Exploring Non‐Coding RNAs in RNAcentral

Sweeney, Blake A.; Tagmazian, Arina A.; Ribas, Carlos Eduardo; Finn, Robert D.; Petrov, Anton I.

doi:10.1002/cpbi.104

Cited by 12 publications

(4 citation statements)

References 35 publications

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“…2C,D). Figure 2 illustrates a secondary structure comparison of ES7 L from G. gallus (R2DT) [31] and the H. sapiens (RNAcentral database) [34]. Most noticeably, the length of tentacle d strongly differs in G. gallus where it consists of 309 nucleotides compared to 89 nucleotides in H. sapiens .…”

Section: Resultsmentioning

confidence: 99%

Cryo‐EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold‐stress conditions

Nurullina,

Terrosu,

Myasnikov

et al. 2024

FEBS Letters

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Here, we present the high‐resolution structure of the Gallus gallus 80S ribosome obtained from cold‐treated chicken embryos. The translationally inactive ribosome complex contains elongation factor eEF2 with GDP, SERPINE1 mRNA binding protein 1 (SERBP1) and deacylated tRNA in the P/E position, showing common features with complexes already described in mammals. Modeling of most expansion segments of G. gallus 28S ribosomal RNA allowed us to identify specific features in their structural organization and to describe areas where a marked difference between mammalian and avian ribosomes could shed light on the evolution of the expansion segments. This study provides the first structure of an avian ribosome, establishing a model for future structural and functional studies on the translational machinery in Aves.

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Section: Resultsmentioning

confidence: 99%

Cryo‐EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold‐stress conditions

Nurullina,

Terrosu,

Myasnikov

et al. 2024

FEBS Letters

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“…Functional annotation and characterization of unannotated genes. The genome-guided assembly reported 13815 new genomic regions on SSRG, which were first annotated with SwissProt (Boutet et al, 2016) for protein-coding genes using the Trinotate (Ghaffari et al, 2014) pipeline; the superTranscripts missing annotations from Swiss-Prot were searched for homology with RNAcentral's plants non-coding RNA database (Sweeney et al, 2020) using BLASTN with parameters pid=90 & qcov=90 for the study of various mi-RNAs and sno-RNAs encoding genes responsible for alternative splicing and silencing. The rest of the superTranscripts that missed annotations from the above two approaches were characterized into putative protein-coding and protein non-coding categories based on their coding potentials with CPC2 (Kang et al, 2017) and further annotated with PLncDB; lncRNA database for sorghum by using BLASTN with parameters pid=90 and qcov=90.…”

Section: Methodsmentioning

confidence: 99%

Unlocking the Genetic Landscape: Enhanced Insights into Sweet Sorghum Genomes through Comprehensive superTranscriptomic Analysis

Nikhil,

Mohideen,

Raja

2023

Preprint

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Sweet sorghum has gained global significance as a versatile crop for food, fodder, and biofuel. Department of Agriculture, USA declared sorghum a sweet alternative for corn and sugarcane. Its cultivated varieties, along with their wild counterparts, contribute to the core genetic pool. We harnessed 223 publicly available RNA-seq datasets from sweet sorghum to construct the superTranscriptome and analyze gene structure. This approach yielded 45,864 Representative Transcript Assemblies (RTA) that showcased intriguing Presence-Absence Variation (PAV) across 15 existing sorghum genomes, even incorporating one wild progenitor. A fascinating outcome was the identification of 301 superTranscripts exclusive to sweet sorghum, encompassing elements such as hexokinases, cytochromes, select lncRNAs, and histones. Moreover, this study enriched sweet sorghum annotations with 2,802 newly identified protein-coding genes, including 559 encoding diverse transcription factors (TFs). This study unveiled 10,059 superTranscripts associated with various non-coding RNAs, including long non-coding RNAs (lncRNAs). The Rio variety displayed elevated expression of light-harvesting complexes (LHCs) and reduced expression of Metallothioneins during internode growth, suggesting the influence of photosynthesis and metal ion transport on sugar accumulation. Intriguingly, specific lncRNAs exhibited significant expression shifts in Rio during internode development, possibly implying their role in sugar accumulation. We validated the superTranscriptome against the Sweet Sorghum Reference Genome (SSRG) using Differential Exon Usage (DEU) and Differential Gene Expression (DGE), which demonstrated superior estimations. This study underscores the superTranscriptome's utility in unraveling fundamental sorghum mechanisms, enhancing genome annotations, and offering a potential alternative to the reference genome.

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“…Trimmed reads were mapped to rat mature and precursor miRNAs using the miRBase -Release 22.1. In addition, custom database for variety of ncRNA was generated by downloading published sequences from RNAcentral, a comprehensive database of ncRNA sequences [48]. Reads were annotated for matches against known ncRNAs related to Rattus norvegicus.…”

Section: Statistical and Bioinformatics Analysismentioning

confidence: 99%

Exploring the Secretome’s Biomarker and Analgesic Potential

Hershfield¹,

Strain²,

Chavez³

et al. 2022

AJPN

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Diagnostic and prognostic biomarkers of nerve injury and/or pain as well as improved pain therapeutics are needed, both on the battlefield to treat injured Service Members and in the civilian sector. Our previous research indicates that there are several differentially expressed (DE) extracellular vesicle-derived microRNAs (EV-miRNAs) isolated from rat plasma following spinal nerve ligation (SNL). As such, EV-miRNAs hold promise as biomarkers and therapeutic targets. The secretome contains biological mediators, including EVs, which are released into the extracellular space. In this study we focus on evaluating EV-non-coding RNAs (ncRNAs), examine effects of SNL on key protein expression in the prefrontal cortex (PFC), and test the secretome's analgesic properties. To accomplish these goals, anesthetized male Sprague Dawley rats underwent SNL and nociceptive behavior measurements, plasma collection followed by EV RNA isolation, small RNA sequencing, and analysis. Expression of several key proteins in the PFC was determined by Wes/Jess analysis. The secretome bath was applied directly to the ligated nerve and the paw withdrawal threshold (PWT) was measured. We identified differences in several classes of ncRNAs such as piRNAs, snoRNAs, and snRNAs post-SNL. Levels of phosphorylated forms of P70S6K and ERK1 were increased in the dorsal PFC at 15 days post-SNL. Bath application of the secretome directly to the ligated nerve resulted in recovery of the reduced PWT (increased mechanical sensitivity) that is induced by SNL. Here, we have identified specific EV-ncRNAs that could contribute to the formation of pain. Furthermore, we have evaluated a novel product for analgesic efficacy that could function to exploit the underlying mechanisms that contribute to pain development, thus reducing acute pain. This is key in treating Service Members on the battlefield in order to prevent pain chronification.

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Exploring Non‐Coding RNAs in RNAcentral

Cited by 12 publications

References 35 publications

Cryo‐EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold‐stress conditions

Cryo‐EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold‐stress conditions

Unlocking the Genetic Landscape: Enhanced Insights into Sweet Sorghum Genomes through Comprehensive superTranscriptomic Analysis

Exploring the Secretome’s Biomarker and Analgesic Potential

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