Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency

Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple...
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Autor*in:	Taolan Zhao [verfasserIn] Qing Huan [verfasserIn] Jing Sun [verfasserIn] Chunyan Liu [verfasserIn] Xiuli Hou [verfasserIn] Xiang Yu [verfasserIn] Ian M. Silverman [verfasserIn] Yi Zhang [verfasserIn] Brian D. Gregory [verfasserIn] Chun-Ming Liu [verfasserIn] Wenfeng Qian [verfasserIn] Xiaofeng Cao [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency

Übergeordnetes Werk:	In: Genome Biology - BMC, 2014, 20(2019), 1, Seite 12
Übergeordnetes Werk:	volume:20 ; year:2019 ; number:1 ; pages:12

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13059-019-1799-8

Katalog-ID:	DOAJ038878038

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520			\|a Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
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allfields	10.1186/s13059-019-1799-8 doi (DE-627)DOAJ038878038 (DE-599)DOAJ409e97ce59b7408c86f3fca23a68684e DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Taolan Zhao verfasserin aut Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression. Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency Biology (General) Genetics Qing Huan verfasserin aut Jing Sun verfasserin aut Chunyan Liu verfasserin aut Xiuli Hou verfasserin aut Xiang Yu verfasserin aut Ian M. Silverman verfasserin aut Yi Zhang verfasserin aut Brian D. Gregory verfasserin aut Chun-Ming Liu verfasserin aut Wenfeng Qian verfasserin aut Xiaofeng Cao verfasserin aut In Genome Biology BMC, 2014 20(2019), 1, Seite 12 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:20 year:2019 number:1 pages:12 https://doi.org/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/article/409e97ce59b7408c86f3fca23a68684e kostenfrei http://link.springer.com/article/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 12
spelling	10.1186/s13059-019-1799-8 doi (DE-627)DOAJ038878038 (DE-599)DOAJ409e97ce59b7408c86f3fca23a68684e DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Taolan Zhao verfasserin aut Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression. Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency Biology (General) Genetics Qing Huan verfasserin aut Jing Sun verfasserin aut Chunyan Liu verfasserin aut Xiuli Hou verfasserin aut Xiang Yu verfasserin aut Ian M. Silverman verfasserin aut Yi Zhang verfasserin aut Brian D. Gregory verfasserin aut Chun-Ming Liu verfasserin aut Wenfeng Qian verfasserin aut Xiaofeng Cao verfasserin aut In Genome Biology BMC, 2014 20(2019), 1, Seite 12 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:20 year:2019 number:1 pages:12 https://doi.org/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/article/409e97ce59b7408c86f3fca23a68684e kostenfrei http://link.springer.com/article/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 12
allfields_unstemmed	10.1186/s13059-019-1799-8 doi (DE-627)DOAJ038878038 (DE-599)DOAJ409e97ce59b7408c86f3fca23a68684e DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Taolan Zhao verfasserin aut Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression. Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency Biology (General) Genetics Qing Huan verfasserin aut Jing Sun verfasserin aut Chunyan Liu verfasserin aut Xiuli Hou verfasserin aut Xiang Yu verfasserin aut Ian M. Silverman verfasserin aut Yi Zhang verfasserin aut Brian D. Gregory verfasserin aut Chun-Ming Liu verfasserin aut Wenfeng Qian verfasserin aut Xiaofeng Cao verfasserin aut In Genome Biology BMC, 2014 20(2019), 1, Seite 12 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:20 year:2019 number:1 pages:12 https://doi.org/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/article/409e97ce59b7408c86f3fca23a68684e kostenfrei http://link.springer.com/article/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 12
allfieldsGer	10.1186/s13059-019-1799-8 doi (DE-627)DOAJ038878038 (DE-599)DOAJ409e97ce59b7408c86f3fca23a68684e DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Taolan Zhao verfasserin aut Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression. Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency Biology (General) Genetics Qing Huan verfasserin aut Jing Sun verfasserin aut Chunyan Liu verfasserin aut Xiuli Hou verfasserin aut Xiang Yu verfasserin aut Ian M. Silverman verfasserin aut Yi Zhang verfasserin aut Brian D. Gregory verfasserin aut Chun-Ming Liu verfasserin aut Wenfeng Qian verfasserin aut Xiaofeng Cao verfasserin aut In Genome Biology BMC, 2014 20(2019), 1, Seite 12 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:20 year:2019 number:1 pages:12 https://doi.org/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/article/409e97ce59b7408c86f3fca23a68684e kostenfrei http://link.springer.com/article/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 12
