Transcriptional control by premature termination: a forgotten mechanism

Kamieniarz-Gdula, Kinga; Proudfoot, Nicholas J.

doi:10.7287/peerj.preprints.27590

Cited by 10 publications

(13 citation statements)

References 100 publications

(162 reference statements)

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“…Cryptic, inactive PAS are often embedded within mammalian introns. Usage of such intronic PAS may be restricted by mechanisms such as limiting levels of CPA factors or more efficient Pol II elongation (Kamieniarz-Gdula and Proudfoot, 2019). Most importantly, U1 antisense morpholino (AMO) that blocks U1 snRNA base pairing with 5’SS often leads to activation of intronic PAS and consequent premature transcriptional termination (PTT) (Kaida et al, 2010; Oh et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

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POINT Technology Illuminates the Processing of Polymerase-Associated Intact Nascent Transcripts

Sousa-Luís

Dujardin

Zukher

et al. 2020

Preprint

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SUMMARYMammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly due to technical limitations in purifying authentic nascent transcripts. We present a new approach to purify and profile nascent RNA, called Polymerase Intact Nascent Transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5’ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano) and profiles whole transcription units (POINT-seq). In particular we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5’P-RNA at polyadenylation sites. Furthermore POINT-nano reveals that splicing occurs either immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing.HIGHLIGHTSPOINT methodology dissects intact nascent RNA processingSpecificity of Xrn2 exonuclease in co-transcriptional RNA degradationSplicing suppresses Xrn2-dependent premature terminationDifferent kinetic classes of co-transcriptional splicing in human genes

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Section: Resultsmentioning

confidence: 99%

“…PTT is a critically important step to fine tune gene expression (Kamieniarz-Gdula and Proudfoot, 2019). Previously U1 snRNP was shown to suppress cleavage at intronic cryptic PAS and thereby restrict PTT by a mechanism referred to as telescripting (Kaida et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

POINT Technology Illuminates the Processing of Polymerase-Associated Intact Nascent Transcripts

Sousa-Luís

Dujardin

Zukher

et al. 2020

Preprint

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“…transcriptional effects. Premature termination has been shown to act as a means of transcriptional control 61 , and while the exact relationship between the use of CLEs and the expression of fulllength transcripts depends on the gene (Fig. 1f, g and Supplementary Fig.…”

Section: Discussionmentioning

confidence: 99%

A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons

et al. 2021

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The RNA-binding protein SFPQ plays an important role in neuronal development and has been associated with several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease. Here, we report that loss of sfpq leads to premature termination of multiple transcripts due to widespread activation of previously unannotated cryptic last exons (CLEs). These SFPQ-inhibited CLEs appear preferentially in long introns of genes with neuronal functions and can dampen gene expression outputs and/or give rise to short peptides interfering with the normal gene functions. We show that one such peptide encoded by the CLE-containing epha4b mRNA isoform is responsible for neurodevelopmental defects in the sfpq mutant. The uncovered CLE-repressive activity of SFPQ is conserved in mouse and human, and SFPQ-inhibited CLEs are found expressed across ALS iPSC-derived neurons. These results greatly expand our understanding of SFPQ function and uncover a gene regulation mechanism with wide relevance to human neuropathologies.

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“…For example, it assumes that RNAPs that initiate transcription gradually make their way all the way along the DNA template to the termination site, with negligible rates of premature termination. The frequency with which premature termination occurs is debated in the literature, with some studies suggesting it occurs at low rates across most genes [16] and others indicating higher rates [19,20]. My hope is that this phenomenon occurs at low enough rates across most of the TU (with the possible exception of locations near the promoter) that it will have at most a minor impact on the rate estimators and hypothesis tests described here, but it could result in appreciable biases.…”

Section: Discussionmentioning

confidence: 89%

A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data

Siepel

2021

Preprint

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Nascent RNA sequencing protocols, such as GRO-seq and PRO-seq, are now widely used in the study of eukaryotic transcription, and these experimental techniques have given rise to a variety of statistical and machine-learning methods for data analysis. These computational methods, however, are generally designed to address specialized signal-processing or prediction tasks, rather than directly describing the dynamics of RNA polymerases as they move along the DNA template. Here, I introduce a general probabilistic model that describes the kinetics of transcription initiation, elongation, pause release, and termination, as well as the generation of sequencing read counts. I show that this generative model enables estimation of separate rates of initiation, pause-release, and termination, up to a proportionality constant. Furthermore, if applied to time-course data in a nonequilibrium setting, the model can be used to estimate elongation rates. This model additionally leads naturally to likelihood ratio tests for differences between genes, conditions, or species in various rates of interest. A version of the model in which read counts are assumed to be Poisson-distributed leads to convenient, closed-form solutions for parameter estimates and likelihood ratio tests. I present extensions to Bayesian inference and to a generalized linear model that can be used to discover genomic features associated with rates of elongation. Finally, I address technicalities concerning estimation of library size, normalization and sequencing replicates. Altogether, this modeling framework enables a unified treatment of many common tasks in the analysis of nascent RNA sequencing data.

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Transcriptional control by premature termination: a forgotten mechanism

Cited by 10 publications

References 100 publications

POINT Technology Illuminates the Processing of Polymerase-Associated Intact Nascent Transcripts

POINT Technology Illuminates the Processing of Polymerase-Associated Intact Nascent Transcripts

A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons

A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data

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