Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails

Liu, Yusheng; Nie, Hu; Liu, Hongxiang; Lu, Falong

doi:10.1038/s41467-019-13228-9

Cited by 93 publications

(133 citation statements)

References 44 publications

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“…This experimental strategy offers high-quality, full-length mRNA sequences, including UTRs and poly(A) tails giving deeper insights into transcriptome shaping, comparing to classical RNAseq experiments 32 . It is characterized by a relative technical simplicity, and in contrast to other RNA-seq methods, no PCR biases are introduced into libraries as in case of other currently used RNA 3ʹ-end research techniques, such as Nascent RNAend-Seq, TAIL-seq, PAL-seq, TED-seq, PAC-Seq, EnD-seq, FLAM-seq, or most recently PAIso-seq 31,[35][36][37][38][39][40][41] . Importantly, despite the recent dynamic expansion of RNA 3ʹ-terminome research, little was known how cytoplasmic ncPAP enzymes contribute to gene expression programs since such techniques were never applied for KOs of individual enzymes in physiological conditions.…”

Section: Discussionmentioning

confidence: 99%

Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C

et al. 2020

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TENT5C is a non-canonical cytoplasmic poly(A) polymerase highly expressed by activated B cells to suppress their proliferation. Here we measure the global distribution of poly(A) tail lengths in responsive B cells using a Nanopore direct RNA-sequencing approach, showing that TENT5C polyadenylates immunoglobulin mRNAs regulating their half-life and consequently steady-state levels. TENT5C is upregulated in differentiating plasma cells by innate signaling. Compared with wild-type, Tent5c −/− mice produce fewer antibodies and have diminished T-cell-independent immune response despite having more CD138 high plasma cells as a consequence of accelerated differentiation. B cells from Tent5c −/− mice also have impaired capacity of the secretory pathway, with reduced ER volume and unfolded protein response. Importantly, these functions of TENT5C are dependent on its enzymatic activity as catalytic mutation knock-in mice display the same defect as Tent5c −/−. These findings define the role of the TENT5C enzyme in the humoral immune response.

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Section: Discussionmentioning

confidence: 99%

Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C

et al. 2020

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“…(iv) PAIso (poly(A) inclusive RNA isoform)-seq: Similar to FLAM-seq, it employs the PacBio platform to enable full-length sequencing of RNA. The 3 0 PCR handles are added by Klenow enzyme, and subsequent reverse transcription with 5 0 template switching enables the creation of circular cDNA libraries (Liu et al, 2019b). (v) PAT (poly(A) test RNA)-seq: RNA fragments bearing poly(A) tails are isolated and used for library construction (Harrison et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

Slobodin

Dikstein

2020

EMBO Reports

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Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine‐tuning of gene expression and the adjustment to constantly changing conditions.

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“…The poly(A) length has long been known to regulate transcript stability and translational efficiency [2,3]. However, investigations into the role of poly(A) length control have just started to emerge [2,8,34,57]. This is primarily due to a lack of sensitive methodologies that allow for accurate determination of the full-length poly(A) tail sequences.…”

Section: Discussionmentioning

confidence: 99%

miRNA-dependent poly(A) length control in uncoupling transcription and translation of haploid male germ cells

Tang

Guo

et al. 2021

Preprint

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As one of the post-transcriptional regulatory mechanisms, transcription and translation’s uncoupling plays an essential role in development and adulthood physiology. However, it remains elusive how thousands of mRNAs get translationally silenced while stability is maintained for up to hours or even days before translation. In addition to oocytes and neurons, developing spermatids have significant uncoupling of transcription and translation for delayed translation. Therefore, spermiogenesis represents an excellent in vivo model for investigating the mechanism underlying uncoupled transcription and translation. Through full-length poly(A) deep sequencing, we discovered dynamic changes in poly(A) length through deadenylation and re-polyadenylation. Deadenylation appeared to be mediated by microRNAs (miRNAs), and transcripts with shorter poly(A) tails tend to be sequestered into ribonucleoproteins (RNPs) for translational repression and stabilization. In contrast, re-polyadenylation allows for translocation of the translationally repressed transcripts from RNPs to polysomes for translation. Overall, our data suggest that miRNA-dependent poly(A) length control represents a novel mechanism underlying uncoupled translation and transcription in haploid male germ cells.

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Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails

Cited by 93 publications

References 44 publications

Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C

Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

miRNA-dependent poly(A) length control in uncoupling transcription and translation of haploid male germ cells

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