SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA

Tichon, Ailone; Perry, Rotem Ben-Tov; Stojic, Lovorka; Ulitsky, Igor

doi:10.1101/gad.309138.117

Cited by 65 publications

(109 citation statements)

References 30 publications

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“…Negative control siRNA and cells without any siRNA treatment were used as controls, for which we observed no systematic differences in the frequencies of each phenotype 15 ( Fig. 1b-d).…”

Section: High-content Phenotypic Screen Identified New Lncrnas Involvmentioning

confidence: 85%

“…Following 48 hr incubation, cells were fixed and processed for immunostaining and subsequent automated image acquisition and analysis. In screen A, antibodies targeting CEP215 (to label centrosomes), a-tubulin (to label the 15 microtubule cytoskeleton), phalloidin (to label the actin cytoskeleton) and Hoechst (to label nuclei) were used. In screen B ( Fig.…”

Section: High-content Phenotypic Screen Identified New Lncrnas Involvmentioning

confidence: 99%

“…For chromosome segregation, we successfully identified the lncRNA NORAD ( Fig. 1c), depletion of which increases the rate of chromosome segregation errors 14,15 . Supplementary Table 2 contains raw data and computed Z-scores for each lncRNA and phenotype.…”

Section: High-content Phenotypic Screen Identified New Lncrnas Involvmentioning

confidence: 99%

“…LncRNAs have been also linked to cell division by regulating the levels of mitotic proteins 10,11 or by modulating the activity of enzymes involved in DNA replication and cohesion 12 . In addition, lncRNAs can regulate chromosome segregation by controlling 15 kinetochore formation via centromeric transcription 13 or by acting as decoys for RNA binding proteins involved in maintaining genome stability 14,15 . All of these lncRNAdependent functions can occur through transcriptional and post-transcriptional gene regulation, chromatin organisation and/or post-translational regulation of protein activity 5 .…”

Section: Introductionmentioning

confidence: 99%

“…We developed new image analysis pipelines to quantify a diverse set of mitotic features in fixed cells, and discovered multiple lncRNAs with roles in mitotic progression, chromosome segregation and cytokinesis. 15 We focused on linc00899, a hitherto uncharacterised lncRNA that regulates mitotic progression by repressing the transcription of the microtubule-stabilising protein TPPP/p25. Our study demonstrates the regulatory function of linc00899 in mitotic microtubule behaviour and provides a comprehensive imaging data resource for further investigation of the roles of lncRNAs in cell division.…”

Section: Introductionmentioning

confidence: 99%

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A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Stojic

Lun

Mascalchi

et al. 2019

Preprint

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ABSTRACTGenome stability relies on proper coordination of mitosis and cytokinesis, where dynamic microtubules capture and faithfully segregate chromosomes into daughter cells. The role of long noncoding RNAs (lncRNAs) in controlling these processes however remains largely unexplored. To identify lncRNAs with mitotic functions, we performed a high-content RNAi imaging screen targeting more than 2,000 human lncRNAs. By investigating major hallmarks of cell division such as chromosome segregation, mitotic duration and cytokinesis, we discovered numerous lncRNAs with functions in each of these processes. The chromatin-associated lncRNA, linc00899, was selected for in-depth studies due to the robust mitotic delay observed upon its depletion. Transcriptome analysis of linc00899-depleted cells together with gain-of-function and rescue experiments across multiple cell types identified the neuronal microtubule-binding protein, TPPP/p25, as a target of linc00899. Linc00899 binds the genomic locus of TPPP/p25 and suppresses its transcription through a cis-acting mechanism. In cells depleted of linc00899, the consequent upregulation of TPPP/p25 alters microtubule dynamics and is necessary and sufficient to delay mitosis. Overall, our comprehensive screen identified several lncRNAs with roles in genome stability and revealed a new lncRNA that controls microtubule behaviour with functional implications beyond cell division.

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“…Negative control siRNA and cells without any siRNA treatment were used as controls, for which we observed no systematic differences in the frequencies of each phenotype 15 ( Fig. 1b-d).…”

Section: High-content Phenotypic Screen Identified New Lncrnas Involvmentioning

confidence: 85%

Section: High-content Phenotypic Screen Identified New Lncrnas Involvmentioning

confidence: 99%

Section: High-content Phenotypic Screen Identified New Lncrnas Involvmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Stojic

Lun

Mascalchi

et al. 2019

Preprint

Self Cite

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Long noncoding RNA SOX2OT promotes the proliferation of pancreatic cancer by binding to FUS

Chen

Zhang

Chen

et al. 2020

Intl Journal of Cancer

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Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors has one of the worst prognoses, and the role of long noncoding RNAs (lncRNAs) in the biological and pathological processes of pancreatic cancer, including tumor cell proliferation, is a popular topic in tumor research. Our previous study revealed the correlation between high levels of the lncRNA-SOX2OT (SOX2OT) with poor survival outcomes. Cell Counting Kit-8, EdU, Flow cytometry and Colony formation assays as well as Xenograft growth of PDAC cells in mice were used for the detection of PDAC cells proliferation progression. Fluorescence in situ hybridization, RNA-binding protein pulldown and RNA immunoprecipitation assays were also used to identify the putative mechanisms of SOX2OT participating in the tumor progression. SOX2OT and its potential downstream targets were verified by Western blot and quantitative real-time polymerase chain reaction (qRT-PCR). SOX2OT was confirmed to promote the proliferation of PDAC cells. It was found to directly physically bind to FUS and we also demonstrated that FUS protein stability was affected by binding with SOX2OT and FUS could suppressed PDAC tumor by regulating cell cycleassociated factors CCND1 and p27. Our findings suggest that SOX2OT may act as a tumor promoter in PDAC through physically binding FUS and regulating its downstream cell cycle-associated factors CCND1 and p27. It may serve as an effective target for antitumor treatment for pancreatic cancer. † L.C., J.Z. and Q.C contributed equally to this work Additional Supporting Information may be found in the online version of this article.

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A high‐throughput approach to predict A‐to‐I effects on RNA structure indicates a change of double‐stranded content in noncoding RNAs

et al. 2022

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RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane‐less organelles such as stress granules. For instance, N6‐methyladenosine (m6A) enhances SG formation and N1‐methyladenosine (m1A) prevents their transition to solid‐like aggregates. Yet, very little is known about adenosine to inosine (A‐to‐I) modification that is very abundant in human cells and not only impacts mRNAs but also noncoding RNAs. Here, we introduce the CROSSalive predictor of A‐to‐I effects on RNA structure based on high‐throughput in‐cell experiments. Our method shows an accuracy of 90% in predicting the single and double‐stranded content of transcripts and identifies a general enrichment of double‐stranded regions caused by A‐to‐I in long intergenic noncoding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD, and XIST, we investigated the relationship between A‐to‐I editing and interactions with RNA‐binding proteins using available CLIP data and catRAPID predictions. We found that A‐to‐I editing is linked to the alteration of interaction sites with proteins involved in phase separation, which suggests that RNP assembly can be influenced by A‐to‐I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive.

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SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA

Cited by 65 publications

References 30 publications

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Long noncoding RNA SOX2OT promotes the proliferation of pancreatic cancer by binding to FUS

A high‐throughput approach to predict A‐to‐I effects on RNA structure indicates a change of double‐stranded content in noncoding RNAs

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