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Increased gene dosage and mRNA expression from chromosomal duplications in C. elegans

Bhavana Ragipani, Sarah Elizabeth Albritton, Ana Karina Morao, Diogo Mesquita, Maxwell Kramer, Sevinç Ercan

Preprint posted on March 23, 2022 https://www.biorxiv.org/content/10.1101/2022.03.22.485368v1

What goes up must come down (or not) – C. elegans lacks dosage compensation mechanism

Selected by Chee Kiang Ewe

Background:

Chromosomal duplications and aneuploidy can be detrimental to organismal health and fitness (Mazzarella & Schlessinger, 1998). However, since 80% of its genome could be isolated as chromosomal duplication in the laboratory, the nematode C. elegans is relatively insensitive to increased gene dosage. (Hodgkin, 2005). Additionally, worm strains carrying protein fusion reporters, which generate copy number variation, often appear superficially wildtype and are routinely used in gene expression analyses (Sarov et al., 2012).

In this important preprint, the authors characterized the effects of increased gene dosage on gene expression and found the absence of a general dosage compensation mechanism acting at mRNA levels. They also uncovered the role of epigenetic regulation in the varied consequences of increased gene dosage in C. elegans.

Major findings:

  1. Increased DNA copy number generally leads to elevated mRNA expression levels with high gene-to-gene variability.

To investigate the effects of increased gene dosage on mRNA expression, the authors sequenced the DNA and mRNA of two C. elegans strains carrying megabase-scale chromosome duplications and found that genes in the duplicated regions were generally upregulated, suggesting the lack of a dosage compensation mechanism. Interestingly, the authors observed a substantial variation in the expression changes of genes located in the same duplication.

  1. Integrated multi-copy transgene causes a ripple effect that alters the transcriptome.

Next, the authors examined whether a multi-copy transgene, like chromosome duplications, might also cause increase in mRNA levels. Indeed, in a transgenic strain that contained multi-copy GFP-tagged pha-4 (which encodes the FOXA transcription factor important for pharynx development), pha-4 was highly upregulated. Importantly, 871 genes were found to be differentially expressed in the presence of the transgene, with only a small fraction of these being the direct targets of PHA-4, highlighting the indirect effect of increased gene dosage on the transcriptome.

  1. Dosage compensation complex (DCC) reduces the mRNA effects of increased gene dosage in X chromosomal duplications.

In C. elegans, X chromosomal genes are repressed during early meiosis in the germline (Reinke et al., 2000). By comparing two duplications – X-to-I and IV-to-X – the authors found that X chromosomal genes attached to chromosome I were silenced in the germline. However, autosomal genes translocated to chromosome X were not affected by germline repression. Finally, the authors showed that DCC, which normally localizes to and attenuates transcription from chromosome X, may repress the expression of X chromosomal genes in autosome.

What I liked about this preprint:

Duplications and protein fusion transgenes are routinely used as genetic balancers and for gene expression analyses in C. elegans, respectively. Hence, this study’s result of the ripple effects of increased gene dosage on the transcriptome will have widespread implications in C. elegans research.

Questions for the authors:

Have you compared the RNA-seq data between the strains with chromosomal duplications and pha-4::EGFP? Is there a common transcriptional response that associates with chromosomal duplications and copy number variation?

References:  

Hodgkin, J. (2005). Karyotype, ploidy, and gene dosage. WormBook : The Online Review of C. Elegans Biology, 1–9. https://doi.org/10.1895/WORMBOOK.1.3.1

Mazzarella, R., & Schlessinger, D. (1998). Pathological Consequences of Sequence Duplications in the Human Genome. Genome Research, 8(10), 1007–1021. https://doi.org/10.1101/GR.8.10.1007

Reinke, V., Smith, H. E., Nance, J., Wang, J., van Doren, C., Begley, R., Jones, S. J. M., Davis, E. B., Scherer, S., Ward, S., & Kim, S. K. (2000). A Global Profile of Germline Gene Expression in C. elegans. Molecular Cell, 6(3), 605–616. https://doi.org/10.1016/S1097-2765(00)00059-9

Sarov, M., Murray, J. I., Schanze, K., Pozniakovski, A., Niu, W., Angermann, K., Hasse, S., Rupprecht, M., Vinis, E., Tinney, M., Preston, E., Zinke, A., Enst, S., Teichgraber, T., Janette, J., Reis, K., Janosch, S., Schloissnig, S., Ejsmont, R. K., … Hyman, A. A. (2012). A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell, 150(4), 855–866. https://doi.org/10.1016/J.CELL.2012.08.001/ATTACHMENT/3B8E8BAF-0932-4191-8385-7E0187BBA430/MMC7.MOV

 

Tags: aneuploidy, dosage compensation, epigenetics

Posted on: 25th April 2022

doi: https://doi.org/10.1242/prelights.31869

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Author's response

Sevinç Ercan shared

A quick look at differentially expressed genes (19 with padj < 0.05) common to the two duplications and the formid integration strain did not pick up statistically significant categories in Wormbase gene enrichment analysis. Interestingly, GO categories for the few genes reported (q value 0.071) were related to defense and immune responses. Differentially expressed genes common to the two duplication strains (86) pulled up metabolism related categories. Work from other organisms suggest that aneuploidies cause metabolic and proteotoxic stress. Perhaps worms also respond to aneuploidy in a similar way and a more careful study addressing stress could highlight the specific genes or pathways that are involved.

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