Combinatorial clustering of distinct DNA motifs directs synergistic binding of Caenorhabditis elegans dosage compensation complex to X chromosomes.
Combinatorial clustering of distinct DNA motifs directs synergistic binding of Caenorhabditis elegans dosage compensation complex to X chromosomes.
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DOI：
10.1073/pnas.2211642119
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发表时间：
2022-09-13
影响因子：
11.1
通讯作者：
Meyer, Barbara J.
中科院分区：
文献类型：
--
作者：
Fuda, Nicholas J.;Brejc, Katjusa;Kruesi, William S.;Ralston, Edward J.;Bigley, Rachel;Shin, Aram;Okada, Miki;Meyer, Barbara J.
多种调节机制平衡哺乳动物、果蝇和线虫（XY/XO 雄性和 XX 雌性/雌雄同体）性别之间的 X 染色体基因表达。我们鉴定了 X 上的 DNA 基序，这些基序在线虫雌雄同体中募集剂量补偿复合物（DCC）以减少 X 染色体表达。 X 上的招募位点（而非常染色体上的区域）包含不同基序的多种组合或一个基序的多个副本。野生型和突变型 X 招募位点的体内和体外 DCC 结合研究验证了基序的使用。我们发现，具有适当方向和间距的不同组合的基序聚类可促进 DCC 结合的协同作用，从而特异性地沿着 X 触发 DCC 组装。我们演示了如何在整个染色体上招募调节复合物以控制其基因表达。通过计算 X 染色体数量来确定性别的生物体利用剂量补偿机制来平衡性别之间的 X 基因表达。通常，调节复合物被招募到一种性别的 X 染色体上以调节基因表达。一个主要的挑战是确定专门针对 X 的调节复合物的机制。在这里，我们鉴定了秀丽隐杆线虫中的关键 X 序列基序，这些基序在雌雄同体中协同作用，以指导剂量补偿复合物（DCC）（一种凝缩蛋白复合物）的 X 特异性募集。我们发现两个 DNA 基序与先前定义的称为 MEX（X 上富集基序）的 12 bp 基序协同介导结合：MEX II（26 bp X 富集基序）和 Motif C（缺乏 X 富集的 9 bp 基序）。将 MEX 和 MEX II 插入 X 上的新位置会创建相当于内源性招募位点的 DCC 结合位点，但仅插入 MEX 或 MEX II 则不会。此外，在具有多个不同基序的内源性招募位点中突变 MEX、MEX II 或基序 C 会显着降低体内 DCC 结合，其程度几乎与突变所有基序相同。改变基序的方向或间距也会减少 DCC 结合。因此，通过基序组合聚类的 DCC 结合协同作用会特异性地在 X 染色体上触发 DCC 组装。使用体外 DNA 结合测定，我们精炼了对于 DCC 结合至关重要的基序和侧翼序列的特征。我们的工作揭示了在整个染色体上招募调节复合物以控制其基因表达的一般原理。
Diverse regulatory mechanisms balance X-chromosome gene expression between sexes in mammals, fruit flies, and nematodes (XY/XO males and XX females/hermaphrodites). We identify DNA motifs on X that recruit dosage compensation complexes (DCCs) in nematode hermaphrodites to reduce X-chromosome expression. Recruitment sites on X, but not regions on autosomes, contain diverse combinations of different motifs or multiple copies of one motif. DCC binding studies in vivo and in vitro of wild-type and mutant X-recruitment sites validate motif usage. We find that clustering of motifs in different combinations with appropriate orientation and spacing promotes synergy in DCC binding, thereby triggering DCC assembly specifically along X. We demonstrate how regulatory complexes can be recruited across an entire chromosome to control its gene expression. Organisms that count X-chromosome number to determine sex utilize dosage compensation mechanisms to balance X-gene expression between sexes. Typically, a regulatory complex is recruited to X chromosomes of one sex to modulate gene expression. A major challenge is to determine the mechanisms that target regulatory complexes specifically to X. Here, we identify critical X-sequence motifs in Caenorhabditis elegans that act synergistically in hermaphrodites to direct X-specific recruitment of the dosage compensation complex (DCC), a condensin complex. We find two DNA motifs that collaborate with a previously defined 12-bp motif called MEX (motif enriched on X) to mediate binding: MEX II, a 26-bp X-enriched motif and Motif C, a 9-bp motif that lacks X enrichment. Inserting both MEX and MEX II into a new location on X creates a DCC binding site equivalent to an endogenous recruitment site, but inserting only MEX or MEX II alone does not. Moreover, mutating MEX, MEX II, or Motif C in endogenous recruitment sites with multiple different motifs dramatically reduces DCC binding in vivo to nearly the same extent as mutating all motifs. Changing the orientation or spacing of motifs also reduces DCC binding. Hence, synergy in DCC binding via combinatorial clustering of motifs triggers DCC assembly specifically on X chromosomes. Using an in vitro DNA binding assay, we refine the features of motifs and flanking sequences that are critical for DCC binding. Our work reveals general principles by which regulatory complexes can be recruited across an entire chromosome to control its gene expression.
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影响因子：
64.5
作者：
CHUANG, PT;ALBERTSON, DG;MEYER, BJ
通讯作者：
MEYER, BJ
影响因子：
56.9
作者：
Chuang, PT;Lieb, JD;Meyer, BJ
通讯作者：
Meyer, BJ
影响因子：
3.3
作者：
Farboud, Behnom;Severson, Aaron F.;Meyer, Barbara J.
通讯作者：
Meyer, Barbara J.
影响因子：
64.5
作者：
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通讯作者：
Meyer BJ
影响因子：
7.7
作者：
Kruesi WS;Core LJ;Waters CT;Lis JT;Meyer BJ
通讯作者：
Meyer BJ