Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4
Jason E Miller1; Liye Zhang2; Haoyang Jiang5,6; Yunfei Li3; B Franklin Pugh5,7; Joseph C Reese4
2018-07
Source PublicationG3 (BETHESDA)
ISSN2160-1836
EISSN2160-1836
Volume8Issue:1Pages:315-330
Status已发表
DOI10.1534/g3.117.300415
Abstract

The Ccr4 (carbon catabolite repression 4)-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a "core" subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae; however, its mRNA targets have not been mapped on a genome-wide scale. Here, we describe a genome-wide approach, RNA immunoprecipitation (RIP) high-throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5 All three proteins were preferentially bound to lowly abundant mRNAs, most often at the 3' end of the transcript. Furthermore, Ccr4, Dhh1, and Puf5 are recruited to mRNAs that are targeted by other RNA-binding proteins that promote decay and mRNA transport, and inhibit translation. Although Ccr4-Not regulates mRNA transcription and decay, Ccr4 recruitment to mRNAs correlates better with decay rates, suggesting it imparts greater control over transcript abundance through decay. Ccr4-enriched mRNAs are refractory to control by the other deadenylase complex in yeast, Pan2/3, suggesting a division of labor between these deadenylation complexes. Finally, Ccr4 and Dhh1 associate with mRNAs whose abundance increases during nutrient starvation, and those that fluctuate during metabolic and oxygen consumption cycles, which explains the known genetic connections between these factors and nutrient utilization and stress pathways.

KeywordCcr4-Not Dhh1 RNA immunoprecipitation-seq mRNA decay
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Cited Times:12[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttps://kms.shanghaitech.edu.cn/handle/2MSLDSTB/126824
Collection生命科学与技术学院_PI研究组_张力烨组
Corresponding AuthorJoseph C Reese
Affiliation1.Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822.
2.School of Life Science and Technology, 100 Haike Rd., Shanghai, 201210, China.
3.Life Technologies, 200 Oyster Point Blvd., South San Francisco, CA 94080
4.Center for Eukaryotic Gene Regulation, Biochemistry and Molecular Biology, Pennsylvania State University, 463A North Frear Laboratory, University Park, PA 16802
5.Center for Eukaryotic Gene Regulation
6.Center for RNA Molecular Biology
7.Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
Recommended Citation
GB/T 7714
Jason E Miller,Liye Zhang,Haoyang Jiang,et al. Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4[J]. G3 (BETHESDA),2018,8(1):315-330.
APA Jason E Miller,Liye Zhang,Haoyang Jiang,Yunfei Li,B Franklin Pugh,&Joseph C Reese.(2018).Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4.G3 (BETHESDA),8(1),315-330.
MLA Jason E Miller,et al."Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4".G3 (BETHESDA) 8.1(2018):315-330.
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