publication . Article . Other literature type . 2021

Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number

Francesca Lopez; Antoine Fort; Luca Tadini; Aline V. Probst; Marcus McHale; James Friel; Peter Ryder; Frédéric Pontvianne; Paolo Pesaresi; Ronan Sulpice; ...
Open Access
  • Published: 02 Feb 2021 Journal: The Plant Cell (eissn: 1532-298X, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract The 45S rRNA genes (rDNA) are amongst the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as ‘back-up’ copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte we reduced 45S rDNA copy number to a plateau of ∼10%. Two independent lines had rDNA copy numbers reduced by up to 90% at the T7 generation, named Low Copy Number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates and steady-state levels remained the s...
Persistent Identifiers
free text keywords: Plant Science, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Settore BIO/18 - Genetica, Regular Issue, Gene dosage, Copy-number variation, Genetics, Segmental duplication, Biology, Low copy number, Genome, Dosage compensation, Ribosomal RNA, Gene
59 references, page 1 of 4

Benoit, M., Simon, L., Desset, S., Duc, C., Cotterell, S., Poulet, A., Le Goff, S., Tatout, C., and Probst, A. V. (2019). Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. New Phytol. 221: 385-398.

Bersaglieri, C. and Santoro, R. (2019). Genome Organization in and around the Nucleolus. Cells 8: 579.

Beying, N., Schmidt, C., Pacher, M., Houben, A., and Puchta, H. (2020). CRISPR-Cas9- mediated induction of heritable chromosomal translocations in Arabidopsis. Nat. Plants 6: 638-645.

Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. [OpenAIRE]

Brandt, S., Fachinger, S., Tohge, T., Fernie, A.R., Braun, H.-P., and Hildebrandt, T.M. (2018). Extended darkness induces internal turnover of glucosinolates in Arabidopsis thaliana leaves. PLoS One 13: e0202153.

Bray, N.L., Pimentel, H., Melsted, P., and Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34: 525-527. [OpenAIRE]

Buescher, P.J., Phillips, R.L., and Brambl, R. (1984). Ribosomal RNA contents of maize genotypes with different ribosomal RNA gene numbers. Biochem. Genet. 22: 923-930.

Chandrasekhara, C., Mohannath, G., Blevins, T., Pontvianne, F., and Pikaard, C.S. (2016). Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in arabidopsis. Genes Dev. 30: 177-190.

Chen, Z.J. and Pikaard, C.S. (1997). Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev. 11: 2124-2136. [OpenAIRE]

Copenhaver, G.P. and Pikaard, C.S. (1996). RFLP and physical mapping with an rDNAspecific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. Plant J. 9: 259-72.

Cubbon, A., Ivancic-Bace, I., and Bolt, E.L. (2018). CRISPR-Cas immunity, DNA repair and genome stability. Biosci. Rep. 38: 1-10.

Feng, W., Hale, C.J., Over, R.S., Cokus, S.J., Jacobsen, S.E., and Michaels, S.D. (2017). Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage. Proc. Natl. Acad. Sci. U. S. A. 114: 406-411.

Folta, K.M. and Kaufman, L.S. (2007). Isolation of Arabidopsis nuclei and measurement of gene transcription rates using nuclear run-on assays. Nat. Protoc. 1: 3094-3100. [OpenAIRE]

French, S.L., Osheim, Y.N., Cioci, F., Nomura, M., and Beyer, A.L. (2003). In Exponentially Growing Saccharomyces cerevisiae Cells, rRNA Synthesis Is Determined by the Summed RNA Polymerase I Loading Rate Rather than by the Number of Active Genes. Mol. Cell. Biol. 23: 1558-1568.

Grob, S., Schmid, M.W., Luedtke, N.W., Wicker, T., and Grossniklaus, U. (2013). Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol. 14: 1-19.

59 references, page 1 of 4
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