Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo and RNA-Seq]

ABSTRACT: Identification hundreds of activity-induced mORFs and uORFs, a subset of which served as robust markers for activity status

ORGANISM(S): Mus musculus

PROVIDER: GSE295656 | GEO | 2026/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo-Seq]

Project description:Neural activity-dependent translation is essential for synaptic plasticity and diverse brain functions. Translation involves not only canonical main open reading frames (mORFs) but also upstream ORFs (uORFs), which may regulate mORF expression. However, due to technical limitations, systematic in-vestigation of activity-dependent uORFs and mORFs in brain tissues remains challenging. Here, we developed a ribosome tagging and purification strategy that bypasses the prolonged turnover of ribo-somal proteins, enabling ribosome profiling with one-hour temporal resolution after neural stimulation. Applying this strategy to mouse hippocampal slices undergoing long-term potentiation, we identified hundreds of activity-induced mORFs and uORFs, a subset of which served as robust markers for ac-tivity status. Notably, ~22% of the upregulated uORFs overlapped with those induced by the integrated stress response, suggesting potential crosstalk between these signaling pathways. This study provides a useful technique and resources for deciphering molecular mechanisms underlying activity- and trans-lation-dependent brain functions in health and disease.

2026-03-01 | GSE317973 | GEO

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [RIP-Seq]

2026-03-01 | GSE317975 | GEO

Ribo-seq analysis elucidates the dynamic translation landscape of yak ovarian tissue across different reproductive stages

Project description:Translation, as a crucial link in the transmission of genetic information, plays an indispensable regulatory role in follicular development, ovulation, corpus luteum formation, and degeneration. In order to deeply analyze the molecular mechanisms of reproductive regulation at the translation level, our study focused on the ovarian tissues of yaks at different reproductive stages to analyze gene expression changes using Ribosome profiling and integrating RNA-seq data. Meanwhile, the small open reading frames (sORFs) of ovarian tissue was characterized, and the impact of the translation efficiency of focused genes on their sequence feature was analyzed. The results showed that over 80% of genes in the two groups exhibited inconsistent changes at the transcription and translation levels, indicated that the changes in genes at both levels were complex and not simply synergistic. Upon the pathway enrichment analysis, the signaling pathways involved in these differentially expressed genes were further clarified, such as the estrogen signaling pathway PI3K-Akt, MAPK, calcium signaling pathway and ovarian steroidogenesis. Further research has found that some genes related to ovarian function have inconsistent expression at two levels and exhibit dynamic changes in translation activity, including PALB2, EGR2, BMP7, SOX9, PIK3R2, and WNT2B. Besides, we identified 66 predicted translatable small open reading frames (sORFs) and also explored the impact of upstream ORFs (uORFs) on the translation efficiency of downstream major ORFs (mORFs). This study systematically revealed the gene expression characteristics of ovarian tissues in yaks at different reproductive stages from the perspective of translational level for the first time, providing a new perspective for a deeper understanding of the physiological mechanisms of yak reproduction.

2025-02-05 | GSE288695 | GEO

The landscape of mRNA translation in tomato roots

Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. Most of the newly identified ORFs are small and difficult to detect with in silico methods. We also identified over thirteen hundreds of upstream ORFs on annotated genes. This data could facilitate gene annotation. Besides, this data also demonstrated that uORFs, miRNAs and antisense RNAs are regulating the expression of associated genes. This study uncovered mechanisms of translational regulation and gene annotation in tomato.

2019-07-05 | GSE124962 | GEO

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo-Seq]

Project description:Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo-Seq]

| PRJNA1416239 | ENA

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo and RNA-Seq]

Project description:Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue [Ribo and RNA-Seq]

| PRJNA1255544 | ENA

Determining Ribosome Translational Status by Ribo-ELISA.

Project description:The Ribo-ELISA was originally developed to elucidate the basis for the ribopuromycylation method (RPM)-based detection of ribosome bound nascent chains. The Ribo-ELISA enables characterization of the translational status of ribosomes, and can be applied to the discovery of super-ribosomal complexes with novel ribosome associated macromolecules that are isolated by physical fractionation in sucrose gradients or other methods.

| S-EPMC5856159 | biostudies-literature

Integrated transcriptome and Ribosome Profiling analyses elucidate the liver response of rainbow trout (Oncorhynchus mykiss) to heat stress [Ribo-seq]

Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.

2024-04-16 | GSE263547 | GEO

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue

Project description:Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue

| PRJNA1416241 | ENA

Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue

Project description:This SuperSeries is composed of the SubSeries listed below.

2026-03-01 | GSE317977 | GEO