CLIP: viewing the RNA world from an RNA-protein interactome perspective

Zhang, Yin; Xie, Shu‐Juan; Xu, Hui; Qu, Liang‐Hu

doi:10.1007/s11427-014-4764-5

Cited by 15 publications

(11 citation statements)

References 149 publications

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“…By sequencing of Argonaute (Ago)-bound RNAs isolated by crosslinking immunoprecipitation (CLIP-Seq, also known as HITS-CLIP), researchers have successfully identified tens of thousands of miRNA-target interactions in various systems [ 31 , 33 – 36 ]. And after, modified forms of this method, such as photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) [ 37 ], individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) [ 38 ], and some other variants [ 39 , 40 ], have been successfully used in decoding RNA–protein interactions.…”

Section: Introductionmentioning

confidence: 99%

Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development

Xie

Chen

et al. 2018

Cell Death Differ

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Skeletal muscle differentiation is controlled by multiple cell signaling pathways, however, the JNK/MAPK signaling pathway dominating this process has not been fully elucidated. Here, we report that the JNK/MAPK pathway was significantly downregulated in the late stages of myogenesis, and in contrast to P38/MAPK pathway, it negatively regulated skeletal muscle differentiation. Based on the PAR-CLIP-seq analysis, we identified six elevated miRNAs (miR-1a-3p, miR-133a-3p, miR-133b-3p, miR-206-3p, miR-128-3p, miR-351-5p), namely myogenesis-associated miRNAs (mamiRs), negatively controlled the JNK/MAPK pathway by repressing multiple factors for the phosphorylation of the JNK/MAPK pathway, including MEKK1, MEKK2, MKK7, and c-Jun but not JNK protein itself, and as a result, expression of transcriptional factor MyoD and mamiRs were further promoted. Our study revealed a novel double-negative feedback regulatory pattern of cell-specific miRNAs by targeting phosphorylation kinase signaling cascade responsible for skeletal muscle development.

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Section: Introductionmentioning

confidence: 99%

Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development

Xie

Chen

et al. 2018

Cell Death Differ

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“…More reliable and user-friendly techniques need to be developed to detect RNA interactions with DNA/RNA/proteins, the spatial localization of low-abundance RNAs, the structures of lncRNA complexes, etc (Zhang et al, 2015;Zhu et al, 2013). For example, to detect chromatin interactions, conformation capture-based assays (HiC, ChIA-PET, etc.)…”

Section: Discussionmentioning

confidence: 99%

Long noncoding RNAs as Organizers of Nuclear Architecture

Cheng

Ming

Zhu

et al. 2016

Sci. China Life Sci.

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In the eukaryotic cell nucleus, chromatin and its associated macromolecules must be organized into a higher-ordered conformation to function normally. However, mechanisms underlying the organization and dynamics of the nucleus remain unclear. Long noncoding RNAs (lncRNAs), i.e., transcripts longer than 200 nucleotides with little or no protein-coding capacity, are increasingly recognized as important regulators in diverse biological processes. Recent studies have shown that some lncRNAs are involved in various aspects of genome organization, including the facilitation of chromosomal interactions and establishment of nuclear bodies, suggesting that lncRNAs act as general organizers of the nuclear architecture. Here, we discuss recent advances in this emerging and intriguing field. long noncoding RNAs, chromatin, nuclear architecture

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“…Here we present a basic overview of some considerations and software for the DGE analysis process and other downstream analyses ( Oshlack et al, 2010 ; Rapaport et al, 2013 ; Williams et al, 2014 ; Finotello and Di Camillo, 2015 ; Conesa et al, 2016 ). Also, note that CLIP studies may require specialized experimental design and analysis using specific software ( Wang et al, 2015 ; Zhang et al, 2015 ). For further help and extra information, the SeqAnswers 2 , Biostars 3 , and StackExchange 4 forums are all excellent resources.…”

Section: High-throughput Assaysmentioning

confidence: 99%

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation

Namjoshi

Raab‐Graham

2017

Front. Mol. Neurosci.

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In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.

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CLIP: viewing the RNA world from an RNA-protein interactome perspective

Cited by 15 publications

References 149 publications

Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development

Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development

Long noncoding RNAs as Organizers of Nuclear Architecture

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation

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