Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

Helwak, Aleksandra; Kudla, Grzegorz; Dudnakova, Tatiana; Tollervey, David

doi:10.1016/j.cell.2013.03.043

Cited by 1,159 publications

(1,488 citation statements)

References 58 publications

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“…The MARGI procedure without either the RNA or the DNA ligation step could not produce a detectable amount of DNA in the final sequencing library. In the second control experiment, we used a mixture of Drosophila S2 cells and human HEK293T cells to estimate the extent of unspecific ligations (cross-species control) [2,3]. After crosslinking and cell lysis, the lysates from the two species were mixed before any subsequent steps.…”

mentioning

confidence: 99%

Systematic Mapping of RNA-Chromatin Interactions In Vivo

Sridhar¹,

Rivas‐Astroza²,

Nguyen³

et al. 2017

Current Biology

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SummaryRNA molecules can attach to chromatin. It remains difficult to know what RNAs are associated with chromatin and where are the genomic target loci of these RNAs. Here, we present MARGI (Mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for human embryonic stem (ES) cells and HEK cells. MARGI revealed hundreds of caRNAs including previously known XIST, SNHG1, NEAT1, MALAT1, as well as each caRNA's genomic interaction loci. Using a cross-species experiment, we estimated that approximately 2.2% of MARGI identified interactions were false positives. In ES and HEK cells, the RNA ends of more than 5% of MARGI read pairs were mapped to distal or inter-chromosomal locations as compared to the locations of their corresponding DNA ends. The majority of transcription start sites are associated with distal or inter-chromosomal caRNAs. ChIP-seq reported H3K27ac and H3K4me3 levels are positively while H3K9me3 is negatively correlated with MARGI reported RNA attachment levels. The MARGI technology should facilitate revealing novel RNA functions and their genomic target regions. Graphical abstractSridhar et al. develop a technology to map global RNA-chromatin interactions in unperturbed cells. They discover hundreds of chromatin associated RNAs. They find that the majority of Correspondence to: Sheng Zhong. 3 Co-first author 4 Lead Contact Supplemental Information: Supplemental Information includes Supplemental Experimental Procedures and four figures and can be found with this article online. All sequencing data are available at Gene Expression Omnibus with access number GSE92345.Author Contributions: B.S., T.C.N., and S.Z. designed the experiments. B.S., T.C.N., and L.H performed the experiments. All authors analyzed and interpreted the data.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. HHS Public Access Results and Discussion Development of the MARGI technologyWe developed MARGI (Mapping RNA-genome interactions), a technology to massively reveal RNA-chromatin interactions from unperturbed cells. MARGI simultaneously identifies all caRNAs and the respective genomic target loci of each caRNA. This changes the paradigm of analyzing one-RNA-at-a-time, and enables the mapping of the native RNAchromatin interaction netwo...

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mentioning

confidence: 99%

Systematic Mapping of RNA-Chromatin Interactions In Vivo

Sridhar¹,

Rivas‐Astroza²,

Nguyen³

et al. 2017

Current Biology

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“…This 5′ region of the miRNA, corresponding to 2 to 7 nt, is essential to target messenger RNAs (mRNAs), mostly in their 3′ untranslated transcript region (3′UTR). More rarely, this targeting could also be localized in the 5′UTR or in the open reading frame (ORF) of mRNAs (Bartel, 2009; Helwak, Kudla, Dudnakova & Tollervey, 2013). The interaction between the miRNA and the target mRNA forms a Watson–Crick pair, resulting in the inhibition of protein synthesis, depending on the pairing of the miRNA and its target.…”

Section: Micrornasmentioning

confidence: 99%

“…For these reasons, miRNAs are currently known as powerful regulators of gene expression. One miRNA has the ability to interact with many target mRNAs and to regulate their expression (Gennarino et al., 2012; Helwak et al., 2013; Hendrickson et al., 2009; Tsang, Ebert & van Oudenaarden, 2010). Currently, 64% of the human miRNAs belong to seed families, which correspond to microRNAs sharing the same or a highly similar seed region (Kozomara & Griffiths‐Jones, 2011).…”

Section: Micrornasmentioning

confidence: 99%

MicroRNAs in hereditary and sporadic premature aging syndromes and other laminopathies

et al. 2018

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SummaryHereditary and sporadic laminopathies are caused by mutations in genes encoding lamins, their partners, or the metalloprotease ZMPSTE24/FACE1. Depending on the clinical phenotype, they are classified as tissue‐specific or systemic diseases. The latter mostly manifest with several accelerated aging features, as in Hutchinson–Gilford progeria syndrome (HGPS) and other progeroid syndromes. MicroRNAs are small noncoding RNAs described as powerful regulators of gene expression, mainly by degrading target mRNAs or by inhibiting their translation. In recent years, the role of these small RNAs has become an object of study in laminopathies using in vitro or in vivo murine models as well as cells/tissues of patients. To date, few miRNAs have been reported to exert protective effects in laminopathies, including miR‐9, which prevents progerin accumulation in HGPS neurons. The recent literature has described the potential implication of several other miRNAs in the pathophysiology of laminopathies, mostly by exerting deleterious effects. This review provides an overview of the current knowledge of the functional relevance and molecular insights of miRNAs in laminopathies. Furthermore, we discuss how these discoveries could help to better understand these diseases at the molecular level and could pave the way toward identifying new potential therapeutic targets and strategies based on miRNA modulation.

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“…mRNA, including the G-to-A point mutation (14) at codon 12 (G12S) and, as a consequence, mismatching for the same region in WT KRAS. Specifically, the amiRs were designed such that the seed mismatch on KRAS WT would fall on different seed bases, between and including nucleotide positions 2 and 7.…”

Section: Significancementioning

confidence: 99%

“…Alternatively, use of microRNAs (miRNAs), a class of endogenous 22-to 24-bp-long sncRNAs involved in multiple cellular processes, pathways, and diseases, including cancer (13), could provide a more tailored targeted therapy design. Generally, miRNAs target the 3′ untranslated region (UTR) of mRNA transcripts, despite having also been proven to bind the CDS, as well as the 5′ UTR (14) like siRNAs, causing translation inhibition and/or inducing mRNA degradation (15). Nevertheless, unlike siRNAs, miRNAs exhibit only partial complementarity to the binding sequence on their targets.…”

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confidence: 99%

Selective targeting of point-mutated KRAS through artificial microRNAs

Acunzo

Romano

Nigita

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Mutated protein-coding genes drive the molecular pathogenesis of many diseases, including cancer. Specifically, mutated KRAS is a documented driver for malignant transformation, occurring early during the pathogenesis of cancers such as lung and pancreatic adenocarcinomas. Therapeutically, the indiscriminate targeting of wild-type and point-mutated transcripts represents an important limitation. Here, we leveraged on the design of miRNA-like artificial molecules (amiRNAs) to specifically target point-mutated genes, such as KRAS, without affecting their wild-type counterparts. Compared with an siRNA-like approach, the requirement of perfect complementarity of the microRNA seed region to a given target sequence in the microRNA/target model has proven to be a more efficient strategy, accomplishing the selective targeting of point-mutated KRAS in vitro and in vivo

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Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

Cited by 1,159 publications

References 58 publications

Systematic Mapping of RNA-Chromatin Interactions In Vivo

Systematic Mapping of RNA-Chromatin Interactions In Vivo

MicroRNAs in hereditary and sporadic premature aging syndromes and other laminopathies

Selective targeting of point-mutated KRAS through artificial microRNAs

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