Despite life’s diversity, studies of variation often remind us of our shared evolutionary past. Abundant genome sequencing and analyses of gene regulatory networks illustrate that genes and entire pathways are conserved, reused, and elaborated in the evolution of diversity. Predating these discoveries, 19th-century embryologists observed that though morphology at birth varies tremendously, certain stages of vertebrate embryogenesis appear remarkably similar across vertebrates. In the mid to late 20th century, anatomical variability of early and late stage embryos and conservation of mid-stages embryos (the ‘phylotypic’ stage) was named the hourglass model of diversification. This model has found mixed support in recent analyses comparing gene expression across species possibly owing to differences in species, embryonic stages, and gene sets compared. We compare 186 microarray and RNA-seq data sets covering embryogenesis in six vertebrate species. We use an unbiased clustering approach to group stages of embryogenesis by transcriptomic similarity and ask whether gene expression similarity of clustered embryonic stages deviates from a null expectation. We characterize expression conservation pattern of each gene at each evolutionary node after correcting for phylogenetic non-independence. We find significant enrichment of genes exhibiting early conservation, hourglass, late conservation patterns in both microarray and RNA-seq data sets. Enrichment of genes showing patterned conservation through embryogenesis indicates diversification of embryogenesis may be temporally constrained. However, the circumstances under which each pattern emerges remain unknown and require both broad evolutionary sampling and systematic examination of embryogenesis across species.
The ribosomal DNA (rDNA) in Saccharomyces cerevisiae is in one tandem repeat array on Chromosome XII. Two regions within each repetitive element, called intergenic spacer 1 (IGS1) and IGS2, are important for organizing the rDNA within the nucleolus. The Smc5/6 complex localizes to IGS1 and IGS2. We show that Smc5/6 has a function in the rDNA beyond its role in homologous recombination (HR) at the replication fork barrier (RFB) located in IGS1. Fob1 is required for optimal binding of Smc5/6 at IGS1 whereas the canonical silencing factor Sir2 is required for its optimal binding at IGS2, independently of Fob1. Through interdependent interactions, Smc5/6 stabilizes Sir2 and Cohibin at both IGS and its recovery at IGS2 is important for nucleolar compaction and transcriptional silencing, which in turn supports rDNA stability and lifespan.
15Despite the diversity of life, studies of variation across animals often remind us of our deep evolutionary 16 past. Abundant genome sequencing over the last ~25 years reveals remarkable conservation of genes and 17 recent analyses of gene regulatory networks illustrate that not only genes but entire pathways are conserved, 18 reused, and elaborated in the evolution of diversity. Predating these discoveries, 19 th -century embryologists 19 observed that though morphology at birth varies tremendously, certain stages of embryogenesis appear 20 remarkably similar across vertebrates. Specifically, while early and late stages are variable across species, 21 anatomy of mid-stages embryos (the phylotypic stage) is conserved. This model of vertebrate development 22
Highlights:• Smc5/6 is important for transcriptional silencing in the rDNA.• Smc5/6 tethers the rDNA array to the periphery.• Transcriptional silencing of ncRNA at NTS1 and NTS2 is differentially regulated.• Smc5/6 has a role in rDNA maintenance independent of HR processing at the RFB.• Fob1-independent disruption of Smc5/6 at NTS2 leads to lifespan reduction .
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