allfieldsSound	10.1186/s13059-019-1799-8 doi (DE-627)DOAJ038878038 (DE-599)DOAJ409e97ce59b7408c86f3fca23a68684e DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Taolan Zhao verfasserin aut Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression. Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency Biology (General) Genetics Qing Huan verfasserin aut Jing Sun verfasserin aut Chunyan Liu verfasserin aut Xiuli Hou verfasserin aut Xiang Yu verfasserin aut Ian M. Silverman verfasserin aut Yi Zhang verfasserin aut Brian D. Gregory verfasserin aut Chun-Ming Liu verfasserin aut Wenfeng Qian verfasserin aut Xiaofeng Cao verfasserin aut In Genome Biology BMC, 2014 20(2019), 1, Seite 12 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:20 year:2019 number:1 pages:12 https://doi.org/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/article/409e97ce59b7408c86f3fca23a68684e kostenfrei http://link.springer.com/article/10.1186/s13059-019-1799-8 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 12
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authorswithroles_txt_mv	Taolan Zhao @@aut@@ Qing Huan @@aut@@ Jing Sun @@aut@@ Chunyan Liu @@aut@@ Xiuli Hou @@aut@@ Xiang Yu @@aut@@ Ian M. Silverman @@aut@@ Yi Zhang @@aut@@ Brian D. Gregory @@aut@@ Chun-Ming Liu @@aut@@ Wenfeng Qian @@aut@@ Xiaofeng Cao @@aut@@
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author	Taolan Zhao
spellingShingle	Taolan Zhao misc QH301-705.5 misc QH426-470 misc Poly(A) tails misc Poly(A)-binding proteins misc PAB binding efficiency misc Poly(A)-tail G-content misc mRNA stability misc Translational efficiency misc Biology (General) misc Genetics Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
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topic_title	QH301-705.5 QH426-470 Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency Poly(A) tails Poly(A)-binding proteins PAB binding efficiency Poly(A)-tail G-content mRNA stability Translational efficiency
topic	misc QH301-705.5 misc QH426-470 misc Poly(A) tails misc Poly(A)-binding proteins misc PAB binding efficiency misc Poly(A)-tail G-content misc mRNA stability misc Translational efficiency misc Biology (General) misc Genetics
topic_unstemmed	misc QH301-705.5 misc QH426-470 misc Poly(A) tails misc Poly(A)-binding proteins misc PAB binding efficiency misc Poly(A)-tail G-content misc mRNA stability misc Translational efficiency misc Biology (General) misc Genetics
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title	Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
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title_sort	impact of poly(a)-tail g-content on arabidopsis pab binding and their role in enhancing translational efficiency
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title_auth	Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
abstract	Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
abstractGer	Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
abstract_unstemmed	Abstract Background Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
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title_short	Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
url	https://doi.org/10.1186/s13059-019-1799-8 https://doaj.org/article/409e97ce59b7408c86f3fca23a68684e http://link.springer.com/article/10.1186/s13059-019-1799-8 https://doaj.org/toc/1474-760X
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It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Results We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. Conclusions Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Poly(A) tails</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Poly(A)-binding proteins</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">PAB binding efficiency</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Poly(A)-tail G-content</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">mRNA stability</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Translational efficiency</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Biology (General)</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Genetics</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Qing Huan</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Jing Sun</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Chunyan Liu</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Xiuli Hou</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Xiang Yu</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Ian M. 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Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency

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