Tools for the assessment of epigenetic regulation

Eaves, Lauren A.; Gardner, Amaree J.; Fry, Rebecca C.

doi:10.1016/b978-0-12-819968-8.00002-0

Cited by 3 publications

(2 citation statements)

References 109 publications

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“…They are repetitive and encode the RNA components of ribosomes, the most ancient and complex of all molecular machines ( Moss et al 2006 ). Despite rDNAs not representing a large proportion of an organism's genome size, they produce around 80–90% of the RNAs found in most cells ( Eaves et al 2020 ) and ribosomal RNAs (rRNAs) accounting for 60% of the ribosomal mass ( O’Connor and Adams 2010 ). Ribosomal DNA repeats are crucial players in maintaining genome stability ( Kobayashi 2006 ) and any disturbance at rDNA loci may have a great impact on cellular processes, including the response to DNA damage and overall cell longevity ( Ganley and Kobayashi 2014 ).…”

Section: Ribosomal Dnas and Transposable Elements: Two Opposing Faces...mentioning

confidence: 99%

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

Garcia,

Kovarik,

Maiwald

et al. 2024

Molecular Biology and Evolution

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Although both are salient features of genomes, at first glance ribosomal DNAs (rDNAs) and transposable elements (TEs) are genetic elements with not much in common: whereas rDNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, TEs are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (rDNAs) versus organization in a dispersed manner (TEs); evolution in a concerted manner (rDNAs) versus evolution by diversification (TEs); and activity that prolongs genomic stability (rDNAs) versus activity that shortens it (TEs). Re-visiting relevant instances in which rDNA-TE interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales; (2) they exchange structural motifs and can enter co-evolution processes; (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging; and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional and evolutionary characteristics of both rDNAs and TEs, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding rDNA-TE associations.

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Section: Ribosomal Dnas and Transposable Elements: Two Opposing Faces...mentioning

confidence: 99%

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

Garcia,

Kovarik,

Maiwald

et al. 2024

Molecular Biology and Evolution

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show abstract

“…Ribosomal RNAs (those encoded by ribosomal DNAs) comprise 80% of the RNA found in a typical cell and account for 60% of the ribosomal mass, having an essential role in protein synthesis (O'Connor and Adams 2010; Eaves et al 2020). In eukaryotes there are four ribosomal RNA genes.…”

Section: Introductionmentioning

confidence: 99%

Evolving together: Cassandra retrotransposons gradually mirror promoter mutations of the 5S rRNA genes

Maiwald

Mann

Garcia

et al. 2023

Preprint

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The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related non-autonomous retrotransposons, so-called Cassandra. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats (LTRs), advantageously providing them with the 5S internal promoter. However, the dynamics of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence information and structural arrangement are still unclear, especially: 1) do we observe repeated or gradual domestication of the highly conserved 5S promoter by Cassandras and 2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements impact Cassandra evolution? Here, we show evidence for gradual co-evolution of Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highly variable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S rDNA promoter mutations of their host genome, likely as an adaptation to the host's specific 5S transcription factors and hence compensating for evolutionary changes in the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem uncorrelated with linked/separated rDNA arrangements. We place all these observations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss Cassandra's origin hypotheses (single or multiple) and Cassandra's possible impact on rDNA and plant genome organization, giving new insights into the interplay of ribosomal genes and transposable elements.

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Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes

Maiwald,

Mann,

Garcia

et al. 2024

Molecular Biology and Evolution

View full text Add to dashboard Cite

The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats, advantageously providing them with the 5S internal promoter. However, the dynamics of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence information and structural arrangement are still unclear, especially: (1) do we observe repeated or gradual domestication of the highly conserved 5S promoter by Cassandras and (2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements impact Cassandra evolution? Here, we show evidence for gradual co-evolution of Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highly variable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S rDNA promoter mutations of their host genome, likely as an adaptation to the host's specific 5S transcription factors and hence compensating for evolutionary changes in the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem uncorrelated with linked/separated rDNA arrangements. We place all these observations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss Cassandra's origin hypotheses (single or multiple) and Cassandra's possible impact on rDNA and plant genome organization, giving new insights into the interplay of ribosomal genes and transposable elements.

show abstract

Tools for the assessment of epigenetic regulation

Cited by 3 publications

References 109 publications

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

Evolving together: Cassandra retrotransposons gradually mirror promoter mutations of the 5S rRNA genes

Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes

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