Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

Zhai, Jixian; Arikit, Siwaret; Simon, Stacey A.; Kingham, Brewster F.

doi:10.1016/j.ymeth.2013.06.025

Cited by 88 publications

(83 citation statements)

References 8 publications

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“…Small RNA and RNA-seq libraries were constructed using TruSeq Small RNA Sample Prep kits and TruSeq RNA Sample Prep kits (Illumina). PARE libraries were constructed as previously described (37). All libraries were sequenced on an Illumina HiSeq 2000 instrument at the Delaware Biotechnology Institute.…”

Section: Methodsmentioning

confidence: 99%

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

Zhai

Zhang

Arikit

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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286

529

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Maize anthers, the male reproductive floral organs, express two classes of phased small-interfering RNAs (phasiRNAs). PhasiRNA precursors are transcribed by RNA polymerase II and map to lowcopy, intergenic regions similar to PIWI-interacting RNAs (piRNAs) in mammalian testis. From 10 sequential cohorts of staged maize anthers plus mature pollen we find that 21-nt phased siRNAs from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, whereas 24-nt phasiRNAs from 176 loci coordinately accumulate during meiosis and persist as anther somatic cells mature and haploid gametophytes differentiate into pollen. Male-sterile ocl4 anthers defective in epidermal signaling lack 21-nt phasiRNAs. Male-sterile mutants with subepidermal defects-mac1 (excess meiocytes), ms23 (defective pretapetal cells), and msca1 (no normal soma or meiocytes)-lack 24-nt phasiRNAs. ameiotic1 mutants (normal soma, no meiosis) accumulate both 21-nt and 24-nt phasiRNAs, ruling out meiotic cells as a source or regulator of phasiRNA biogenesis. By in situ hybridization, miR2118 triggers of 21-nt phasiRNA biogenesis localize to epidermis; however, 21-PHAS precursors and 21-nt phasiRNAs are abundant subepidermally. The miR2275 trigger, 24-PHAS precursors, and 24-nt phasiRNAs all accumulate preferentially in tapetum and meiocytes. Therefore, each phasiRNA type exhibits independent spatiotemporal regulation with 21-nt premeiotic phasiRNAs dependent on epidermal and 24-nt meiotic phasiRNAs dependent on tapetal cell differentiation. Maize phasiRNAs and mammalian piRNAs illustrate putative convergent evolution of small RNAs in male reproduction. phasiRNAs | anther development | piRNAs | tapetum | tasiRNAs D iverse small RNAs exist in male reproductive cells of animals and plants. In animals, PIWI proteins, a subfamily of the ARGONAUTEs, and their interacting piRNAs are required for spermatogenesis; mutants defective for the PIWI-encoding genes fail to produce mature sperm (1-3). Whereas most Drosophila piRNAs are repeat-derived and function to silence transposable elements (TEs) (4, 5), mammalian piRNAs predominantly map to unique intergenic regions and have unclear but essential roles during gonad development. Based on their expression timing, different sizes, and distinctive PIWI partners, mammalian piRNAs are further classified as prepachytene or pachytene (6). Given the continuum of developmental stages in the testes, the prepachytene class is characteristic of gonads in which no cells have reached pachytene, whereas the pachytene-associated small RNAs are characteristic of gonads in which the most advanced germ line cells have reached this meiotic stage and all prior stages are also present in the more immature zone of the gonad.In flowering plants, the anther is equivalent to the mammalian testes in that it consists of multiple somatic cell types required to support the premeiotic, meiotic, and postmeiotic haploid cells. In contrast to the continuum of mammalian gonads, however, an entire anther progres...

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Section: Methodsmentioning

confidence: 99%

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

Zhai

Zhang

Arikit

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

286

529

View full text Add to dashboard Cite

show abstract

“…Therefore, we undertook PARE to profile the RNA degradome, capturing uncapped precursor siRNA template molecules. This procedure captures all uncapped and polyadenylated mRNA molecules in the transcriptome using a custom variation on the Illumina sRNA and mRNA library preparation protocols, providing a snapshot of the degradome (Zhai et al, 2014). Using these data, we can calculate the degradome abundance associated with the mRNA for a particular gene.…”

Section: Profiling Rna Degradome Dynamics During Stress and Recoverymentioning

confidence: 99%

“…siRNA clusters were overlapped with TAIR10 gene and TE annotations, downloaded from TAIR, using bedtools intersect (v2.24.0) with default parameters. PARE PARE libraries were prepared as per Zhai et al (2014) with minor modifications included below. PARE libraries capture a 20-to 21-nucleotide tag of the 5ʹ end of all uncapped (5ʹ monophosphate) mRNA molecules by ligation of a 5ʹ adapter incorporating the recognition site of the Type II restriction endonuclease MmeI.…”

Section: Rna Half-life Calculationmentioning

confidence: 99%

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

et al. 2017

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Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5ʹ-3ʹ RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.

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“…Total RNA isolated by PureLink Plant RNA Reagent (Thermo Fisher) and MaxTract high-density gel tubes (Qiagen) was used for PARE library construction following the protocol published previously (Zhai et al, 2014). PARE libraries were constructed with ;80 mg total RNA and then sequenced on the Illumina HiSeq 2500 platform.…”

Section: Pare Library Construction and Sequencingmentioning

confidence: 99%

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

et al. 2016

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High-throughput approaches for profiling the 59 ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 59-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). Based on this analysis, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nucleotide periodicity in the position of free 59 RNA ends and a bias toward the translational frame. By examining conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice, we found a predominance of 59 termini of RNA degradation intermediates that were separated by a length equal to a ribosome-protected mRNA fragment. Through the analysis of RNA degradome data, we discovered uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, our analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a noncleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.

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Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

Cited by 88 publications

References 8 publications

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

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