Chromatin epimutations in transgenerational epigenetic inheritance. Chromatin epimutations in transgenerational epigenetic inheritance

Epigenetic inheritance is the transmission of altered gene expression states across dividing cells without DNA sequence variation. Induced epigenetic changes (epimutations) have been extensively studied, but importantly, epimutations also occur spontaneously in a manner reminiscent of DNA sequence change. Small RNAs are established as a source of spontaneous epimutations which transmit gene expression changes over multiple generations in C.elegans. These changes are generally short lived, but rarely long-lived changes occur. Given that chromatin state is a critical regulator of gene expression, we explored whether chromatin states also undergo spontaneous change and whether this could be a potential alternative mechanism for transgenerational epigenetic inheritance. We compared the chromatin profiles and gene expression profiles at matched time points from a twenty generation bottlenecked lineage of C.elegans. We found that heritable changes in gene expression arose at a higher rate than the estimate for DNA sequence variation, indicating that these were true epigenetic events. In addition to recapitulating the known role for small RNAs, we provide evidence for chromatin mediated epimutations as an alternative mechanism driving epigenetic inheritance. Chromatin epimutations were heritable, enriched in the germline and synchronised with inherited gene expression changes. As with small RNA mediated epimutations, they were generally short lived with a tendency to resolve to baseline after 2-3 generations. A subset of chromatin epimutations however were long lasting, and these were uniquely enriched in piRNA clusters. Genes with long lived epimutations were implicated in multiple components of xenobiotic response pathways. This points to a mechanism for epigenetic ‘anticipation’ of environmental stressors. Adaptive traits driven by epimutations may be selected for under adverse conditions and lost on return to normal conditions, enabling soft adaptation in the absence of genetic sequence change. Overall design: Examination of time matched RNA, ATAC and small RNA from 10 time points across 3 independent lineages of C.elegans

表观遗传（Epigenetic inheritance）指不发生DNA序列变异（DNA sequence variation）的前提下，将基因表达（gene expression）的改变状态传递至分裂子代细胞的遗传过程。诱导产生的表观遗传改变（表观突变，epimutations）已得到广泛研究，但值得注意的是，表观突变也可自发产生，其发生模式与DNA序列变异的发生模式类似。小RNA（small RNAs）已被证实为自发表观突变的来源之一，这类突变可在秀丽隐杆线虫（C.elegans）中跨多代传递基因表达的改变。这类改变通常仅短暂存在，但极少数情况下会出现长期维持的改变。
鉴于染色质（chromatin）状态是基因表达的关键调控因子，本研究探讨了染色质状态是否也会发生自发改变，以及这是否可能成为跨代表观遗传（transgenerational epigenetic inheritance）的潜在替代机制。我们对经过20代瓶颈培养的秀丽隐杆线虫（C.elegans）谱系的匹配时间点样本，开展了染色质谱（chromatin profiles）与基因表达谱（gene expression profiles）的对比分析。研究发现，可遗传的基因表达改变的发生速率高于DNA序列变异的预估速率，表明这类改变属于真正的表观遗传事件。除了验证了小RNA在表观遗传中的已知作用外，本研究还提供了证据，证明染色质介导的表观突变（chromatin mediated epimutations）是驱动表观遗传的另一类机制。
染色质表观突变具有可遗传性，在生殖系（germline）中富集，且与遗传获得的基因表达改变同步发生。与小RNA介导的表观突变类似，这类突变通常也仅短暂存在，往往在2-3代后恢复至基线水平。但有一部分染色质表观突变可长期维持，这类突变仅在piRNA簇（piRNA clusters）中富集。携带长期维持的表观突变的基因，涉及异生物质应答通路（xenobiotic response pathways）的多个组分。这提示存在一种表观遗传层面的环境应激“预适应”机制。由表观突变驱动的适应性性状，可在逆境条件下被选择保留，在恢复至正常环境后又可丢失，从而在不发生DNA序列变异的情况下实现柔性适应。
实验整体设计：对3个独立的秀丽隐杆线虫（C.elegans）谱系的10个匹配时间点样本，开展RNA、转座酶可及性染色质测序（ATAC）与小RNA的检测分析。