Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil.
Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA.
DNA Res. 2018 Apr 1;25(2):137-147. doi: 10.1093/dnares/dsx044.
Satellite DNA (satDNA) is an abundant class of non-coding repetitive DNA that is preferentially found as tandemly repeated arrays in gene-poor heterochromatin but is also present in gene-rich euchromatin. Here, we used DNA- and RNA-seq from Gryllus assimilis to address the content and transcriptional patterns of satDNAs. We also mapped RNA-seq libraries for other Gryllus species against the satDNAs found in G. assimilis and G. bimaculatus genomes to investigate their evolutionary conservation and transcriptional profiles in Gryllus. Through DNA-seq read clustering analysis using RepeatExplorer, dotplots analysis and fluorescence in situ hybridization mapping, we found that ∼4% of the G. assimilis genome is represented by 11 well-defined A + T-rich satDNA families. These are mainly located in heterochromatic areas, with some repeats able to form high-order repeat structures. By in silico transcriptional analysis we identified satDNAs that are conserved in Gryllus but differentially transcribed. The data regarding satDNA presence in G. assimilis genome were discussed in an evolutionary context, with transcriptional data enabling comparisons between sexes and across tissues when possible. We discuss hypotheses for the conservation and transcription of satDNAs in Gryllus, which might result from their role in sexual differentiation at the chromatin level, heterochromatin formation and centromeric function.
卫星 DNA（satDNA）是一类丰富的非编码重复 DNA，它优先作为串联重复的基因贫异染色质的阵列存在，但也存在于基因丰富的常染色质中。在这里，我们使用来自 Gryllus assimilis 的 DNA 和 RNA-seq 来解决 satDNA 的内容和转录模式问题。我们还将其他 Gryllus 物种的 RNA-seq 文库映射到在 G. assimilis 和 G. bimaculatus 基因组中发现的 satDNAs 上，以研究它们在 Gryllus 中的进化保守性和转录谱。通过使用 RepeatExplorer 进行 DNA-seq 读聚类分析、点图分析和荧光原位杂交作图，我们发现 G. assimilis 基因组的约 4%由 11 个定义明确的 A+T 丰富的 satDNA 家族组成。这些主要位于异染色质区域，一些重复序列能够形成高级重复结构。通过计算机转录分析，我们鉴定了在 Gryllus 中保守但转录差异的 satDNA。关于 satDNA 在 G. assimilis 基因组中存在的数据在进化背景下进行了讨论，并且在可能的情况下，转录数据能够进行性别和组织之间的比较。我们讨论了 satDNA 在 Gryllus 中保守和转录的假说，这可能是由于它们在染色质水平的性别分化、异染色质形成和着丝粒功能中的作用。
