Giemsa staining of metaphase chromosomes results in a characteristic banding useful for identification of chromosomes and its alterations. We have investigated in silico whether Giemsa bands (G bands) correlate with epigenetic and topological features of the interphase genome. Staining of G‐positive bands decreases with GC content; nonetheless, G‐negative bands are GC heterogeneous. High GC bands are enriched in active histone marks, RNA polymerase II, and SINEs and associate with gene richness, gene expression, and early replication. Low GC bands are enriched in repressive marks, lamina‐associated domains, and LINEs. Histone H1 variants distribute heterogeneously among G bands: H1X is enriched at high GC bands and H1.2 is abundant at low GC, compacted bands. According to epigenetic features and H1 content, G bands can be organized in clusters useful to compartmentalize the genome. Indeed, we have obtained Hi‐C chromosome interaction maps and compared topologically associating domains (TADs) and A/B compartments to G banding. TADs with high H1.2/H1X ratio strongly overlap with B compartment, late replicating, and inaccessible chromatin and low GC bands. We propose that GC content is a strong driver of chromatin compaction and 3D genome organization, that Giemsa staining recapitulates this organization denoted by high‐throughput techniques, and that H1 variants distribute at distinct chromatin domains.

中文翻译：

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富含组蛋白H1.2的TAD与B区隔，染色质难以接近以及富含AT的Giemsa谱带强烈重叠

中期染色体的Giemsa染色导致特征性条带，可用于鉴定染色体及其变异。我们在计算机上进行了调查Giemsa谱带（G谱带）是否与相间基因组的表观遗传和拓扑特征相关。G阳性条带的染色随着GC含量的降低而降低；但是，G负带是GC异质的。高GC谱带富含活性组蛋白标记，RNA聚合酶II和SINE，并与基因丰富度，基因表达和早期复制相关。低GC谱带富含抑制标记，与椎板相关的结构域和LINE。组蛋白H1变体在G条带之间异质分布：H1X在高GC条带富集，而H1.2在低GC压缩条带中富集。根据表观遗传学特征和H1含量，可以将G条带组织成簇，用于分隔基因组。的确，我们已经获得了Hi-C染色体相互作用图谱，并将拓扑关联域（TAD）和A / B区室与G条带进行了比较。具有高H1.2 / H1X比率的TAD与B区室，晚期复制，难以获得的染色质和低GC谱带强烈重叠。我们认为，GC含量是染色质紧实和3D基因组组织的强大驱动力，Giemsa染色概括了这种由高通量技术表示的组织，并且H1变体分布在不同的染色质结构域。