What Are 3′ UTRs Doing?

Mayr, Christine

doi:10.1101/cshperspect.a034728

Cited by 373 publications

(317 citation statements)

References 123 publications

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“…Therefore-as also supported by results from a recent in vitro study 53 -3'UTR editing could be used to upregulate the expression of many or most of these genes in their native chromatin context. At the same time, it is increasingly recognised that 3'UTRs can have other functions, such as regulating mRNA localization or protein-protein interactions [54][55][56] , which are likely to limit the use of the 3'UTR editing for gene Knock Up. However, once relevant motifs are identified, it could be feasible to retain the sequences required for these other functions by selecting appropriate gRNAs for Cas9-mediated excision, or by incorporating those motifs into the FLEx cassette, thus expanding the list of potential target genes for the Knock Up approach.…”

Section: Discussionmentioning

confidence: 99%

Gene Knock Up via 3’UTR editing to study gene functionin vivo

Mätlik

Olfat

et al. 2019

Preprint

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Currently available genetic tools do not allow researchers to upregulate ('Knock Up') the levels of a given protein while retaining its cell-type-specific regulation. As a result, we have limited ability to develop overexpression-related disease models, to study the contribution of single genes in diseases caused by copy number variations and to identify disease pathways for drug targets. Here we develop two approaches for endogenous gene upregulation: conditional Knock Up (cKU) utilizing the Cre/lox system, and CRISPR-Cas9 mediated gene Knock Up (KU) in wild-type mouse embryos and human cells. Using glial cell line derived neurotrophic factor (GDNF) as a proof of concept, we show that both approaches resulted in upregulation of endogenous GDNF levels without disturbing Gdnf's expression pattern. Furthermore, CNS-specific GDNF cKU resulted in dopaminergic abnormalities and schizophrenia-like phenotypes. Our results suggest that gene Knock Up can reveal unknown gene functions and provide novel entry points for studying neurological disease.

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Section: Discussionmentioning

confidence: 99%

Gene Knock Up via 3’UTR editing to study gene functionin vivo

Mätlik

Olfat

et al. 2019

Preprint

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“…Since mRNA stability is closely regulated by RNA-binding proteins (RBPs) [49][50][51][52] , we next asked whether RBPs are involved in the modulation of mRNA abundance by RNA editing sites. To this end, we analyzed enhanced ultraviolet crosslinking and immunoprecipitation (eCLIP) datasets of 126 RBPs in two cell lines (HepG2 and K562) from ENCODE 46,53 .…”

Section: Ilf3 As An Editing-dependent Regulator Of Mrna Abundancementioning

confidence: 99%

Differential RNA editing between epithelial and mesenchymal tumors impacts mRNA abundance in immune response pathways

Chan

Bahn

et al. 2020

Preprint

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Recent studies revealed global shifts in RNA editing, the modification of RNA sequences, across many cancers. Besides a few sites implicated in tumorigenesis or metastasis, most tumor-associated sites, predominantly in noncoding regions, have unknown function. Here, we characterize editing profiles between epithelial (E) and mesenchymal (M) phenotypes in seven cancer types, as epithelial-mesenchymal transition (EMT) is a key paradigm for metastasis. We observe distinct editing patterns between E and M tumors and EMT induction upon loss of ADAR enzymes in cultured cells. E-M differential sites are highly enriched in genes involved in immune and viral processes, some of which regulate mRNA abundance of their respective genes. We identify a novel mechanism in which ILF3 preferentially stabilizes edited transcripts. Among editing-dependent ILF3 targets is the transcript encoding PKR, a crucial player in immune response. Our study demonstrates the broad impact of RNA editing in cancer and relevance of editing to cancer-related immune pathways.

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“…UTRs offer a critical source of regulation for messages through specific ciselements, which can bind microRNAs and/or proteins to regulate pathways including RNA decay and translation (12). To probe for novel cis-elements within 3'UTRs, we specifically targeted 3'UTR within known essential genes.…”

Section: Crispr Targeting Of the 3' Utrs Of Essential Genes Identifiementioning

confidence: 99%

“…Untranslated regions (UTRs) of messages are important for regulating stability, translation and localization (12). Sequences within the UTRs (cis-elements) can function in microRNA binding, structure and/or protein binding (13).…”

Section: 'Utr-targeting Guides and Identification Of Potential Cis-ementioning

confidence: 99%

“…In addition to identifying essential genes in macrophages we also aimed to understand what regulatory mechanisms could be involved in controlling expression of these genes. We know that the untranslated regions (UTRs) of messages are important for regulating stability, translation and localization (reviewed in (12)). Sequences within the UTRs (cis-elements) can function in microRNA binding, structure and/or protein binding (13).…”

Section: Introductionmentioning

confidence: 99%

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High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways

Covarrubias

Vollmers

Capili

et al. 2019

Preprint

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Macrophages are critical cells of the innate immune system involved in the recognition and destruction of invading microbes in addition to the resolution of inflammation and maintenance of homeostasis. Understanding the genes involved in all aspects of macrophage biology is essential to gaining new insights into immune system dysregulation during diseases that range from autoinflammatory to cancer. Here we utilize high throughput clustered regularly interspaced short palindromic repeats (CRISPR) screening to generate a resource that identifies genes required for macrophage viability and function. First, we employ a pooled based CRISPR/Cas nuclease active screening approach to identify essential genes required for macrophage viability by targeting genes within coding exons. In addition, we also target 3'UTRs to gain insights into new cis-regulatory regions that control expression of these essential genes. Second, using our recently generated NF-κB reporter macrophage line, we perform a fluorescence-activated cell sorting (FACS)-based high-throughput genetic screen to identify regulators of inflammation. We identify a number of novel positive and negative regulators of the NF-κB pathway as well as unraveling complexities of the TNF signaling cascade showing it can function in an autocrine manner to negatively regulate the pathway. Utilizing a single complex library design we are capable of interrogating various aspects of macrophage biology, generating a resource for future studies. SignificanceExcess inflammation is associated with a variety of autoimmune diseases and cancers. Macrophages are important mediators of this inflammatory response. Defining the genes involved in their viability and effector function is needed to completely understand these two important aspects of macrophage biology. Here we screened over 21,000 genes and generated a resource guide of genes required for macrophage viability as well as novel positive and negative regulators of NF-κB signaling. We reveal important regulatory aspects of TNF signaling and showing that membrane-bound TNF primarily functions in an autocrine fashion to negatively regulate inflammation. /body

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What Are 3′ UTRs Doing?

Cited by 373 publications

References 123 publications

Gene Knock Up via 3’UTR editing to study gene functionin vivo

Gene Knock Up via 3’UTR editing to study gene functionin vivo

Differential RNA editing between epithelial and mesenchymal tumors impacts mRNA abundance in immune response pathways

High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways

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