Long non-coding RNA: Classification, biogenesis and functions in blood cells

Molecular Immunology, Journal Year: 2019, Volume and Issue: 112, P. 82 - 92

Published: May 9, 2019

Language: Английский

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Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function

PLANT PHYSIOLOGY, Journal Year: 2017, Volume and Issue: 176(1), P. 254 - 269

Published: Nov. 20, 2017

Discoveries illuminate highly regulated dynamics of mRNA translation, sequestration, and degradation within the cytoplasm plants.

Language: Английский

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Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications

Molecular Plant, Journal Year: 2021, Volume and Issue: 15(1), P. 104 - 124

Published: Dec. 24, 2021

Language: Английский

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Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(6), P. 1762 - 1786

Published: Feb. 4, 2023

Abstract Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to variety regulatory processes. Functionally characterized lncRNAs play critical roles plants, ranging from regulating flowering controlling lateral root formation. However, findings the past decade have revealed thousands present plant transcriptomes, characterization has lagged far behind identification. In this setting, distinguishing function noise is challenging. community been at forefront discovery lncRNA biology, providing many functional mechanistic insights increased our understanding gene class. review, we examine key discoveries made biology over two half decades. We describe how pregenomics era informed efforts identify functionally characterize subsequent provide an overview archetypes into which fit speculate on new avenues research may uncover yet more archetypes. Finally, review discusses challenges facing field some exciting molecular computational approaches help inform comparative analyses.

Language: Английский

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CodLncScape Provides a Self‐Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs

Advanced Science, Journal Year: 2024, Volume and Issue: 11(22)

Published: April 11, 2024

Abstract Recent studies have revealed that numerous lncRNAs can translate proteins under specific conditions, performing diverse biological functions, thus termed coding lncRNAs. Their comprehensive landscape, however, remains elusive due to this field's preliminary and dispersed nature. This study introduces codLncScape, a framework for lncRNA exploration consisting of codLncDB, codLncFlow, codLncWeb, codLncNLP. Specifically, it contains manually compiled knowledge base, encompassing 353 entries validated by experiments. Building upon codLncFlow investigates the expression characteristics these their diagnostic potential in pan‐cancer context, alongside association with spermatogenesis. Furthermore, codLncWeb emerges as platform storing, browsing, accessing concerning within various programming environments. Finally, codLncNLP serves knowledge‐mining tool enhance timely content inclusion updates codLncDB. In summary, offers well‐functioning, content‐rich ecosystem research, aiming accelerate systematic field.

Language: Английский

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Evolutionary flexibility in flooding response circuitry in angiosperms

Science, Journal Year: 2019, Volume and Issue: 365(6459), P. 1291 - 1295

Published: Sept. 19, 2019

Flood-resistance from gene regulation Some plants tolerate flooding better than others. Reynoso et al. compared regulatory networks activated by in rice, which is adapted to flooding, with those species less flooding. Flood-related was characterized according chromatin accessibility as well transcription. Although flood response circuitry evident dryland well, its activation greater wetland rice. Science , this issue p. 1291

Language: Английский

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Mechanisms of Long Non-Coding RNAs in Cancers and Their Dynamic Regulations

Cancers, Journal Year: 2020, Volume and Issue: 12(5), P. 1245 - 1245

Published: May 15, 2020

Long non-coding RNA (lncRNA), which is a kind of noncoding RNA, generally characterized as being more than 200 nucleotide transcripts in length. LncRNAs exhibit many biological activities, including, but not limited to, cancer development. In this review, search the PubMed database was performed to identify relevant studies published English. The term “lncRNA or long RNA” combined with range terms related core focus review: mechanism, structure, regulation, and cancer. eligibility retrieved mainly based on abstract. decision whether study included review made after careful assessment its content. reference lists were also checked any other that could be review. We first summarized molecular mechanisms lncRNAs tumorigenesis, including competing endogenous (ceRNA) mechanisms, epigenetic decoy scaffold mRNA protein stability transcriptional translational miRNA processing architectural role lncRNAs, will help broad audience better understand how work Second, we introduced recent elucidate structure there link between lncRNA function visualizing domains vital understanding their function. Third, explored emerging evidence for regulators expression, turnover, modifications (including 5-methylcytidine, N6-methyladenosine, adenosine inosine editing), highlighting dynamics lncRNAs. Finally, used autophagy an example interpret diverse clinical trials lncRNA-based therapies.

Language: Английский

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A gene expression map of shoot domains reveals regulatory mechanisms

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Jan. 8, 2019

Abstract Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from SAM peripheral zone. After initiation, develop polarity patterns to form a planar shape. Here we compare translating RNAs among and leaf domains. Using ribosome affinity purification RNA sequencing quantify expression target domains, generate translatome map covering representative vegetative stage We discuss predicted cellular functions of these domains provide evidence that dome seemingly unrelated utilize common modules. Experimental follow up shows RABBIT EARS HANABA TARANU transcription factors have roles axillary initiation. This dataset provides community resource for further study response internal environmental signals.

Language: Английский

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Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(30), P. 7831 - 7836

Published: June 18, 2018

Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced transcription factors such as HY5. However, few detailed analyses have been carried out on the control start sites (TSSs). Of various wavelengths light, it blue (BL) that regulates physiological responses hypocotyl elongation and flowering time. To understand how controlled not only transcript abundance but also TSS selection, we examined genome-wide profiles Arabidopsis seedlings after exposure BL irradiation following initial growth dark. Thousands use multiple TSSs, some transcripts upstream ORFs (uORFs) take precedence over main ORF (mORF) encoding proteins. The uORFs often function translation inhibitors mORF or triggers nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream 220 enhanced exposure. This type regulation found HY5 HYH, major regulators light-dependent expression. Translation efficiencies showing usage these increased upon We show 45 genes, including HY5, accumulated a mutant NMD. These results suggest controls enhancing transcriptions choosing TSS, evade uORF-mediated inhibition ensure high light-regulated genes.

Language: Английский

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Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation

Trends in Genetics, Journal Year: 2018, Volume and Issue: 35(3), P. 186 - 198

Published: Dec. 31, 2018

Language: Английский

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