Leitch Andrew R, Ma Lu, Dodsworth Steven, Fuchs Jörg, Houben Andreas, Leitch Ilia J
School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
Plants (Basel). 2023 May 30;12(11):2159. doi: 10.3390/plants12112159.
Angiosperm genome sizes (GS) range ~2400-fold and comprise genes and their regulatory regions, repeats, semi-degraded repeats, and 'dark matter'. The latter represents repeats so degraded that they can no longer be recognised as repetitive. In exploring whether the histone modifications associated with chromatin packaging of these contrasting genomic components are conserved across the diversity of GS in angiosperms, we compared immunocytochemistry data for two species whose GS differ ~286-fold. We compared published data for with a small genome (GS = 157 Mbp/1C) with newly generated data from , which has a giant genome (GS = 45,000 Mbp/1C). We compared the distributions of the following histone marks: H3K4me1, H3K4me2, H3K9me1, H3K9me2, H3K9me3, H3K27me1, H3K27me2, and H3K27me3. Assuming these histone marks are associated with the same genomic features across all species, irrespective of GS, our comparative analysis enables us to suggest that while H3K4me1 and H3K4me2 methylation identifies genic DNA, H3K9me3 and H3K27me3 marks are associated with 'dark matter', H3K9me1 and H3K27me1 mark highly homogeneous repeats, and H3K9me2 and H3K27me2 mark semi-degraded repeats. The results have implications for our understanding of epigenetic profiles, chromatin packaging and the divergence of genomes, and highlight contrasting organizations of the chromatin within the nucleus depending on GS itself.
被子植物的基因组大小（GS）范围相差约2400倍，包括基因及其调控区域、重复序列、半降解重复序列和“暗物质”。后者指那些降解程度极高以至于无法再被识别为重复序列的重复片段。在探究与这些截然不同的基因组成分的染色质包装相关的组蛋白修饰在被子植物的各种GS中是否保守时，我们比较了GS相差约286倍的两个物种的免疫细胞化学数据。我们将已发表的一个小基因组（GS = 157 Mbp/1C）的数据与来自一个大基因组（GS = 45,000 Mbp/1C）的新生成数据进行了比较。我们比较了以下组蛋白标记的分布：H3K4me1、H3K4me2、H3K9me1、H3K9me2、H3K9me3、H3K27me1、H3K27me2和H3K27me3。假设这些组蛋白标记在所有物种中都与相同的基因组特征相关，而与GS无关，我们的比较分析使我们能够提出，虽然H3K4me1和H3K4me2甲基化识别基因DNA，但H3K9me3和H3K27me3标记与“暗物质”相关，H3K9me1和H3K27me1标记高度同质的重复序列，H3K9me2和H3K27me2标记半降解的重复序列。这些结果对我们理解表观遗传图谱、染色质包装和基因组的分化具有启示意义，并突出了细胞核内染色质根据GS本身的不同组织形式。
