Root-derived small peptides: Key regulators of plant development, stress resilience, and nutrient acquisition

Plant Science, Journal Year: 2025, Volume and Issue: unknown, P. 112433 - 112433

Published: Feb. 1, 2025

Language: Английский

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Comparative Transcriptomic Analysis Provides Insight into Spatiotemporal Expression Patterns of Pivotal Genes During Critical Growth Stages in Min Pig Breed

Biomolecules, Journal Year: 2025, Volume and Issue: 15(2), P. 180 - 180

Published: Jan. 26, 2025

The growth and development of animals are dynamic processes characterized by fluctuations. Min pigs, a local breed renowned for their superior meat quality, present an intriguing yet poorly understood relationship between this quality patterns. To elucidate relationship, we employed multi-faceted approach that included comparative transcriptomics, quantitative real-time PCR (qRT-PCR), selection pressure analysis key genes, three-dimensional protein structure simulations. Our findings revealed 150 days (150 d) age represented pivotal turning point in the pigs. Thirteen genes exhibiting significant differential expression early late stages were identified. Notably, CDK2 gene demonstrated specific high hind limb muscles adipose tissues during later stages. Comparative with African warthog while remained conserved, base mutations upstream downstream non-coding regions resulted strong positive on gene. These results suggest plays crucial role defining spatiotemporal characteristics domestication This study provides critical insights into patterns domestic pigs offers robust scientific foundation improving traits through domestication.

Language: Английский

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Current Perspectives on Functional Involvement of Micropeptides in Virus–Host Interactions

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3651 - 3651

Published: April 12, 2025

Micropeptides (miPEPs), encoded by short open reading frames (sORFs) within various genomic regions, have recently emerged as critical regulators of multiple biological processes. In particular, these small molecules are now increasingly being recognized for their role in modulating viral replication, pathogenesis, and host immune responses. Both miPEPs virus-derived been noted ability to regulate virus–host interactions through diversified mechanisms such altering protein stability protein–protein interactions. Although thousands sORFs annotated having the potential encode miPEPs, only a number experimentally validated so far, with some directly linked subset associated modulation, indicating that investigation is still its infancy. The systematic identification, translational status assessment, in-depth characterization, functional analysis substantial fraction encoding remain largely underexplored. Further studies anticipated uncover intricate underlying interactions, broader functions miPEPs. This article will review emerging roles immunity, discuss challenges future perspectives miPEP studies.

Language: Английский

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Microsatellite expansions hidden within the human dark genome are translated in novel and toxic proteins causing muscle and neurodegenerative diseases

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

The vast majority of the human genome is non-coding with one-half composed repeated DNA elements, including microsatellites that are short sequences 1 to 6 nucleotides. Expansion a subset these leading cause over 60 neurological diseases. However, most tandem repeat expansions located in annotated as non-coding, thus questioning how mutations pathogenic. Here, we found GGC causing various diseases, oculopharyngodistal myopathy or without leukoencephalopathy (OPDM/OPML) and neuronal intranuclear inclusion disease (NIID), while embedded considered reality within small previously unrecognized ORFs, resulting their translation into novel diverse polyglycine-containing proteins. Antibodies developed against proteins stain p62-positive inclusions typical Importantly, sole expression recapitulates key features OPDM/OPML/NIID, namely formation protein aggregates locomotor skeletal muscle alterations associated neurodegeneration cell, fly mouse models. Moreover, polyglycine show unexpected variations interactants, half-life, aggregation toxicity. These results stress role specific ORF hosting repeats modulate toxic properties central core. Finally, identified pharmacological compound targeting proteins, raising hope develop common therapy for neuromuscular neurodegenerative Overall, uncover unified pathogenic mechanism diseases where translated driving aggregates, well cell dysfunctions. this work highlights complexity richness “dark” proteome importance yet ORFs pathologies.

Language: Английский

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From non‐coding RNAs to cancer regulators: The fascinating world of micropeptides

International Journal of Cancer, Journal Year: 2025, Volume and Issue: unknown

Published: April 25, 2025

Abstract Micropeptides are commonly identified as peptides encoded by non‐coding RNAs (ncRNAs). In the short open reading frame (sORF) of ncRNAs, there is a base sequence encoding functional micropeptides, which great significance in biological field. Recently, micropeptides regulate diverse processes, including mitochondrial metabolism, calcium transport, mRNA splicing, signal transduction, myocyte fusion, and cellular senescence, regulating homeostasis internal environment cancer's incidence progression. Especially, study cancer about potential regulatory mechanism will be conducive to further understanding process initiation development. More more research shows have been confirmed play an essential role emergence multiple kinds cancers, Breast cancer, Colon Colorectal Glioma, Glioblastoma, Liver cancer. This review presents comprehensive synthesis latest advancements our roles cells, with particular focus on networks involving oncogenesis. The new mode action provides innovative ideas for diagnosis treatment. Moreover, we explored significant capacity diagnostic biomarkers targets anti‐cancer therapies clinical settings, highlighting their development micropeptide‐based tools therapeutics.

