Drosophila TDP-43 RNA-Binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers and Polycomb Response Elements.
Drosophila TDP-43 RNA-Binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers and Polycomb Response Elements.
复制标题
DOI：
10.1371/journal.pgen.1006331
复制
发表时间：
2016-09
期刊：
影响因子：
4.5
通讯作者：
Dorsett D
中科院分区：
文献类型：
--
作者：
Swain A;Misulovin Z;Pherson M;Gause M;Mihindukulasuriya K;Rickels RA;Shilatifard A;Dorsett D
内聚蛋白复合物介导姐妹染色单体内聚并参与调节生长和发育的基因的转录控制。黏结蛋白活性的大量降低改变了许多基因的转录，而不破坏染色体分离。果蝇Nipped-B蛋白将粘聚蛋白装载到染色体上，并且Nipped-B和粘聚蛋白一起占据了所有活性转录增强子和大部分活性基因。目前尚不清楚为什么有些活性基因能结合高水平的黏结蛋白，而有些则不能。本研究表明TBPH和Lark rna结合蛋白影响Nipped-B和黏结蛋白与基因和基因调控序列的结合。在体外，TBPH和Lark蛋白特异性结合由Nipped-B和黏结蛋白占据的基因产生的rna。通过基因组染色质免疫沉淀，这些rna结合蛋白也结合到染色体内聚蛋白结合基因、增强子和多梳反应元件（PREs）上。RNAi缺失表明TBPH促进了Nipped-B和黏结蛋白与基因和调控序列的关联。云雀减少了Nipped-B和黏结蛋白在许多启动子上的结合，并帮助它们与几个大的增强子结合。相反，Nipped-B促进TBPH和Lark与基因和调控序列的关联，并在亲和层析和免疫沉淀实验中与TBPH和Lark相互作用。阻断转录不会切断Nipped-B和rna结合蛋白与染色体的结合，这表明一旦建立了结合，就不需要转录来维持结合。这些发现表明，rna结合蛋白有助于控制姐妹染色单体内聚蛋白与基因和增强子的结合。当细胞分裂时，内聚蛋白复合体结合染色体以促进它们正确分裂成两个子细胞。内聚蛋白和将内聚蛋白装载到染色体上的Nipped-B蛋白也与基因和调节基因的区域结合，以确保基因产生适当数量的RNA。nipned - b和粘接蛋白优先结合对生长发育重要的基因子集，粘接蛋白活性的微小变化会导致严重的出生缺陷。为什么黏结蛋白结合了一些基因而不是其他基因，这是未知的。我们测试了这样一种想法，即特异性结合基因产生的RNA序列的蛋白质可能有助于确定哪些基因结合内聚蛋白。我们发现果蝇TBPH和云雀的RNA结合蛋白结合了由结合Nipped-B和黏结蛋白的基因产生的RNA。它们还与染色体上的这些基因以及调节它们的染色体区域结合。TBPH确保了Nipped-B和黏结蛋白在调控区域和基因上的高水平存在。云雀抑制了niped - b和黏结蛋白与某些基因的结合，并增加了它们与某些调控区域的结合。Nipped-B与这两种rna结合蛋白相互作用并促进它们与基因的结合。这些发现表明，rna结合蛋白有助于确定哪些基因结合了Nipped-B和内聚蛋白。
The cohesin protein complex mediates sister chromatid cohesion and participates in transcriptional control of genes that regulate growth and development. Substantial reduction of cohesin activity alters transcription of many genes without disrupting chromosome segregation. Drosophila Nipped-B protein loads cohesin onto chromosomes, and together Nipped-B and cohesin occupy essentially all active transcriptional enhancers and a large fraction of active genes. It is unknown why some active genes bind high levels of cohesin and some do not. Here we show that the TBPH and Lark RNA-binding proteins influence association of Nipped-B and cohesin with genes and gene regulatory sequences. In vitro, TBPH and Lark proteins specifically bind RNAs produced by genes occupied by Nipped-B and cohesin. By genomic chromatin immunoprecipitation these RNA-binding proteins also bind to chromosomes at cohesin-binding genes, enhancers, and Polycomb response elements (PREs). RNAi depletion reveals that TBPH facilitates association of Nipped-B and cohesin with genes and regulatory sequences. Lark reduces binding of Nipped-B and cohesin at many promoters and aids their association with several large enhancers. Conversely, Nipped-B facilitates TBPH and Lark association with genes and regulatory sequences, and interacts with