Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer. DOI Open Access
Shea H. Siwik, Aleksandra J. Wierzba, Shelby R. Lennon

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, thereby revealing novel aspects RNA metabolism and dynamics. While a diverse set been developed, new generation are beginning to exploit the ring-opening spirocyclic rhodamine dyes achieve robust performance live mammalian cells. These fluorophores have two chemical states: colorless, cell-permeable state fluorescent zwitterionic state. Recently, developed dye SpyRho555 almost exclusively adopts closed solution becomes complex RhoBAST aptamer. To understand basis for RhoBAST-SpyRho555 fluorogenicity, we determined crystal structures 5-carboxytetramethylrhodamine analogue, MaP555. is organized by perfect four-way junction that positions loops form dye-binding pocket. The core ligand resides between tri-adenine floor single guanine base, largely driven π-stacking interactions. Importantly, unpaired interacts 3-position group MaP555 stabilize open conformation, supported mutagenesis data, may play an active role promoting conformation dye. Graphical

Language: Английский

Deciphering the epigenetic role of long non‐coding RNAs in mood disorders: Focus on human brain studies DOI Creative Commons
Bhaskar Roy,

Anuj Kumar Verma,

Yu Funahashi

et al.

Clinical and Translational Medicine, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

Language: Английский

Citations

1
Decoding the complex journeys of RNAs along neurons DOI Creative Commons
Jenna L. Wingfield, Sathyanarayanan V. Puthanveettil

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: April 10, 2025

Abstract Neurons are highly polarized, specialized cells that must overcome immense challenges to ensure the health and survival of organism in which they reside. They can spread over meters persist for decades yet communicate at sub-millisecond millimeter scales. Thus, neurons require extreme levels spatial-temporal control. employ molecular motors transport coding noncoding RNAs distal synapses. Intracellular trafficking enables locally regulate protein synthesis synaptic activity. The way get loaded onto transported their target locations, particularly following plasticity, is explored below.

Language: Английский

Citations

0
Non-coding RNA and memory DOI
Sarbani Samaddar, Sourav Banerjee

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
lncRNA ADEPTR loss-of-function elicits sex-specific behavioral and spine deficits DOI Creative Commons
Kaushik Chanda,

Jackson P. Carter,

Hirofumi Nishizono

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 26, 2024

Abstract Activity-dependent changes in neuronal connections are fundamental to learning and long-term memory storage. However, the precise contribution of long noncoding RNAs (lncRNAs) these modifications remains unclear. In this study, we assessed role lncRNA ADEPTR, a cAMP-modulated localized dendrites, which is crucial for synapse morphology. By generating two different mouse models—one with deletion ADEPTR (L-ADEPTR) one its protein interaction region (S-ADEPTR)—we investigated sex-specific impacts loss function on learning, memory, dendritic arborization, Our behavioral analyses revealed reduction anxiety adult male mice, while remained unaffected both models. Systematic evaluations morphology across various developmental stages (∼3-day-old postnatal cultures 14- 42-day-old female mice) uncovered substantial deficits architecture S- L-ADEPTR cultures. At day 42, contrast their counterparts, mice exhibited significant deficiency thin spines. Additionally, found that expression plasticity-related gene BDNF, immediate early cFOS were enhanced cortex hippocampus suggesting activation compensatory mechanism protecting against deficits. Collectively, observations underscore shaping behavior.

Language: Английский

Citations

0
lncRNA ADEPTR Loss-of-Function Elicits Sex-Specific Behavioral and Spine Deficits DOI
Kaushik Chanda, Jackson Carter, Hirofumi Nishizono

et al.

Published: Jan. 1, 2024

Language: Английский

Citations

0
Profiling hippocampal expression of long non-coding RNA GM12371 in a rat model of vascular dementia DOI Creative Commons
Etrat Hooshmandi, Somayeh Akbari, Negin Gharbi

et al.

Egyptian Journal of Medical Human Genetics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Oct. 6, 2024

Abstract Background Dementia, characterized by synaptic dysfunction and memory loss, presents a significant challenge in medical research. Long non-coding RNAs (lncRNAs), known for their crucial roles regulating gene expression, represent gap knowledge regarding specific involvement structure, transmission, plasticity. This study aims to investigate the dynamic changes hippocampal lncRNA GM12371 expression response acute chronic hypoperfusion rat brain using 2VO model. Methods The model was induced permanently occluding common carotid arteries. Quantitative real-time polymerase chain reaction (qRT-PCR) used evaluate at both (day 4) 28) stages post-2VO surgery. Comparative analysis conducted with sham-operated group. Results A notable reduction observed hippocampus on day 4 following surgery compared sham group ( P < 0.05). However, there no difference between 2VO-28 groups. Conclusion These findings suggest that downregulation of is blood flow but tends normalize during phase cerebral hypoperfusion. regulation may be adaptive vascular dementia. Further clinical studies are warranted potential peripheral alterations individuals

Language: Английский

Citations

0
Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer. DOI Open Access
Shea H. Siwik, Aleksandra J. Wierzba, Shelby R. Lennon

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, thereby revealing novel aspects RNA metabolism and dynamics. While a diverse set been developed, new generation are beginning to exploit the ring-opening spirocyclic rhodamine dyes achieve robust performance live mammalian cells. These fluorophores have two chemical states: colorless, cell-permeable state fluorescent zwitterionic state. Recently, developed dye SpyRho555 almost exclusively adopts closed solution becomes complex RhoBAST aptamer. To understand basis for RhoBAST-SpyRho555 fluorogenicity, we determined crystal structures 5-carboxytetramethylrhodamine analogue, MaP555. is organized by perfect four-way junction that positions loops form dye-binding pocket. The core ligand resides between tri-adenine floor single guanine base, largely driven π-stacking interactions. Importantly, unpaired interacts 3-position group MaP555 stabilize open conformation, supported mutagenesis data, may play an active role promoting conformation dye. Graphical

Language: Английский

Citations

0