Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.
Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.
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DOI：
10.1371/journal.pgen.1010705
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发表时间：
2023-04
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影响因子：
4.5
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中科院分区：
文献类型：
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尽管最近在体外凝缩蛋白活性的单分子和结构分析方面取得了进展，但导致特定染色体组织的功能性凝缩蛋白装载和环挤压的机制仍不清楚。在酿酒酵母中，最突出的凝聚蛋白装载位点是染色体XII上的rDNA位点，但其重复性阻碍了对单个基因的严格分析。一个同样突出的非rdna凝聚蛋白位点位于染色体III （chrIII）上。它位于一种被称为RDT1的非编码RNA基因的启动子中，该基因位于重组增强子（RE）的一个片段中，该片段决定了mata特异性的chrIII组织。在这里，我们意外地发现凝聚蛋白通过与Fob1、Tof2和cohibin （Lrs4/Csm1）的分层相互作用被募集到MATa细胞的RDT1启动子上，这组核核因子也将凝聚蛋白募集到rDNA上。Fob1在体外直接与该位点结合，而其在体内的结合依赖于邻近的Mcm1/α2结合位点，该位点提供了MATa细胞特异性。我们还发现了由Fob1和cohibin锚定在RDT1上的凝缩蛋白驱动的环挤压的证据，该环向chrIII右臂的MATa方向单向延伸，支持在交配型转换过程中供体偏好。因此，酿酒酵母chrii为程序化凝缩蛋白介导的染色体构象的研究提供了一个新的平台。凝缩蛋白是一种保守的蛋白质复合物，在有丝分裂过程中通过蛋白质相互作用和DNA环挤压的结合使染色体紧密。关于凝缩蛋白装载到染色质上的机制和环挤压过程的方向性，这可能是生物体特异性的，目前有积极的讨论。在出芽酵母中，单凝聚蛋白复合物在体外进行单侧环挤压，但没有特定凝聚蛋白招募位点的例子，在体内可以机械地研究环挤压。我们之前在III号染色体的重组增强子位点上发现了一个新的凝聚蛋白招募位点，它控制着顺式结构的构象。我们现在报告了凝聚蛋白在染色体III上募集的机制，发现它是通过Fob1锚定在染色质上的“核核”蛋白复合物发生的，也被称为将凝聚蛋白募集到核糖体DNA上。在III号染色体上，Fob1与MADS-box转录因子Mcm1合作，特异性募集MATa细胞中的凝缩蛋白，从而提供细胞类型调节。此外，我们在III号染色体上观察到由Fob1锚定的凝缩蛋白介导的环挤压的证据。在未来，酵母III号染色体应该提供一个强大的遗传工具，以了解可调节的凝聚蛋白装载和环挤出，从体内的一个位点组织染色体组织。
Despite recent advances in single-molecule and structural analysis of condensin activity in vitro, mechanisms of functional condensin loading and loop extrusion that lead to specific chromosomal organization remain unclear. In Saccharomyces cerevisiae, the most prominent condensin loading site is the rDNA locus on chromosome XII, but its repetitiveness deters rigorous analysis of individual genes. An equally prominent non-rDNA condensin site is located on chromosome III (chrIII). It lies in the promoter of a putative non-coding RNA gene called RDT1, which is in a segment of the recombination enhancer (RE) that dictates MATa-specific chrIII organization. Here, we unexpectedly find that condensin is recruited to the RDT1 promoter in MATa cells through hierarchical interactions with Fob1, Tof2, and cohibin (Lrs4/Csm1), a set of nucleolar factors that also recruit condensin to the rDNA. Fob1 directly binds to this locus in vitro, while its binding in vivo depends on an adjacent Mcm1/α2 binding site that provides MATa cell specificity. We also uncover evidence for condensin-driven loop extrusion anchored by Fob1 and cohibin at RDT1 that unidirectionally extends toward MATa on the right arm of chrIII, supporting donor preference during mating-type switching. S. cerevisiae chrIII therefore provides a new platform for the study of programmed condensin-mediated chromosome conformation. Condensin is a conserved protein complex that compacts chromosomes during mitosis through a combination of protein-protein interactions and DNA loop extrusion. There is active discussion regarding the mechanisms of condensin loading onto chromatin and directionality of the loop extrusion process, which may be organism specific. In budding yeast, the single condensin complex performs one-sided loop extrusion in vitro, but there are no examples of specific condensin recruitment sites where loop extrusion can be mechanistically studied in vivo. We previously identified a novel condensin recruitment site on chromosome III at the recombination enhancer locus, which controls structural conformation in cis. We now report the mechanism of condensin recruitment onto chromosome III, discovering it occurs through a complex of ‘nucleolar’ proteins anchored onto chromatin by Fob1, also known to recruit condensin onto the ribosomal DNA. On chromosome III, Fob1 cooperates with a MADS-box transcription factor, Mcm1, to specifically recruit condensin in MATa cells, thus providing cell type regulation. Furthermore, we observed evidence of condensin-mediated loop extrusion anchored by Fob1 on chromosome III. In the future, yeast chromosome III should provide a powerful genetic tool for understanding regulatable condensin loading and loop extrusion that organizes chromosome organization from a single site in vivo.
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影响因子：
16
作者：
Ivessa, AS;Lenzmeier, BA;Zakian, VA
通讯作者：
Zakian, VA
DOI：
10.1126/science.aar7831
发表时间：
2018-04-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Ganji M;Shaltiel IA;Bisht S;Kim E;Kalichava A;Haering CH;Dekker C
通讯作者：
Dekker C
DOI：
10.1073/pnas.88.23.10966
发表时间：
1991-12-01
影响因子：
11.1
作者：
ELBLE, R;TYE, BK
通讯作者：
TYE, BK
影响因子：
48
作者：
Hsieh, Tsung-Han S.;Fudenberg, Geoffrey;Rando, Oliver J.
通讯作者：
Rando, Oliver J.
影响因子：
10.5
作者：
Huang, Julie;Brito, Ilana L.;Moazed, Danesh
通讯作者：
Moazed, Danesh