X染色体剂量补偿的机制已在代表共有性染色体祖先进化枝的一些模型物种中进行了广泛研究。然而,作为性染色体进化的功能,每个进化枝的多样性在很大程度上是未知的。这里,我们将自己锚定在线虫秀丽隐杆线虫上,通过专门的染色体结构维持(SMC)复合物,发生了经过充分研究的剂量补偿机制,并探讨线虫周围系统发育中剂量补偿的多样性。通过对C.elegan剂量补偿复合体的系统发育分析和对其表观遗传特征的调查,包括X特异性拓扑关联域(TADs)和H4K20me1的X富集,我们发现凝缩素介导的机制最近在谱系中进化,通过SMC-4复制导致秀丽隐杆线虫。有趣的是,Pristionchuspacificus中SMC-4的独立重复和X特异性TAD的存在表明凝缩素介导的剂量补偿不止一次。在几种线虫物种中基因表达的mRNA-seq分析表明,剂量补偿本身是祖先的,正如古代XO性别决定系统所预期的那样。表明祖先机制,H4K20me1富集在动物的X染色体上,它不包含X特异性TAD或SMC-4旁系同源物。一起,我们的结果表明,在C.线虫剂量补偿系统是令人惊讶的新,凝集素可能在线虫中被反复增选,这表明进化剂量补偿的全染色体基因调控机制的过程受到限制。
■X染色体剂量补偿机制在性染色体进化过程中响应Y染色体变性而进化。然而,建立剂量补偿不是终点。随着性染色体的改变,剂量补偿策略也可能发生了变化。在这项研究中,我们进行了围绕秀丽隐杆线虫的系统发育和表观基因组分析,发现秀丽隐杆线虫的凝缩蛋白介导的剂量补偿机制是令人惊讶的新,并在祖先机制的存在下进化。有趣的是,基于凝缩素的剂量补偿可能在线虫谱系中不止一次进化,另一次是在Pristionchus.一起,我们的工作强调了一个以前未被重视的剂量补偿机制的多样性,并提出了在现有机制存在的情况下发展新机制的制约因素。
Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegans dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae, which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained.
UNASSIGNED: X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus. Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.