Nucleolar dominance and ribosomal RNA gene silencing

Tucker, Sarah; Vitins, Alexa P.; Pikaard, Craig S.

doi:10.1016/j.ceb.2010.03.009

Cited by 108 publications

(97 citation statements)

References 58 publications

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“…Moreover, the classic hybrid-and allopolyploid-associated phenomenon of "nucleolar dominance," i.e., selectively silencing rRNA genes of one parental origin in a hybrid/allopolyploid genome, has been mechanistically established as being dictated by localized epigenetic difference (Chen and Pikaard 1997;Tucker et al 2010). Taken together, these results have pointed to the intriguing possibility that epigenetic mechanisms may indeed have played a prominent role in allopolyploidy-mediated speciation and evolution in plants, which warrants further investigation.…”

Section: Discussionmentioning

confidence: 85%

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

Zhao

Zhu

et al. 2011

Genetics

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Allopolyploidy has played a prominent role in organismal evolution, particularly in angiosperms. Allohexaploidization is a critical step leading to the formation of common wheat as a new species, Triticum aestivum, as well as for bestowing its remarkable adaptability. A recent study documented that the initial stages of wheat allohexaploidization was associated with rampant genetic and epigenetic instabilities at genomic regions flanking a retrotransposon family named Veju. Although this finding is in line with the prevailing opinion of rapid genomic instability associated with nascent plant allopolyploidy, its relevance to speciation of T. aestivum remains unclear. Here, we show that genetic instability at genomic regions flanking the Veju, flanking a more abundant retroelement BARE-1, as well as at a large number of randomly sampled genomic loci, is all extremely rare or nonexistent in preselected individuals representing three sets of independently formed nascent allohexaploid wheat lines, which had a transgenerationally stable genomic constitution analogous to that of T. aestivum. In contrast, extensive and transgenerationally heritable repatterning of DNA methylation at all three kinds of genomic loci were reproducibly detected. Thus, our results suggest that rampant genetic instability associated with nascent allohexaploidization in wheat likely represents incidental and anomalous phenomena that are confined to by-product individuals inconsequential to the establishment of the newly formed plants toward speciation of T. aestivum; instead, extensive and heritable epigenetic remodeling coupled with preponderant genetic stability is generally associated with nascent wheat allohexaploidy, and therefore, more likely a contributory factor to the speciation event(s).

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Section: Discussionmentioning

confidence: 85%

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

Zhao

Zhu

et al. 2011

Genetics

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“…The opposite pattern was clear for the 45S rDNA repeat sequence, which showed an almost 2-fold enrichment over G1 in the late S reads. A much smaller fraction of the 45S rDNA replicates in early and mid S and likely corresponds to a small fraction of 45S copies that are transcriptionally active (Buescher et al, 1984;Tucker et al, 2010). Both of the knob repeat sequences, knob180 and TR-1, replicate almost entirely in the late S fraction, where they are enriched by 1.7-and 3-fold, respectively, relative to G1.…”

Section: Analysis Of Tandem Repeat Sequences In Repli-seq Readsmentioning

confidence: 99%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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“…A particularly clear example of epigenetic control of rDNA is provided by nucleolar dominance in hybrids where the NORs of one parental genome are active, whereas those of the other are inactive (Tucker et al, 2010). An RNAi approach has been used with Arabidopsis suecica, a hybrid of Arabidopsis and Arabidopsis arenosa, to determine factors involved in nucleolar dominance.…”

Section: Nucleolar Chromatin and Epigeneticsmentioning

confidence: 99%