Determinants and implications of mRNA poly(A) tail size – Does this protein make my tail look big?

Jalkanen, Aimee; Coleman, Stephen J.; Wilusz, Jeffrey

doi:10.1016/j.semcdb.2014.05.018

Cited by 124 publications

(102 citation statements)

References 114 publications

(163 reference statements)

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“…After nuclear export, poly(A) length is dynamically regulated by the interplay of 3 ′ -to-5 ′ degradation through exoribonucleases, poly(A) tail stabilization via poly(A) tail binding proteins, and elongation by cytoplasmic Poly(A)polymerases (Diez and Brawerman 1974;Clegg and Pikó 1982;Hake and Richter 1994;Mendez et al 2000;Read et al 2002). While it has been shown that the poly(A) tail has a regulatory role, it is still not fully understood whether a specific length allows for specific regulatory outcomes (Jalkanen et al 2014). A minimal poly(A) tail is needed to prevent quick 3 ′ -to-5 ′ exonuclease degradation (Ford et al 1997), yet hyperadenylated RNAs are marked for fast RNA degradation in the nucleus (Bresson and Conrad 2013;Jalkanen et al 2014).…”

Section: Introductionmentioning

confidence: 99%

“…While it has been shown that the poly(A) tail has a regulatory role, it is still not fully understood whether a specific length allows for specific regulatory outcomes (Jalkanen et al 2014). A minimal poly(A) tail is needed to prevent quick 3 ′ -to-5 ′ exonuclease degradation (Ford et al 1997), yet hyperadenylated RNAs are marked for fast RNA degradation in the nucleus (Bresson and Conrad 2013;Jalkanen et al 2014). Besides regulating RNA degradation, poly(A) tail length has been shown to correlate with translation efficiency during embryonic development (Beilharz and Preiss 2007;Subtelny et al 2014), possibly by favoring a closed-loop structure of the mRNA.…”

Section: Introductionmentioning

confidence: 99%

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tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Krause

Niazi

Labun

et al. 2019

RNA

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Polyadenylation at the 3 ′ ′ ′ ′ ′ -end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3 ′ ′ ′ ′ ′ -ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr, an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr's performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Krause

Niazi

Labun

et al. 2019

RNA

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“…3′ end processing of most eukaryotic mRNAs is a multistep maturation involving co‐transcriptional recognition of pre‐mRNA cis ‐elements, following by cleavage of the nascent RNA and non‐templated addition of ~200 adenosine residues in human cells. These mRNA 3′ end modifications confer stability and translational efficiency to the transcripts (Bentley, ; Jalkanen, Coleman, & Wilusz, ; Proudfoot, ; Y. Shi & Manley, ). Conversely, removal of the poly(A) tail by deadenylation can signal mRNA decay and/or translational repression of poly(A) + transcripts (Aström, Aström, & Virtanen, ; Mayya & Duchaine, ; Nicholson & Pasquinelli, ; Webster et al, ; Yi et al, ; X. Zhang, Kleiman, & Devany, ).These modifications in the 3′ end are controlled by cis ‐acting elements present in the mRNA and trans ‐acting regulatory factors, such as RNA binding proteins (RBPs) and RNAs with complementary base‐pairing, such as, but not restricted to, microRNAs (miRNAs).…”

Section: Introductionmentioning

confidence: 99%

Connections between 3′ end processing and DNA damage response: Ten years later

Murphy

Kleiman

2019

WIREs RNA

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Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady‐state levels due to turnover of the transcripts. The 3′ end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene‐specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3′ end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins‐mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3′ End Processing RNA‐Based Catalysis > Miscellaneous RNA‐Catalyzed Reactions RNA in Disease and Development > RNA in Disease

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“…It is essential that the 3′ end of virtually all eukaryotic RNA polymerase II transcripts is being processed and forming mature polyadenylated mRNA. The polyadenylation signal is located approximately 10–30 nucleotides upstream of the poly(A) addition site in most mRNAs; the poly(A) tails are indispensable structural and functional elements of eukaryotic mRNAs, and they are also crucial for the regulation of mRNA stability . In the HIV‐1 genome, the HIV‐1 poly(A) site can fold into a stable stem‐loop structure, which is highly conserved among different simian and human immunodeficiency viruses .…”

Section: Functions Of Rna Conformational Transitionsmentioning

confidence: 99%

Regulatory effects of cotranscriptional RNA structure formation and transitions

Liu

Zhang

2016

WIREs RNA

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RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website.

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Determinants and implications of mRNA poly(A) tail size – Does this protein make my tail look big?

Cited by 124 publications

References 114 publications

tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Connections between 3′ end processing and DNA damage response: Ten years later

Regulatory effects of cotranscriptional RNA structure formation and transitions

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