TBPH and Lark in affinity chromatography and immunoprecipitation experiments. Blocking transcription does not ablate binding of Nipped-B and the RNA-binding proteins to chromosomes, indicating transcription is not required to maintain binding once established. These findings demonstrate that RNA-binding proteins help govern association of sister chromatid cohesion proteins with genes and enhancers. The cohesin protein complex binds chromosomes to facilitate their proper division into two daughter cells when a cell divides. Cohesin and the Nipped-B protein that loads cohesin onto chromosomes also bind to genes and regions that regulate genes to ensure that genes produce proper amounts of RNA. Nipped-B and cohesin preferentially bind a subset of genes important for growth and development, and small changes in cohesin activity cause severe birth defects. Why cohesin binds some genes and not others is unknown. We tested the idea that proteins that specifically bind the RNA sequences being produced by genes may help determine which genes bind cohesin. We find that the Drosophila TBPH and Lark RNA-binding proteins bind RNA produced by genes that bind Nipped-B and cohesin. They also bind to these genes on chromosomes and the chromosomal regions that regulate them. TBPH ensures that Nipped-B and cohesin are present at high levels on regulatory regions and genes. Lark inhibits Nipped-B and cohesin binding to some genes and increases their binding to some regulatory regions. Nipped-B interacts with both RNA-binding proteins and promotes their binding to genes. These findings show that RNA-binding proteins help determine which genes bind Nipped-B and cohesin.
登录
查看更多内容
影响因子：
64.8
作者：
Deardorff, Matthew A.;Bando, Masashige;Nakato, Ryuichiro;Watrin, Erwan;Itoh, Takehiko;Minamino, Masashi;Saitoh, Katsuya;Komata, Makiko;Katou, Yuki;Clark, Dinah;Cole, Kathryn E.;De Baere, Elfride;Decroos, Christophe;Di Donato, Nataliya;Ernst, Sarah;Francey, Lauren J.;Gyftodimou, Yolanda;Hirashima, Kyotaro;Hullings, Melanie;Ishikawa, Yuuichi;Jaulin, Christian;Kaur, Maninder;Kiyono, Tohru;Lombardi, Patrick M.;Magnaghi-Jaulin, Laura;Mortier, Geert R.;Nozaki, Naohito;Petersen, Michael B.;Seimiya, Hiroyuki;Siu, Victoria M.;Suzuki, Yutaka;Takagaki, Kentaro;Wilde, Jonathan J.;Willems, Patrick J.;Prigent, Claude;Gillessen-Kaesbach, Gabriele;Christianson, David W.;Kaiser, Frank J.;Jackson, Laird G.;Hirota, Toru;Krantz, Ian D.;Shirahige, Katsuhiko
通讯作者：
Shirahige, Katsuhiko
影响因子：
16
作者：
Bartman CR;Hsu SC;Hsiung CC;Raj A;Blobel GA
通讯作者：
Blobel GA
影响因子：
5.3
作者：
Lin, JC;Tarn, WY
通讯作者：
Tarn, WY
影响因子：
7
作者：
Faure AJ;Schmidt D;Watt S;Schwalie PC;Wilson MD;Xu H;Ramsay RG;Odom DT;Flicek P
通讯作者：
Flicek P
影响因子：
5.6
作者：
Ayala, YM;Pantano, S;Baralle, FE
通讯作者：
Baralle, FE