Widespread inter-individual gene expression variability in<i>Arabidopsis thaliana</i>

Cortijo, Sandra; Aydın, Zeynep Gökçe Gayretli; Ahnert, Sebastian E.; Locke, James

doi:10.1101/335380

Cited by 17 publications

(37 citation statements)

References 66 publications

(69 reference statements)

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“…Indeed, the only regularity that seems to operate in both vertebrates and invertebrates, involves the aforementioned association of high levels of DNA methylation with low expression noise. This generalization may even extend to plants, as suggested by recent studies of Arabidopsis thaliana, which indicate that genes with less expression variability are depleted in DNA methylation (Cortijo et al 2019). It is true that the diversity of models studied in this sense is too small (a mammal, a cockroach, and a mustard plant) to draw definitive conclusions.…”

Section: Discussionmentioning

confidence: 94%

DNA methylation in cockroaches is essential in early embryo development and reduces gene expression noise

Ventós-Alfonso

Ylla

Montanyes

et al. 2020

Preprint

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The influence of DNA methylation on gene behavior, and its consequent phenotypic effects appear to be very important, but the details are not well understood. Insects offer a diversity of DNA methylation modes, making them an excellent lineage for comparative analyses. However, functional studies have tended to focus on quite specialized holometabolan species, such as wasps, bees, beetles, and flies. Here we have studied DNA methylation in a hemimetabolan insect, the cockroach Blattella germanica, a model of early-branching insects. In this cockroach, one of the main genes responsible for DNA methylation, DNA methyltransferase 1 (DNMT1), is expressed in early embryogenesis. In our experiments, DNMT1 interference by RNAi reduces DNA methylation and impairs blastoderm formation. Using Reduced Representation Bisulfite Sequencing (RRBS) and transcriptomic analyses, we observed that hypermethylated genes are associated with metabolism and are highly expressed, whereas hypomethylated genes are related to signaling and have low expression levels. Moreover, the expression change in hypermethylated genes is greter than that in hypomethylated genes, whereas hypermethylated genes have less expression variability than hypomethylated genes. The latter observation has also been reported for humans and in Arabidopsis plants. A reduction in expression noise may therefore be one of the few universal effects of DNA methylation.

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Section: Discussionmentioning

confidence: 94%

DNA methylation in cockroaches is essential in early embryo development and reduces gene expression noise

Ventós-Alfonso

Ylla

Montanyes

et al. 2020

Preprint

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“…We can learn much from single cell expression studies of a single accession of A. thaliana, but it is known that gene expression varies considerably among genotypes of this species (Cortijo et al, 2019), and that the response even to autopolyploidy in Arabidopsis varies among accessions (Yu et al, 2010;Song et al, 2020), so we look forward to the availability in expression atlases (e.g., Papatheodorou et al, 2019) of single cell data for roots and other tissues of additional individuals and accessions, and also from other species. Interspecific data would allow us to hypothesize ancestral states with far more confidence, particularly data from Cleomaceae, the sister family to Brassicaceae, whose common ancestor pre-dates the alpha WGD event (Edger et al, 2018).…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots

et al. 2020

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Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralog pairs rapidly return to single copy status whereas, in other pairs, both paralogs are retained and may diverge in expression pattern or function. The effect of a geneits site of expression and thus the initial locus of its function-occurs at the level of a cell comprising a single cell type at a given state of the cell's development. Using Arabidopsis thaliana single cell transcriptomic data we categorized patterns of expression for 11,470 duplicate gene pairs across 36 cell clusters comprising nine cell types and their developmental states. Among these 11,470 pairs, 10,187 (88.8%) had at least one copy expressed in at least one of the 36 cell clusters. Pairs produced by WGD more often had both paralogs expressed in root cells than did pairs produced by small scale duplications. Three quarters of gene pairs expressed in the 36 cell clusters (7,608/10,187) showed extreme expression bias in at least one cluster, including 352 cases of reciprocal bias, a pattern consistent with expression subfunctionalization. More than twice as many pairs showed reciprocal expression bias between cell states than between cell types or between roots and leaves. A group of 33 gene pairs with reciprocal expression bias showed evidence of concerted divergence of gene networks in stele vs. epidermis. Pairs with both paralogs expressed without bias were less likely to have paralogs with divergent mutant phenotypes; such bias-free pairs showed evidence of preservation by maintenance of dosage balance. Overall, we found considerable evidence of shifts in gene expression following duplication, including in >80% of pairs encoding 7,653 genes expressed ubiquitously in all root cell types and states for which we inferred the polarity of change.

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“…Another limitation of our study is high interindividual variability in gene expression levels (high SD values) observed for many samples. While a relatively high level of molecular noise is common in gene expression studies [86,87], high interindividual variability in gene expression was particularly pronounced in genes that are involved in environmental responses in Arabidopsis thaliana [88]. This is an indication that harsh environmental conditions may be causing pronouncedly volatile gene expression levels on the interindividual, or possibly even intraindividual, levels on relatively short time scales, but this hypothesis warrants further studies.…”

Section: Discussionmentioning

confidence: 92%

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

Zhao

Yin

et al. 2020

FEBS Open Bio

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Goji berries have been used as food and medicine for millennia. Due to their high morphological similarity, fruits of two distinct species belonging to the family Solanaceae, Lycium barbarum (LB) and Lycium chinense (Chinese boxthorn), are usually marketed together as goji berries, but nearly 90% of all commercially available goji berries belong to the former species. A third closely related species, a wild perennial thorny shrub native to north‐western China, Lycium ruthenicum (LR; known as Russian box thorn, and its fruit as black wolfberry), has become a popular choice for combating soil desertification and for alleviating soil salinity/alkalinity due to its high resistance to the harsh environment of saline deserts. Despite the phylogenetic closeness of LB and LR, their fruits are very different. To identify the genes involved in these distinct phenotypes, here we studied expression patterns of 22 transcriptional regulators that may be crucial drivers of these differences during five developmental stages. BAM1 may contribute to higher sugar content in LB. High expression of BFRUCT in ripe LR is likely to be an evolutionary adaptation to fruit ripening in an arid environment. Two arogenate dehydratase paralogues, CHS and LDOX, are probably crucial elements of the mechanism by which LR accumulates much higher levels of anthocyanin. DXS2 (carotenoid accumulation in LB) and CCD4 (carotenoid degradation in ripe LR fruit) may be crucial drivers behind the much higher content of carotenoids in LB. EIL3 and ERF5 are two transcription factors that may contribute to the higher abiotic stress resilience of LR. GATA22‐like appears to have more important roles in growth than ripening in LB fruit and vice versa in LR. HAT5‐like exhibited opposite temporal patterns in two fruits: high in the 1st stage in LB and high in the 5th stage in LR. PED1 was expressed at a much lower level in LR. Finally, we hypothesise that the poorly functionally characterised SCL32 gene may play a part in the increased resistance to environmental stress of LR. We suggest that BAM1, BFRUCT, EIL3, ERF5, ADT paralogues (for functional redundancy), PED1, GATA22‐like, HAT5‐like and SCL32 warrant further functional studies.

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Widespread inter-individual gene expression variability inArabidopsis thaliana

Abstract: 10

Cited by 17 publications

References 66 publications

DNA methylation in cockroaches is essential in early embryo development and reduces gene expression noise

DNA methylation in cockroaches is essential in early embryo development and reduces gene expression noise

Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

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