Cis- and Trans-Regulatory Mechanisms of Gene Expression in the ASJ Sensory Neuron of Caenorhabditis elegans

Ascidians present a striking dichotomy between conserved phenotypes and divergent genomes: embryonic cell lineages and gene expression patterns are conserved between distantly related species. Much research has focused on Ciona or Halocynthia spp. but development in other ascidians remains poorly characterized. In this study, we surveyed the multipotent myogenic B7.5 lineage in Molgula spp. Comparisons to the homologous lineage in Ciona revealed identical cell division and fate specification events that result in segregation of larval, cardiac, and pharyngeal muscle progenitors. Moreover, the expression patterns of key regulators are conserved, but cross-species transgenic assays uncovered incompatibility, or ‘unintelligibility’, of orthologous cis-regulatory sequences between Molgula and Ciona. These sequences drive identical expression patterns that are not recapitulated in cross-species assays. We show that this unintelligibility is likely due to changes in both cis- and trans-acting elements, hinting at widespread and frequent turnover of regulatory mechanisms underlying otherwise conserved aspects of ascidian embryogenesis.

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Cis-regulatory mechanisms of gene expression in an olfactory neuron type in Caenorhabditis elegans

Developmental Dynamics ◽

10.1002/dvdy.22147 ◽

2009 ◽

Vol 238 (12) ◽

pp. 3080-3092 ◽

Cited By ~ 14

Author(s):

Eva B. Nokes ◽

Alexander M. Van Der Linden ◽

Caron Winslow ◽

Saikat Mukhopadhyay ◽

Kristin Ma ◽

...

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Regulatory Mechanisms ◽

Olfactory Neuron ◽

Neuron Type

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Faculty Opinions recommendation of MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1004969.57959 ◽

2002 ◽

Author(s):

Bruce Bowerman

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Cell Polarity ◽

Interacting Proteins

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tiRNAs & tRFs Biogenesis and Regulation of Diseases: A Review

Current Medicinal Chemistry ◽

10.2174/0929867326666190124123831 ◽

2019 ◽

Vol 26 (31) ◽

pp. 5849-5861 ◽

Cited By ~ 3

Author(s):

Pan Jiang ◽

Feng Yan

Keyword(s):

Gene Expression ◽

Protein Synthesis ◽

Metabolic Diseases ◽

Viral Infections ◽

Regulatory Mechanisms ◽

Biological Functions ◽

Reverse Transcriptases ◽

Dna Damage Responses ◽

Potential Applications ◽

Viral Reverse Transcriptases

tiRNAs & tRFs are a class of small molecular noncoding tRNA derived from precise processing of mature or precursor tRNAs. Most tiRNAs & tRFs described originate from nucleus-encoded tRNAs, and only a few tiRNAs and tRFs have been reported. They have been suggested to play important roles in inhibiting protein synthesis, regulating gene expression, priming viral reverse transcriptases, and the modulation of DNA damage responses. However, the regulatory mechanisms and potential function of tiRNAs & tRFs remain poorly understood. This review aims to describe tiRNAs & tRFs, including their structure, biological functions and subcellular localization. The regulatory roles of tiRNAs & tRFs in translation, neurodegeneration, metabolic diseases, viral infections, and carcinogenesis are also discussed in detail. Finally, the potential applications of these noncoding tRNAs as biomarkers and gene regulators in different diseases is also highlighted.

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Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading

Nature Communications ◽

10.1038/s41467-021-22503-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Christopher A. Brosnan ◽

Alexander J. Palmer ◽

Steven Zuryn

Keyword(s):

Caenorhabditis Elegans ◽

Regulatory Networks ◽

Regulatory Mechanisms ◽

Cell Type ◽

A Genome ◽

Temporal Flexibility ◽

Small Regulatory Rnas ◽

Cell Type Specific ◽

Single Cell Type ◽

Regulated Gene Expression

AbstractMulticellularity has coincided with the evolution of microRNAs (miRNAs), small regulatory RNAs that are integrated into cellular differentiation and homeostatic gene-regulatory networks. However, the regulatory mechanisms underpinning miRNA activity have remained largely obscured because of the precise, and thus difficult to access, cellular contexts under which they operate. To resolve these, we have generated a genome-wide map of active miRNAs in Caenorhabditis elegans by revealing cell-type-specific patterns of miRNAs loaded into Argonaute (AGO) silencing complexes. Epitope-labelled AGO proteins were selectively expressed and immunoprecipitated from three distinct tissue types and associated miRNAs sequenced. In addition to providing information on biological function, we define adaptable miRNA:AGO interactions with single-cell-type and AGO-specific resolution. We demonstrate spatial and temporal dynamicism, flexibility of miRNA loading, and suggest miRNA regulatory mechanisms via AGO selectivity in different tissues and during ageing. Additionally, we resolve widespread changes in AGO-regulated gene expression by analysing translatomes specifically in neurons.

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Caenorhabditis elegans Genes Affecting Interindividual Variation in Life-span Biomarker Gene Expression

The Journals of Gerontology Series A ◽

10.1093/gerona/glw349 ◽

2017 ◽

Vol 72 (10) ◽

pp. 1305-1310 ◽

Cited By ~ 11

Author(s):

Alexander Mendenhall ◽

Matthew M Crane ◽

Patricia M Tedesco ◽

Thomas E Johnson ◽

Roger Brent

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Life Span ◽

Interindividual Variation

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R2R3-MYB transcription factors, StmiR858 and sucrose mediate potato flavonol biosynthesis

Horticulture Research ◽

10.1038/s41438-021-00463-9 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Sen Lin ◽

Rajesh K. Singh ◽

Moehninsi ◽

Duroy A. Navarre

Keyword(s):

Gene Expression ◽

Abiotic Stress ◽

Feedback Loop ◽

Regulatory Mechanisms ◽

Phenylpropanoid Metabolism ◽

Biotic And Abiotic Stress ◽

Health Promoting ◽

Transient Overexpression ◽

R2r3 Myb ◽

R2r3 Myb Transcription Factors

AbstractFlavonols and other phenylpropanoids protect plants from biotic and abiotic stress and are dietarily desirable because of their health-promoting properties. The ability to develop new potatoes (Solanum tuberosum) with optimal types and amounts of phenylpropanoids is limited by lack of knowledge about the regulatory mechanisms. Exogenous sucrose increased flavonols, whereas overexpression of the MYB StAN1 induced sucrolytic gene expression. Heterologous StAN1 protein bound promoter fragments from sucrolytic genes (SUSY1 and INV1). Two additional MYBs and one microRNA were identified that regulated potato flavonols. Overexpression analysis showed MYB12A and C increased amounts of flavonols and other phenylpropanoids. Endogenous flavonol amounts in light-exposed organs were much higher those in the dark. Expression levels of StMYB12A and C were high in flowers but low in tubers. Transient overexpression of miR858 altered potato flavonol metabolism. Endogenous StmiR858 expression was much lower in flowers than leaves and correlated with flavonol amounts in these organs. Collectively, these findings support the hypothesis that sucrose, MYBs, and miRNA control potato phenylpropanoid metabolism in a finely tuned manner that includes a feedback loop between sucrose and StAN1. These findings will aid in the development of potatoes with phenylpropanoid profiles optimized for crop performance and human health.

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