DCC binding and function (ChIP-chip: SDC-2)

In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X gene products between males (1X) and females (2X). Here we identify cis-acting regulatory elements that target the C. elegans X chromosome for repression by the DCC. The DCC binds to discrete, dispersed sites on X of two types. rex sites recruit the DCC in an autonomous, DNA sequence-dependent manner using a 12 bp consensus motif that is enriched on X. This motif is critical for DCC binding, is clustered in rex sites, and confers much of X-chromosome specificity. Motif variants enriched on X by 3.8-fold or more are highly predictive (95%) for rex sites. In contrast, dox sites lack the X-enriched variants and cannot bind the DCC when detached from X. dox sites are more prevalent than rex sites and, unlike rex sites, reside preferentially in promoters of some expressed genes. These findings fulfill predictions for a targeting model in which the DCC binds to recruitment sites on X and disperses to discrete sites lacking autonomous recruitment ability. To relate DCC binding to function, we identified dosage-compensated and non-compensated genes on X. Unexpectedly, many genes of both types have bound DCC, but many do not, suggesting the DCC acts over long distances to repress X gene expression. Remarkably, the DCC binds to autosomes, but at far fewer sites and rarely at consensus motifs. DCC disruption causes opposite effects on expression of X and autosomal genes. The DCC thus acts at a distance to impact expression throughout the genome. Keywords: dosage compensation, condensin, X chromosome, gene expression, epigenetics, C. elegans ChIP-chip experiments included: biological duplicates of SDC-2.

在众多物种中，剂量补偿复合物（dosage compensation complex, DCC）会被靶向至某一性别的X染色体，以平衡雄性（1条X染色体）与雌性（2条X染色体）之间的X染色体基因产物水平。本研究鉴定出可靶向秀丽隐杆线虫（C. elegans）X染色体、并介导DCC对其进行转录抑制的顺式作用调控元件。DCC可结合于X染色体上两类离散分散的结合位点。rex位点可通过X染色体上富集的12bp共有基序，以自主的、依赖DNA序列的方式招募DCC。该基序对DCC结合至关重要，且在rex位点中成簇分布，同时赋予了DCC结合的主要X染色体靶向特异性。在X染色体上富集3.8倍及以上的基序变异体，对rex位点具有高达95%的预测准确率。与之相反，dox位点不含X染色体富集的基序变异体，且当脱离X染色体时无法结合DCC。dox位点的数量多于rex位点，且与rex位点不同，dox位点优先分布于部分活跃表达基因的启动子区域。上述研究结果验证了靶向模型的相关预测：DCC先结合于X染色体上的招募位点，随后扩散至不具备自主招募能力的离散结合位点。为了将DCC结合与其功能关联起来，本研究鉴定了X染色体上受剂量补偿调控与不受剂量补偿调控的基因。出乎意料的是，两类基因中均有部分可结合DCC，但也有大量基因无法结合，这表明DCC可通过远距离作用抑制X染色体基因的表达。值得注意的是，DCC也可结合于常染色体，但结合位点数量远少于X染色体，且极少结合共有基序。破坏DCC会对X染色体与常染色体基因的表达产生相反的调控效果。由此可见，DCC可通过远距离作用影响全基因组的基因表达。关键词：剂量补偿，凝缩蛋白，X染色体，基因表达，表观遗传学，秀丽隐杆线虫；本研究包含的染色质免疫沉淀芯片（ChIP-chip）实验包括：SDC-2的生物学重复两组。