale and Incarnato discuss how the application of sequencing-based RNA structure mapping methods to entire transcriptomes in living cells is providing insight into the RNA structurome, the dynamics of RNA ensembles and how RNA structure regulates cellular processes.

Robert C. Spitale
Danny Incarnato
Reviews08 Nov 2022
Nature Reviews Genetics

Volume: 24, P: 178-196
p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response

The p140Cap adaptor protein is a tumour suppressor associated with improved prognosis in breast cancer. Here, the authors identify a role for p140Cap in preventing the immunosuppressive and pro-tumour function of polymorphonuclear myeloid-derived suppressor cells via downmodulation of the β-Catenin/Tumor Initiating Cells/G-CSF axi

Vincenzo Salemme
Mauro Vedelago
Paola Defilippi
ResearchOpen Access11 May 2023
Nature Communications

Volume: 14, P: 1-22
Extracellular nicotinate phosphoribosyltransferase binds Toll like receptor 4 and mediates inflammation

The enzyme nicotinate phosphoribosyltransferase (NAPRT) mediates the rate-limiting step in NAD salvage pathway starting from nicotinic acid. Here the authors show that NAPRT can be detected extracellularly, binds to Toll like receptor 4, and activates NF-kB signaling and cytokine production in macrophage via NAD synthesis-independent pathways.

Antonella Managò
Valentina Audrito
Silvia Deaglio
ResearchOpen Access11 Sept 2019
Nature Communications

Volume: 10, P: 1-14
Genome-scale deconvolution of RNA structure ensembles

The DRACO algorithm deconvolutes coexisting RNA structures from mutational profiling experiments, and can be applied to bacterial regulatory structures and elements from the SARS-CoV-2 genome.

Edoardo Morandi
Ilaria Manfredonia
Danny Incarnato
Research22 Feb 2021
Nature Methods

Volume: 18, P: 249-252
TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway

F Neri
D Dettori
S Oliviero
Research03 Nov 2014
Oncogene

Volume: 34, P: 4168-4176
SiO₂ nanoparticles modulate the electrical activity of neuroendocrine cells without exerting genomic effects

C. Distasi
F. A. Ruffinatti
D. Lovisolo
ResearchOpen Access09 Feb 2018
Scientific Reports

Volume: 8, P: 1-12
Mutations in NOTCH1 PEST domain orchestrate CCL19-driven homing of chronic lymphocytic leukemia cells by modulating the tumor suppressor gene DUSP22

F Arruga
B Gizdic
S Deaglio
Research26 Dec 2016
Leukemia

Volume: 31, P: 1882-1893

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Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis

Author Correction: CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells

SHAPE-guided RNA structure homology search and motif discovery

Probing the dynamic RNA structurome and its functions

p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response

Extracellular nicotinate phosphoribosyltransferase binds Toll like receptor 4 and mediates inflammation

Genome-scale deconvolution of RNA structure ensembles

TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway

SiO₂ nanoparticles modulate the electrical activity of neuroendocrine cells without exerting genomic effects

Mutations in NOTCH1 PEST domain orchestrate CCL19-driven homing of chronic lymphocytic leukemia cells by modulating the tumor suppressor gene DUSP22

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