A first exon termination checkpoint preferentially suppresses extragenic transcription

Austenaa, Liv; Piccolo, Viviana; Russo, Mara; Prosperini, Elena; Polletti, Sara; Polizzese, Danilo; Ghisletti, Serena; Barozzi, Iros; Diaferia, Giuseppe R.; Natoli, Gioacchino

doi:10.1038/s41594-021-00572-y

Cited by 40 publications

(54 citation statements)

References 76 publications

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“…For example, ZC3H4, a CCCH zinc finger domain-containing RBP, occupies broad promoter regions and represses non-coding transcription events in human cells [ 27 ]. With WDR82 that binds Ser5-phosphorylated RNA Pol II, ZC3H4 forms a complex that suppresses lncRNAs transcribed from enhancers and promoters by transcription termination, which is activated by the inefficiently spliced first exon of lncRNAs [ 28 ]. Collectively, RBPs can function as regulatory proteins and control the expression of lncRNAs in multiple ways.…”

Section: Introductionmentioning

confidence: 99%

Integrated Analysis of RNA Binding Protein-Related lncRNA Prognostic Signature for Breast Cancer Patients

Xie

Zhou

et al. 2022

Genes

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Long non-coding RNAs (lncRNAs) have been well known for their multiple functions in the tumorigenesis, development, and prognosis of breast cancer (BC). Mechanistically, their production, function, or stability can be regulated by RNA binding proteins (RBPs), which were also involved in the carcinogenesis and progression of BC. However, the roles and clinical implications of RBP-related lncRNAs in BC remain largely unknown. Therefore, we herein aim to construct a prognostic signature with RBP-relevant lncRNAs for the prognostic evaluation of BC patients. Firstly, based on the RNA sequencing data of female BC patients from The Cancer Genome Atlas (TCGA) database, we screened out 377 differentially expressed lncRNAs related to RBPs. The univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were then performed to establish a prognostic signature composed of 12-RBP-related lncRNAs. Furthermore, we divided the BC patients into high- and low-risk groups by the prognostic signature and found the overall survival (OS) of patients in the high-risk group was significantly shorter than that of the low-risk group. Moreover, the 12-lncRNA signature exhibited independence in evaluating the prognosis of BC patients. Additionally, a functional enrichment analysis revealed that the prognostic signature was associated with some cancer-relevant pathways, including cell cycle and immunity. In summary, our 12-lncRNA signature may provide a theoretical reference for the prognostic evaluation or clinical treatment of BC patients.

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Section: Introductionmentioning

confidence: 99%

Integrated Analysis of RNA Binding Protein-Related lncRNA Prognostic Signature for Breast Cancer Patients

Xie

Zhou

et al. 2022

Genes

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“…This observed positive correlation might also be explained by effects of splicing on nuclear export [ 43 ], or on RNA stability [ 40 , 44 ], that can both enhance steady-state RNA levels per gene. Additionally, it was shown that splicing and transcription occur simultaneously [ 13 ], and it was recently demonstrated in mammalian cells that inefficient splicing of non-coding RNA can lead to transcription termination [ 45 ]. In addition, this correlation could be explained by an effect of transcription rate on splicing but we estimate that this explanation is less likely since all variants in the library are transcribed using the same promoter.…”

Section: Resultsmentioning

confidence: 99%

A broad analysis of splicing regulation in yeast using a large library of synthetic introns

et al. 2021

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RNA splicing is a key process in eukaryotic gene expression, in which an intron is spliced out of a pre-mRNA molecule to eventually produce a mature mRNA. Most intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient regulation of gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Introns are defined by three functional sites, the 5’ donor site, the branch site, and the 3’ acceptor site. Using a combinatorial design of synthetic introns, we demonstrate how non-consensus splice site sequences in each of these sites affect splicing efficiency. We then show that S. cerevisiae splicing machinery tends to select alternative 3’ splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns’ 3’ ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organism’s splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, demonstrating that merely a synthetic fusion of two introns might be suffice to facilitate alternative splicing in yeast. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome. In addition, it provides a valuable resource to study the regulation of constitutive and alternative splicing in a model organism.

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“…However, we show that the effect of 5'SSs goes beyond this role, to stimulate transcription more broadly. We propose that changes in RNAPII conformation that occur upon U1 binding make it intrinsically more processive, and/or prevent association of other termination machineries, such as Integrator 2,41 and WDR82/ZC3H4 42,43 . Providing a molecular mechanism for 5'SS-mediated transcription stimulation and identifying additional sequence elements that regulate transcription elongation will be important for future work, and we anticipate that our newly developed methodology can be leveraged towards these goals.…”

Section: Discussionmentioning

confidence: 99%

Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential

Vlaming

Martin

et al. 2021

Preprint

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Organismal growth and development rely on RNA Polymerase II (RNAPII) synthesizing the appropriate repertoire of messenger RNAs (mRNAs) from protein-coding genes. Productive elongation of full-length transcripts is essential for mRNA function, however what determines whether an engaged RNAPII molecule will terminate prematurely or transcribe processively remains poorly understood. Notably, despite a common process for transcription initiation across RNAPII-synthesized RNAs, RNAPII is highly susceptible to termination when transcribing non-coding RNAs such as upstream antisense RNAs (uaRNAs) and enhancers RNAs (eRNAs), suggesting that differences arise during RNAPII elongation. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in uaRNAs and eRNAs, rather than specific sequence motifs, underlies the propensity for RNAPII termination on these transcripts. Further, we demonstrate that 5' splice sites exert both splicing-dependent and autonomous, splicing-independent stimulation of transcription, even in the absence of polyadenylation signals. Together, our results reveal a potent role for transcribed sequence in dictating gene output at mRNA and non-coding RNA loci, and demonstrate the power of INSERT-seq towards illuminating these contributions.

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A first exon termination checkpoint preferentially suppresses extragenic transcription

Cited by 40 publications

References 76 publications

Integrated Analysis of RNA Binding Protein-Related lncRNA Prognostic Signature for Breast Cancer Patients

Integrated Analysis of RNA Binding Protein-Related lncRNA Prognostic Signature for Breast Cancer Patients

A broad analysis of splicing regulation in yeast using a large library of synthetic introns

Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential

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