Binding of an X-specific condensin correlates with a reduction in active histone modifications at gene regulatory elements

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In C. elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using ChIP-seq and mRNA-seq. Across the X, DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements. Overall design: Included are ChIP-seq profiles data from C. elegans mixed stage embryos and L3 larva. Data was collected from two to three replicates. ChIP-seq data sets in N2, H3K9me3 null (GW638), X;A fusion (15eh1, YPT41), DCC mutant (CB428), and DCC RNAi knockdown (DPY-27 RNAi) strains were generated using antibodies against three dosage compensation complex proteins (SDC-3, CAPG-1, and DPY-27), histone modifications H3K4me3, H3K27ac, H4K16ac, H4panAc, H3ac, H3K4me1, H3K27me1, H3K27me2, H3K9me3, and H4K20me1, the histone protein H3, IgG, and chromatin associated proteins MDT-15, CBP-1, PQN-85, AMA-1, RNA Pol II, and PHA-4::GFP. PHA-4 was pulled down using anti-GFP in OP37[PHA-4::GFP] strain. We additionally include four replicates of RNA-seq data in L3 larva N2 and X;II and X;V fusion strains.

凝缩蛋白（Condensins）是一类进化保守的蛋白质复合物，既参与细胞分裂过程中的染色体分离，也在细胞间期维持基因组的正常三维构象。
在秀丽隐杆线虫（C. elegans）中，一类特化的凝缩蛋白构成了剂量补偿复合物（DCC）的核心组分，能够结合X染色体并抑制其转录。
本研究采用染色质免疫共沉淀测序（ChIP-seq）与mRNA测序（mRNA-seq）技术，分析了DCC的定位特征，以及DCC缺失对组蛋白修饰、转录因子结合与基因表达的调控影响。
在X染色体全域，DCC特异性富集于活跃染色质的可及基因调控位点，而非异染色质区域。
DCC可显著降低激活型组蛋白修饰（包括H3K4me3与H3K27ac）的水平，但对抑制型组蛋白修饰H3K9me3无明显调控作用。
在X染色体-常染色体融合染色体中，DCC向常染色体序列的扩散可局部抑制基因表达，从而直接建立了DCC结合与转录抑制之间的因果关联。
综合上述实验结果，本研究证实DCC介导的转录抑制与X染色体基因调控元件的活性降低密切相关。
实验设计概述：本数据集涵盖秀丽隐杆线虫混合阶段胚胎与L3期幼虫的ChIP-seq谱数据，所有数据均设置2-3次生物学重复。
本次ChIP-seq实验覆盖以下品系：野生型N2品系、H3K9me3敲除品系（GW638）、X-常染色体融合品系（15eh1、YPT41）、DCC突变体品系（CB428）以及DCC RNA干扰敲低品系（DPY-27 RNAi）。实验所用抗体靶向三类DCC核心蛋白（SDC-3、CAPG-1与DPY-27）、12种组蛋白修饰（H3K4me3、H3K27ac、H4K16ac、H4panAc、H3ac、H3K4me1、H3K27me1、H3K27me2、H3K9me3与H4K20me1）、组蛋白H3、免疫球蛋白G（IgG），以及7种染色质相关蛋白（MDT-15、CBP-1、PQN-85、AMA-1、RNA聚合酶II（RNA Pol II）与PHA-4::GFP融合蛋白）。其中PHA-4融合蛋白通过抗GFP抗体在OP37[PHA-4::GFP]品系中完成免疫沉淀富集。
本数据集额外包含L3期幼虫野生型N2品系、X;II融合品系与X;V融合品系的4次生物学重复RNA-seq数据。