LARP7-Mediated U6 snRNA Modification Ensures Splicing Fidelity and Spermatogenesis in Mice

Wang, Xin; Li, Zhitong; Yan, Yue; Lin, Penghui; Tang, Wei; Hasler, Daniele; Meduri, Rajyalakshmi; Li, Ye; Hua, Min-Min; Qi, Hui-Tao; Lin, Di-Hang; Shi, Huijuan; Hui, Jingyi; Li, Jinsong; Li, Dangsheng; Yang, Jianhua; Lin, Jinzhong; Meister, Gunter; Fischer, Utz; Lin, Li

doi:10.1016/j.molcel.2020.01.002

Cited by 43 publications

(47 citation statements)

References 75 publications

(110 reference statements)

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“…RNA modifications are key regulators of a wide range of biological processes (Frye et al, 2018;Li and Mason, 2014;Roundtree et al, 2017). They can modulate the fate of RNA molecules, such as mRNA splicing (Louloupi et al, 2018;Wang et al, 2020;Zhou et al, 2019) or mRNA decay (Guo et al, 2017;Lee et al, 2020), as well as affect major cell and organism-level decisions, including cellular differentiation (Geula et al, 2015;Weng et al, 2018) and sex determination (Haussmann et al, 2016;Kan et al, 2017;Lence et al, 2016). While the biological relevance of RNA modifications is out of question, a major difficulty in studying them is the need for tailored protocols to map each modification individually (Novoa et al, 2017;Schaefer et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

Begik

Lucas

Pryszcz

et al. 2020

Preprint

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SUMMARYA broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification individually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify diverse RNA modification types present in native RNA molecules, using rRNA as the exemplar, and show that each RNA modification type results in distinct and characteristic base-calling ‘error’ signatures. We demonstrate the value of these signatures for de novo prediction of pseudouridine (Y) modifications transcriptome-wide, confirming known Y modifications in rRNAs, snRNAs and mRNAs, and uncovering a novel Pus4-dependent Y modification in yeast mitochondrial rRNA. Using a machine learning classifier, we show that the stoichiometry of modified sites can be quantified by identifying current intensity alterations in individual RNA reads. Finally, we explore the dynamics of pseudouridylation across a battery of environmental stresses, revealing novel heat-sensitive Y-modified sites in both snRNAs and snoRNAs. Altogether, our work demonstrates that Y RNA modifications can be predicted de novo and in a quantitative manner using native RNA nanopore sequencing.

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Section: Discussionmentioning

confidence: 99%

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

Begik

Lucas

Pryszcz

et al. 2020

Preprint

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“…LARP7 family members likewise bind the 3′end of Pol III transcripts. However, they have apparently developed specificity for a subset of Pol III RNA targets [ 32 , 33 , 34 ], and facilitate specific functions, such as the stabilization of 7SKRNA or the 2′O methylation of the spliceosomal U6 small nuclear ribonucleic acid (snRNA) [ 35 , 36 , 37 , 38 , 39 ]…”

Section: Introductionmentioning

confidence: 99%

Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1

et al. 2020

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Eukaryotic cells determine the protein output of their genetic program by regulating mRNA transcription, localization, translation and turnover rates. This regulation is accomplished by an ensemble of RNA-binding proteins (RBPs) that bind to any given mRNA, thus forming mRNPs. Poly(A) binding proteins (PABPs) are prominent members of virtually all mRNPs that possess poly(A) tails. They serve as multifunctional scaffolds, allowing the recruitment of diverse factors containing a poly(A)-interacting motif (PAM) into mRNPs. We present the crystal structure of the variant PAM motif (termed PAM2w) in the N-terminal part of the positive translation factor LARP4B, which binds to the MLLE domain of the poly(A) binding protein C1 cytoplasmic 1 (PABPC1). The structural analysis, along with mutational studies in vitro and in vivo, uncovered a new mode of interaction between PAM2 motifs and MLLE domains.

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“…Besides epigenetic regulation, AS is another mechanism by which cancer cells transiently and dynamically regulate genes that enable metastasis (42)(43)(44). Two studies recently described a role for LARP7, a RNA-binding protein that mediates the interaction between U6 and U6-targeting snoRNAs like Snord67 (45,46). Knockout of LARP7 in human embryonic kidney cells resulted in loss of methylation at all known U6 sites, as well as resultant changes in AS.…”

Section: Discussionmentioning

confidence: 99%

Snord67 promotes lymph node metastasis and regulates U6-mediated alternative splicing in breast cancer

Chao

Zhu

Tsai

et al. 2020

Preprint

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Small nucleolar RNAs (snoRNAs) have long been considered “housekeeping genes”, important for ribosomal biogenesis and protein synthesis. However, there is increasing evidence that this largely ignored class of non-coding RNAs (ncRNAs) also have wide-ranging, non-canonical functions in diseases, including cancer. SnoRNAs have been shown to have both oncogenic and tumor suppressor roles, yet whether snoRNAs regulate metastasis is unknown. Here we show that expression of certain snoRNAs are enriched in lymph node (LN) metastases in a micro-surgical, immune-competent mouse model of breast cancer. We identify the snoRNA Snord67 as a key regulator of LN metastasis. Knockout of Snord67 resulted in significantly decreased LN tumor growth and subsequent development of distant metastases. This was associated with loss of targeted 2’-O-methylation on the small nuclear RNA U6, a component of the spliceosome. RNA sequencing revealed distinct alternative splicing patterns in Snord67 knockout cells. Using rapid autopsy breast cancer cases, we found that matched human primary tumor and LN metastases revealed similar alternatively spliced genes, including several that are known to contribute to cancer. These results demonstrate that Snord67 is critical for growth of LN metastases and subsequent spread to distant metastases, and suggest that snoRNA-guided modifications of the spliceosome represent a previously unappreciated, yet targetable pathway in cancer.

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LARP7-Mediated U6 snRNA Modification Ensures Splicing Fidelity and Spermatogenesis in Mice

Cited by 43 publications

References 75 publications

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1

Snord67 promotes lymph node metastasis and regulates U6-mediated alternative splicing in breast cancer

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