Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

ABSTRACTAmong the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA line). Compared to the wild-type Col-0, the 20rDNA line shows several signs of genomic instability, such as variations in 3D genome organization, spontaneous double-strand breaks accumulation, transcriptomic changes, and higher DNA methylation level. Strikingly, using genomic and microscopic approaches, we identified seven large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. As a consequence, more than 600 genes were duplicated, often associated with an increase in their expression level. Among them, we found several upregulated genes involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and we discuss their potential implications on plant genome evolution.

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Do the microRNAs we eat affect gene expression?

Nature ◽

10.1038/d41586-020-01767-x ◽

2020 ◽

Vol 582 (7812) ◽

pp. S10-S11 ◽

Cited By ~ 1

Author(s):

Kristina Campbell

Keyword(s):

Gene Expression ◽

Affect Gene Expression

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Faculty Opinions recommendation of Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.

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

10.3410/f.14061961.15528062 ◽

2012 ◽

Author(s):

Job Dekker

Keyword(s):

Gene Expression ◽

Noncoding Rnas ◽

Affect Gene Expression

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Phenotypic plasticity

10.1093/oso/9780198797500.003.0005 ◽

2018 ◽

Author(s):

Karen D. Williams ◽

Marla B. Sokolowski

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Environmental Change ◽

Behavioral Plasticity ◽

Behavioral Flexibility ◽

Insect Behavior ◽

Behavioral Variability ◽

Gene By Environment Interactions ◽

Affect Gene Expression

Why is there so much variation in insect behavior? This chapter will address the sources of behavioral variability, with a particular focus on phenotypic plasticity. Variation in social, nutritional, and seasonal environmental contexts during development and adulthood can give rise to phenotypic plasticity. To delve into mechanism underlying behavioral flexibility in insects, examples of polyphenisms, a type of phenotypic plasticity, will be discussed. Selected examples reveal that environmental change can affect gene expression, which in turn can affect behavioral plasticity. These changes in gene expression together with gene-by-environment interactions are discussed to illuminate our understanding of insect behavioral plasticity.

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Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids

Nature Ecology & Evolution ◽

10.1038/s41559-021-01523-y ◽

2021 ◽

Vol 5 (10) ◽

pp. 1382-1393

Author(s):

Xinyu Jiang ◽

Qingxin Song ◽

Wenxue Ye ◽

Z. Jeffrey Chen

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Small Rnas ◽

Structural Variation ◽

Self Incompatibility ◽

Polyploid Evolution ◽

Genomic Variations ◽

Conserved Gene ◽

Arabidopsis Suecica ◽

Affect Gene Expression

AbstractDuring evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsisthaliana (TT) and Arabidopsisarenosa (AA). A. suecica shows conserved gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inherited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution.

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Developmentally Regulated Oscillations in the Expression of UV Repair Genes in a Soilborne Plant Pathogen Dictate UV Repair Efficiency and Survival

mBio ◽

10.1128/mbio.02623-19 ◽

2019 ◽

Vol 10 (6) ◽

Author(s):

Shira Milo-Cochavi ◽

Sheera Adar ◽

Shay Covo

Keyword(s):

Gene Expression ◽

Fusarium Oxysporum ◽

Plant Pathogen ◽

Uv Light ◽

Sun Exposure ◽

The Sun ◽

Repair Gene ◽

Repair Capacity ◽

Content Type ◽

Repair Genes

ABSTRACT The ability to withstand UV damage shapes the ecology of microbes. While mechanisms of UV tolerance were extensively investigated in microorganisms regularly exposed to the sun, far less is known about UV repair of soilborne microorganisms. Fusarium oxysporum is a soilborne fungal plant pathogen that is resistant to UV light. We hypothesized that its UV repair capacity is induced to deal with irregular sun exposure. Unlike the SOS paradigm, our analysis revealed only sporadic increases and even decreases in UV repair gene expression following UVC irradiation or exposure to visible light. Strikingly, a major factor determining the expression of UV repair genes was the developmental status of the fungus. At the early stages of germination, the expression of photolyase increased while the expression of UV endonuclease decreased, and then the trend was reversed. These gene expression oscillations were dependent on cell cycle progression. Consequently, the contribution of photoreactivation to UV repair and survival was stronger at the beginning of germination than later when a filament was established. F. oxysporum germinates following cues from the host. Early on in germination, it is most vulnerable to UV; when the filament is established, the pathogen is protected from the sun because it is already within the host tissue. IMPORTANCE Fusarium oxysporum infects plants through the roots and therefore is not exposed to the sun regularly. However, the ability to survive sun exposure expands the distribution of the population. UV from the sun is toxic and mutagenic, and to survive sun exposure, fungi encode several DNA repair mechanisms. We found that Fusarium oxysporum has a gene expression program that activates photolyase at the first hours of germination when the pathogen is not established in the plant tissue. Later on, the expression of photolyase decreases, and the expression of a light-independent UV repair mechanism increases. We suggest a novel point of view to a very fundamental question of how soilborne microorganisms defend themselves against sudden UV exposure.

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