Cytoplasmic Drosha activity generated by alternative splicing

Dai, Li-Shang; Chen, Kevin; Youngren, Brenda; Kulina, Julia; Yang, Acong; Guo, Zhengyu; Jin, Li; Yu, Peng; Gu, Shuo

doi:10.1093/nar/gkw668

Cited by 39 publications

(42 citation statements)

References 59 publications

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“…These cells also express a lower molecular weight isoform of DGCR8 ( Figure 3E). Different isoforms of DROSHA with distinct cytoplasmic or nuclear localization have been recently identified [35,36]. However, it is still not clear whether the isoforms detected here are the same as those previously described.…”

Section: Plekha7 and Rnai Components Are Mis-localized In Human Colonsupporting

confidence: 61%

Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer

Nair-Menon

Daulagala

Connor

et al. 2020

IJMS

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The RNA interference (RNAi) machinery is an essential component of the cell, regulating miRNA biogenesis and function. RNAi complexes were thought to localize either in the nucleus, such as the microprocessor, or in the cytoplasm, such as the RNA-induced silencing complex (RISC). We recently revealed that the core microprocessor components DROSHA and DGCR8, as well as the main components of RISC, including Ago2, also associate with the apical adherens junctions of well-differentiated cultured epithelial cells. Here, we demonstrate that the localization of the core RNAi components is specific and predominant at apical areas of cell-cell contact of human normal colon epithelial tissues and normal primary colon epithelial cells. Importantly, the apical junctional localization of RNAi proteins is disrupted or lost in human colon tumors and in poorly differentiated colon cancer cell lines, correlating with the dysregulation of the adherens junction component PLEKHA7. We show that the restoration of PLEKHA7 expression at adherens junctions of aggressively tumorigenic colon cancer cells restores the junctional localization of RNAi components and suppresses cancer cell growth in vitro and in vivo. In summary, this work identifies the apical junctional localization of the RNAi machinery as a key feature of the differentiated colonic epithelium, with a putative tumor suppressing function.

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Section: Plekha7 and Rnai Components Are Mis-localized In Human Colonsupporting

confidence: 61%

Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer

Nair-Menon

Daulagala

Connor

et al. 2020

IJMS

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“…Because GSK3b activity is regulated by various extracellular signals (Beurel et al, 2015), it is possible that serum starvation might cause an inhibition of GSK3b and mediate dephosphorylation of Ser 300/302 of Drosha, resulting in the accumulation in the cytoplasm. An alternatively spliced form of Drosha skipping exon 6, which encodes the putative nuclear localization signal, is reported to localize in both the cytoplasm and the nucleus (Dai et al, 2016;Link et al, 2016). However, the molecular size of cytoplasmic Drosha after serum starvation is equivalent to full-length Drosha (159 kDa) and indistinguishable from nuclear Drosha, thus it is unlikely that alternative splicing is involved in the change of nuclear/cytoplasmic ratio of Drosha upon serum starvation.…”

Section: Discussionmentioning

confidence: 99%

Control of ribosomal protein synthesis by Microprocessor complex

Jiang

Prabhakar

Voorn

et al. 2020

Preprint

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Ribosome biogenesis in eukaryotes requires stoichiometric production and assembly of 80 ribosomal proteins (RPs) and 4 ribosomal RNAs, and its rate must be coordinated with cellular growth. The indispensable regulator of RP biosynthesis is the 5'-terminal oligopyrimidine (TOP) motif, spanning the transcription start site of all RP genes. Here we show that the Microprocessor complex, previously linked to the first step of processing microRNAs (miRNAs), coregulates RP expression by binding the TOP motif of nascent RP mRNAs and stimulating transcription elongation via resolution of DNA/RNA hybrids. Cell growth arrest triggers nuclear export and degradation of the Microprocessor protein Drosha by the E3 ubiquitin ligase Nedd4, accumulation of DNA/RNA hybrids at RP gene loci, decreased RP synthesis, and ribosome deficiency, hence synchronizing ribosome production with cell growth. Conditional deletion of Drosha in erythroid progenitors phenocopies human ribosomopathies, in which ribosomal insufficiency leads to anemia. Outlining a miRNA-independent role of the Microprocessor complex at the interphase between cell growth and ribosome biogenesis offers a new paradigm by which cells alter their protein biosynthetic capacity and cellular metabolism.in response to the change in cellular growth environment remains to be identified (Meyuhas and Kahan, 2015; Patursky-Polischuk et al., 2014).During transcription, a three-stranded nucleic acid structure known as an R-loop spontaneously forms(García-Muse and Aguilera, 2019). It is composed of a DNA/RNA hybrid (a single-stranded template DNA (ssDNA) hybridized with a nascent mRNA) and an associated non-template ssDNA (García-Muse and Aguilera, 2019;Sanz and Chédin, 2019;Sanz et al., 2016). R-loops are critical modulator of gene expression and DNA repair (García-Muse and Aguilera, 2019;Sanz and Chédin, 2019;Sanz et al., 2016), and their extended persistence during transcription is inhibitory to gene expression (Gowrishankar et al., 2013;Nudler, 2012). The abundance of R-loops is determined by the balance between its formation and resolution of DNA/RNA hybrids and various factors, including transcription factors, helicases, ribonucleases, topoisomerases, chromatin remodelers, proteins in DNA repair and RNA surveillance, have been identified to control R-loop homeostasis(García-Muse and Aguilera, 2019). Deregulation of R-loops, which results in aberrant gene expression and chromatin structure, increased DNA breaks, and genome instability, contributes to human disease, including neurological disorders and tumorigenesis (García-Muse and Aguilera, 2019;Groh and Gromak, 2014;Sanz et al., 2016).The Microprocessor complex comprises two core components, the ribonuclease (RNase) III Drosha and its cofactor Dgcr8. It is essential for the biogenesis of most microRNAs (miRNAs), short RNAs that repress gene expression by binding to messenger RNAs and targeting them for degradation and/or preventing their translation (Han et al., 2004;Siomi and Siomi, 2010). The Microprocessor localizes predom...

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“…To identify the DAS events, we performed DAS analysis 57,58,59,60,61 . Briefly, the raw RNA-Seq reads first were aligned to mouse genome (mm9) using STAR 62 with default settings, and those uniquely mapped reads were retained to calculate the counts of the reads for each exon and each exon-exon junction annotated in the UCSC knownGene (mm9) table 63 using the Python package HTSeq 64 .…”

Section: Das Analysis Using Rna-seq Datamentioning

confidence: 99%

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors

Jin

Deng

et al. 2020

Preprint

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A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that coldinduced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.

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Cytoplasmic Drosha activity generated by alternative splicing

Cited by 39 publications

References 59 publications

Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer

Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer

Control of ribosomal protein synthesis by Microprocessor complex

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors

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