Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion

Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401727 ◽

2020 ◽

Vol 10 (11) ◽

pp. 4129-4146

Author(s):

Leonardo G. de Lima ◽

Stacey L. Hanlon ◽

Jennifer L. Gerton

Keyword(s):

Repetitive Sequences ◽

Specific Pattern ◽

Evolutionary Patterns ◽

Satellite Dnas ◽

Evolutionary Pattern ◽

Functional Roles ◽

Drosophila Phylogeny ◽

Species Specific ◽

Future Work ◽

Eukaryotic Genomes

Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.

Download Full-text

Chromosome Y genetic variants: impact in animal models and on human disease

Physiological Genomics ◽

10.1152/physiolgenomics.00074.2015 ◽

2015 ◽

Vol 47 (11) ◽

pp. 525-537 ◽

Cited By ~ 17

Author(s):

J. W. Prokop ◽

C. F. Deschepper

Keyword(s):

Animal Models ◽

Genetic Variants ◽

Repetitive Sequences ◽

Cellular Functions ◽

Chromosome Y ◽

Functional Roles ◽

Disease States ◽

Regulatory Changes ◽

Causal Variants ◽

The Many

Chromosome Y (chrY) variation has been associated with many complex diseases ranging from cancer to cardiovascular disorders. Functional roles of chrY genes outside of testes are suggested by the fact that they are broadly expressed in many other tissues and correspond to regulators of basic cellular functions (such as transcription, translation, and protein stability). However, the unique genetic properties of chrY (including the lack of meiotic crossover and the presence of numerous highly repetitive sequences) have made the identification of causal variants very difficult. Despite the prior lack of reliable sequences and/or data on genetic polymorphisms, earlier studies with animal chrY consomic strains have made it possible to narrow down the phenotypic contributions of chrY. Some of the evidence so far indicates that chrY gene variants associate with regulatory changes in the expression of other autosomal genes, in part via epigenetic effects. In humans, a limited number of studies have shown associations between chrY haplotypes and disease traits. However, recent sequencing efforts have made it possible to greatly increase the identification of genetic variants on chrY, which promises that future association of chrY with disease traits will be further refined. Continuing studies (both in humans and in animal models) will be critical to help explain the many sex-biased disease states in human that are contributed to not only by the classical sex steroid hormones, but also by chrY genetics.

Download Full-text

Intron size minimisation in teleosts

10.21203/rs.3.rs-362877/v1 ◽

2021 ◽

Author(s):

Lars Martin Jakt ◽

Arseny Dubin ◽

Steinar Daae Johansen

Keyword(s):

Rna Splicing ◽

Metabolic Cost ◽

Intron Size ◽

Evolutionary Time ◽

Functional Roles ◽

Mature Transcript ◽

Genome Size Evolution ◽

Size Evolution ◽

Random Manner ◽

Suitable System

Abstract BackgroundSpliceosomal introns are parts of primary transcripts that are removed by RNA splicing. Although introns apparently do not contribute to the function of the mature transcript, in vertebrates they comprise the majority of the transcribed region increasing the metabolic cost of transcription. The persistence of long introns across evolutionary time suggests functional roles that can offset this metabolic cost. The teleosts comprise one of the largest vertebrate clades. They have unusually compact and variable genome sizes and provide a suitable system for analysing intron evolution. ResultsWe have analysed intron lengths in 172 vertebrate genomes and show that teleost intron lengths are relatively short, highly variable and bimodally distributed. Introns that were long in teleosts were also found to be long in mammals and were more likely to be found in regulatory genes and to contain conserved sequences. Our results argue that intron length has decreased in parallel in a non-random manner throughout teleost evolution and represent a deviation from the ancestral state.ConclusionOur observations indicate an accelerated rate of intron size evolution in the teleosts and that teleost introns can be divided into two classes by their length. Teleost intron sizes have evolved primarily as a side-effect of genome size evolution and small genomes are dominated by short introns ( < 256 bp). However, a non-random subset of introns has resisted this process across the teleosts and these are more likely have functional roles in all vertebrate clades

Download Full-text