The regulatory role of Pcf11-similar-4 (PCFS4) in Arabidopsis development by genome-wide physical interactions with target loci

文献类型： 外文期刊

第一作者： Xing, Denghui

作者： Xing, Denghui;Wang, Yajun;Xu, Ruqiang;Li, Qingshun Q.;Ye, Xinfu;Yang, Dewei;Li, Qingshun Q.;Li, Qingshun Q.;Li, Qingshun Q.

作者机构：

关键词： Transcription;Polyadenylation factor;RNA processing;Alternative processing;ChIP-seq

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2013 年 14 卷

页码：

收录情况： SCI

摘要： Background: The yeast and human Pcf11 functions in both constitutive and regulated transcription and pre-mRNA processing. The constitutive roles of PCF11 are largely mediated by its direct interaction with RNA Polymerase II C-terminal domain and a polyadenylation factor, Clp1. However, little is known about the mechanism of the regulatory roles of Pcf11. Though similar to Pcf11 in multiple aspects, Arabidopsis Pcf11-similar-4 protein (PCFS4) plays only a regulatory role in Arabidopsis gene expression. Towards understanding how PCFS4 regulates the expression of its direct target genes in a genome level, ChIP-Seq approach was employed in this study to identify PCFS4 enrichment sites (ES) and the ES-linked genes within the Arabidopsis genome. Results: A total of 892 PCFS4 ES sites linked to 839 genes were identified. Distribution analysis of the ES sites along the gene bodies suggested that PCFS4 is preferentially located on the coding sequences of the genes, consistent with its regulatory role in transcription and pre-mRNA processing. Gene ontology (GO) analysis revealed that the ES-linked genes were specifically enriched in a few GO terms, including those categories of known PCFS4 functions in Arabidopsis development. More interestingly, GO analysis suggested novel roles of PCFS4. An example is its role in circadian rhythm, which was experimentally verified herein. ES site sequences analysis identified some over-represented sequence motifs shared by subsets of ES sites. The motifs may explain the specificity of PCFS4 on its target genes and the PCFS4's functions in multiple aspects of Arabidopsis development and behavior. Conclusions: Arabidopsis PCFS4 has been shown to specifically target on, and physically interact with, the subsets of genes. Its targeting specificity is likely mediated by cis-elements shared by the genes of each subset. The potential regulation on both transcription and mRNA processing levels of each subset of the genes may explain the functions of PCFS4 in multiple aspects of Arabidopsis development and behavior.

分类号：

  • 相关文献

[1]Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development. Zhang, Huanan,Kuang, Rui,Cheng, Feng,Wang, Xiaowu,Xiao, Yuguo,Kang, Xiaojun,Ni, Min. 2017

[2]Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. Wu, Xiaohui,Gaffney, Bobby,Hunt, Arthur G.,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.. 2014

[3]Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants. Hunt, Arthur G.,Xing, Denghui,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.. 2012

[4]Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. Wu, Xiaohui,Zeng, Yong,Guan, Jinting,Ji, Guoli,Huang, Rongting,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.,Ji, Guoli. 2015

[5]A R2R3 MYB transcription factor from ash positively regulates salt response in tobacco. Li, Tian,Sun, Jingkuan,Li, Tian,Bi, Yuping. 2017

[6]The cloning and sequencing of a cDNA encoding a WD repeat protein in cotton (Gossypium hirsutum L.). HONG Y. DUAN,FU G. LI,XU D. WU,DONG M. MA,MAO WANG,YU X. HOU.

