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

Zhao, Taolan; Huan, Qing; Sun, Jing; Liu, Chunyan; Hou, Xiuli; Yu, Xiang; Silverman, Ian M.; Zhang, Yi; Gregory, Brian D.; Liu, Chunming; Qian, Wenfeng; Cao, Xiaofeng

doi:10.1186/s13059-019-1799-8

Cited by 53 publications

(68 citation statements)

References 61 publications

(80 reference statements)

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“…Due to the increasing appreciation of the importance of poly(A) tails in regulating translation and transcriptome [33,34], developing NGS-based methods to profile the 3' poly(A) tails remains a high research priority in recent years [8,14,[21][22][23][24][25]27]. Direct sequencing the poly (A) tails is attractive not only because it is straight-forward, but also for studying 3' uridylation that controls mRNA decay and mixed tailing associated with RNA binding protein interaction and regulation [12,33,35,36]. Nanopore sequencing, FLAM-seq, PAlso-seq using single molecule sequencing technologies have been applied to directly sequencing poly(A) tails from the 3'-UTR into the poly(A) regions [23,25,27].…”

Section: Discussionmentioning

confidence: 99%

Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails

Yu¹,

Cheng²,

Wang³

et al. 2020

PLoS ONE

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Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly (A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development-and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.

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Section: Discussionmentioning

confidence: 99%

Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails

Yu¹,

Cheng²,

Wang³

et al. 2020

PLoS ONE

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“…In Arabidopsis, the poly(A) tail length (PAL) of HSP21 increased under severe heat stress (Osteryoung et al, 1993). In general, however, PAL is poorly studied and is currently mostly limited to individual transcripts (Zhao et al, 2019). Furthermore, the contribution of PAL to plant thermotolerance remains unclear on a transcriptome level.…”

Section: Introductionmentioning

confidence: 99%

Heat Shock Responsive Gene Expression Modulated by mRNA Poly(A) Tail Length

Wang

et al. 2020

Front. Plant Sci.

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Poly(A) tail length (PAL) has been implicated in the regulation of mRNA translation activities. However, the extent of such regulation at the transcriptome level is less understood in plants. Herein, we report the development and optimization of a largescale sequencing technique called the Assay for PAL-sequencing (APAL-seq). To explore the role of PAL on post-transcriptional modification and translation, we performed PAL profiling of Arabidopsis transcriptome in response to heat shock. Transcripts of 2,477 genes were found to have variable PAL upon heat treatments. Further study of the transcripts of 14 potential heat-responsive genes identified two distinct groups of genes. In one group, PAL was heat stress-independent, and in the other, PAL was heat stresssensitive. Meanwhile, the protein expression of HSP70 and HSP17.6C was determined to test the impact of PAL on translational activity. In the absence of heat stress, neither gene demonstrated protein expression; however, under gradual or abrupt heat stress, both transcripts showed enhanced protein expression with elongated PAL. Interestingly, HSP17.6C protein levels were positively correlated with the severity of heat treatment and peaked when treated with abrupt heat. Our results suggest that plant genes have a high variability of PALs and that PAL contributes to swift posttranslational stress responses.

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“…This releases the polypeptide from the P-site and a final ATP hydrolysis by ABCE1 promotes the disassembly of the 80S components, to be recycled for another round of protein synthesis. For details refer to Browning and Bailey-Serres (2015) Vaughn, & von Arnim, 2007;Martinez-Silva, Aguirre-Martinez, Flores-Tinoco, Alejandri-Ramirez, & Dinkova, 2012;Tiruneh, Kim, Gallie, Roy, & von Arnim, 2013), while others, such as those in eIF3k and the poly (A)-binding proteins (PABPs) had surprisingly subtle consequences (Tiruneh et al, 2013) unless PABP gene dosage was severely curtailed (T. Zhao et al, 2019). Genetic perturbations have been particularly informative when paired with short-term environmental treatments (Cho et al, 2019;Lokdarshi, Guan, et al, 2020;Merchante et al, 2015;.…”

Section: Control Of the Translatome By Environmental Perturbationmentioning

confidence: 99%

“…The PABPs are considered core translation factors. In Arabidopsis PAB2, PAB4, and PAB8 are jointly expressed in the diploid phase of the life cycle and are partially functionally redundant (Gallie, 2017;T. Zhao et al, 2019).…”

Section: Elongation Termination and Recyclingmentioning

confidence: 99%

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Translational gene regulation in plants: A green new deal

2020

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The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants.

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

Cited by 53 publications

References 61 publications

Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails

Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails

Heat Shock Responsive Gene Expression Modulated by mRNA Poly(A) Tail Length

Translational gene regulation in plants: A green new deal

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