Language: Английский

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Novel insights into small open reading frame-encoded micropeptides in hepatocellular carcinoma: A potential breakthrough

Cancer Letters, Journal Year: 2024, Volume and Issue: 587, P. 216691 - 216691

Published: Feb. 14, 2024

Language: Английский

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How to overcome constraints imposed by microsporidian genome features to ensure gene prediction?

Journal of Eukaryotic Microbiology, Journal Year: 2024, Volume and Issue: 71(5)

Published: June 27, 2024

Since the advent of sequencing techniques and due to their continuous evolution, it has become easier less expensive obtain complete genome sequence any organism. Nevertheless, elucidate all biological processes governing organism development, quality annotation is essential. In annotation, predicting gene structure one most important captivating challenges for computational biology. This aspect requires continual optimization, particularly genomes as unusual those microsporidia. Indeed, this group fungal-related parasites exhibits specific features (highly reduced sizes, sequences with high rate evolution) linked evolution intracellular parasites, requiring implementation approaches consider these features. review aimed outline characteristics assess increasingly efficient tools that have enhanced accuracy prediction microsporidia, both in terms sensitivity specificity. Subsequently, a final part will be dedicated postgenomic at reinforcing data generated by software. These include characterization other understudied genes, such encoding regulatory noncoding RNAs or very small proteins, which also play crucial roles life cycle microorganisms.

Language: Английский

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MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(2), P. 880 - 880

Published: Jan. 10, 2024

With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions these microorganisms, complete genome sequencing is routinely used. Nevertheless, proper prediction their gene catalogue challenging due to taxon-specific evolutionary features. As innovative annotation strategies are needed obtain representative snapshot overall lifestyle parasites, MicroAnnot tool, dedicated workflow for microsporidian sequence using data from curated databases accurately annotated genes, has been developed. Furthermore, specific modules have implemented perform small (<300 bp) transposable element identification. Finally, functional was performed signature-based InterProScan software. MicroAnnot's accuracy verified by re-annotation four genomes which structural had previously validated. its comparative approach transcriptional signal identification method, provides an accurate translation initiation sites, efficient elements, as well high specificity sensitivity including those under 300 bp.

Language: Английский

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Rules and impacts of nonsense‐mediated mRNA decay in the degradation of long noncoding RNAs

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2024, Volume and Issue: 15(3)

Published: May 1, 2024

Abstract Nonsense‐mediated mRNA decay (NMD) is a quality‐control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3′UTR. NMD detects such and rapidly them during initial rounds of translation in the eukaryotic cells. Since translation‐dependent cytoplasmic surveillance process, noncoding RNAs were initially believed to be NMD‐resistant. The sequence feature‐based analysis has revealed many putative (lncRNAs) have short frames, most which potential. Subsequent transcriptome‐based molecular studies showed an association large set lncRNAs with translating ribosomes, some produce stable functionally active micropeptides. translationally typically relatively longer unprotected 3′UTR, can induce their NMD‐dependent degradation. This review defines mechanism regulation degradation its impact on biological processes related functions encoded article categorized under: RNA Turnover Surveillance > Turnover/Surveillance Mechanisms Regulation Stability Disease Development

Language: Английский

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Roles of small peptides encoded by non-coding RNAs in tumor invasion and migration

Frontiers in Pharmacology, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 16, 2024

Non-coding RNAs (ncRNAs), which are usually considered not to encode proteins, widely involved in important activities including signal transduction and cell proliferation. However, recent studies have shown that small peptides encoded by ncRNAs (SPENs) roles the development of malignant tumors. Some SPENs participate regulation skeleton reorganization, intercellular adhesion, signaling other processes tumor cells, with effects on invasive migratory abilities cells. Therefore, potential applications as therapeutic targets biomarkers Invasion migration cells main reasons for poor prognosis cancer patients represent most challenging aspects treatment Currently, treatments tumors include surgery, radiotherapy, targeted drug therapy. Surgery, however, is reserved early stages carries risks costs. Radiotherapy therapy serious side effects. This review describes mechanisms their invasion migration, aim providing new diagnosis treatment.

Language: Английский

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