[7]DNA-Bound peptides control the mRNA transcription through CDK7. Lv, Xiaowen,Lv, Feijie,Qin, Yuchang,Wang, Jing,Dong, Zhiyuan. 2009

[8]Identification and genetic effect of haplotypes in the promoter region of porcine myostatin gene. Liu, D.,Xu, Q.,Zang, L.,Liang, S.,Jiang, Y.,Wu, Y.,Wei, S.. 2011

[9]Structure and transcription of the Helicoverpa armigera densovirus (HaDV2) genome and its expression strategy in LD652 cells. Wu, Kongming,Xu, Pengjun,Graham, Robert I.,Wilson, Kenneth. 2017

[10]Characterization of ribulose-1, 5-bisphosphate carboxylase/oxygenase and transcriptional analysis of its related genes in Saccharina japonica (Laminariales, Phaeophyta). Shao Zhanru,Li Qiuying,Yao Jianting,Duan Delin,Liu Fuli,Shao Zhanru,Li Qiuying. 2014

[11]DROUGHT-INDUCED TRANSCRIPTION OF RESISTANT AND SENSITIVE COMMON MILLET VARIETIES. Wang, R. Y.,Liu, X. Y.,Lian, S.,Wang, R. Y.,Wang, H. G.,Chen, L.,Qiao, Z. J.,Wang, L.,McInerney, C. E.. 2017

[12]Comparative Morphology, Transcription, and Proteomics Study Revealing the Key Molecular Mechanism of Camphor on the Potato Tuber Sprouting Effect. Zou, Xue,Deng, Meng-Sheng,Peng, Jie,Huang, Xue-Li,Lu, Xue,Fang, Chen-Cheng,Wang, Xi-Yao,Zou, Xue. 2017

[13]The ecdysteroid UDP-glucosyltransferase gene promoter from Autographa californica multicapsid nucleopolyhedrovirus. Shen, XJ,Yi, YZ,Tang, SM,Zhang, ZF,Li, YR,He, JL.

[14]High Oxygen Concentration Increases the Abundance and Activity of Bacterial Rather than Archaeal Nitrifiers in Rice Field Soil. Ke, Xiubin,Lu, Wei,Ke, Xiubin,Conrad, Ralf.

[15]Isolated and characterization of a cDNA encoding ethylene-responsive element binding protein (EREBP)/AP2-type protein, RCBF2, in Oryza sativa L.. Liu, Jin-Ge,Zhang, Zhen,Qin, Qiu-Lin,Peng, Ri-He,Xiong, Ai-Sheng,Chen, Jian-Min,Xu, Fang,Zhu, Hong,Yao, Quan-Hong.

[16]Cloning of multiple cellulase cDNAs from Volvariella volvacea and their differential expression during substrate colonization and fruiting. Ding, Shaojun,Ge, Wei,Buswell, John A..

[17]Antagonistic HLH/bHLH Transcription Factors Mediate Brassinosteroid Regulation of Cell Elongation and Plant Development in Rice and Arabidopsis. Zhang, Li-Ying,Bai, Ming-Yi,Zhu, Jia-Ying,Wang, Hao,Wang, Wenfei,Zhao, Jun,Yang, Hongjuan,Xu, Yunyuan,Lin, Wen-Hui,Chong, Kang,Wang, Zhi-Yong,Zhang, Li-Ying,Zhu, Jia-Ying,Wang, Hao,Wang, Wenfei,Zhao, Jun,Bai, Ming-Yi,Sun, Yu,Wang, Zhi-Yong,Wu, Jinxia,Zhang, Zhiguo,Sun, Xuehui,Lu, Tiegang,Kim, Soo-Hwan,Fujioka, Shozo.

[18]Studies on resistance characteristic and cDNA sequence conservation of transferrin from crucian carp, Carassius auratus. Long, Hua,Yu, Qi-Xing.

[19]Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets. Gebelin, Virginie,Argout, Xavier,Engchuan, Worrawat,Pitollat, Bertrand,Duan, Cuifang,Montoro, Pascal,Leclercq, Julie,Engchuan, Worrawat,Duan, Cuifang. 2012

[20]Molecular cloning and characterization of the promoter region of the porcine apolipoprotein E gene. Xia, Jihan,Hu, Bingjun,Mu, Yulian,Xin, Leilei,Yang, Shulin,Li, Kui.

作者其他论文 更多>>

微信小程序