Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14

Using TSG101 pre-mRNA, we previously discovered cancer-specific re-splicing of mature mRNA that generates aberrant transcripts/proteins. The fact that mRNA is aberrantly re-spliced in various cancer cells implies there must be an important mechanism to prevent deleterious re-splicing on the spliced mRNA in normal cells. We thus postulated that mRNA re-splicing is controlled by specific repressors, and we searched for repressor candidates by siRNA-based screening for mRNA re-splicing activity. We found that knock-down of EIF4A3, which is a core component of the exon junction complex (EJC), significantly promoted mRNA re-splicing. Remarkably, we could recapitulate cancer-specific mRNA re-splicing in normal cells by knock-down of any of the core EJC proteins, EIF4A3, MAGOH, or RBM8A (Y14), implicating the EJC core as the repressor of mRNA re-splicing often observed in cancer cells. We propose that the EJC core is a critical mRNA quality control factor to prevent over-splicing of mature mRNA.

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Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster

eLife ◽

10.7554/elife.19881 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 13

Author(s):

Subhendu Roy Choudhury ◽

Anand K Singh ◽

Tina McLeod ◽

Marco Blanchette ◽

Boyun Jang ◽

...

Keyword(s):

Specific Interaction ◽

Polytene Chromosomes ◽

Exon Junction Complex ◽

Exon Junction ◽

Cell Extracts ◽

Intronless Genes ◽

Core Proteins ◽

Central Protein ◽

Nascent Transcripts

Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosomes. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells. The association of the EJC proteins with nascent transcripts does not require CWC22 and that of Y14 and MAGO is independent of eIF4AIII. We also show that eIF4AIII associates with both polysomal and monosomal RNA in S2 cell extracts, whereas Y14 and MAGO fractionate separately. Cumulatively, our data indicate a global role of eIF4AIII in gene expression, which would be independent of Y14 and MAGO, splicing, and of the EJC, as currently understood.

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CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex

Nucleic Acids Research ◽

10.1093/nar/gkaa564 ◽

2020 ◽

Vol 48 (15) ◽

pp. 8626-8644 ◽

Cited By ~ 1

Author(s):

Jennifer V Gerbracht ◽

Volker Boehm ◽

Thiago Britto-Borges ◽

Sebastian Kallabis ◽

Janica L Wiederstein ◽

...

Keyword(s):

Exon Junction Complex ◽

Core Component ◽

Mrna Isoforms ◽

Nonsense Mediated Decay ◽

Exon Junction ◽

Endonucleolytic Cleavage ◽

Core Proteins ◽

Messenger Ribonucleoprotein ◽

Cytoplasmic Processes

Abstract The exon junction complex (EJC) is an essential constituent and regulator of spliced messenger ribonucleoprotein particles (mRNPs) in metazoans. As a core component of the EJC, CASC3 was described to be pivotal for EJC-dependent nuclear and cytoplasmic processes. However, recent evidence suggests that CASC3 functions differently from other EJC core proteins. Here, we have established human CASC3 knockout cell lines to elucidate the cellular role of CASC3. In the knockout cells, overall EJC composition and EJC-dependent splicing are unchanged. A transcriptome-wide analysis reveals that hundreds of mRNA isoforms targeted by nonsense-mediated decay (NMD) are upregulated. Mechanistically, recruiting CASC3 to reporter mRNAs by direct tethering or via binding to the EJC stimulates mRNA decay and endonucleolytic cleavage at the termination codon. Building on existing EJC-NMD models, we propose that CASC3 equips the EJC with the persisting ability to communicate with the NMD machinery in the cytoplasm. Collectively, our results characterize CASC3 as a peripheral EJC protein that tailors the transcriptome by promoting the degradation of EJC-dependent NMD substrates.

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Regulation of vertebrate embryogenesis by the exon junction complex core component Eif4a3

Developmental Dynamics ◽

10.1002/dvdy.22330 ◽

2010 ◽

Vol 239 (7) ◽

pp. 1977-1987 ◽

Cited By ~ 16

Author(s):

Tomomi Haremaki ◽

Jyotsna Sridharan ◽

Shira Dvora ◽

Daniel C. Weinstein

Keyword(s):

Exon Junction Complex ◽

Core Component ◽

Exon Junction ◽

Complex Core

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Regulation of vertebrate embryogenesis by the Exon Junction Complex core component Eif4a3

Developmental Biology ◽

10.1016/j.ydbio.2010.05.343 ◽

2010 ◽

Vol 344 (1) ◽

pp. 508

Author(s):

Daniel C. Weinstein ◽

Tomomi Haremaki ◽

Jyotsna Sridharan ◽

Shira Dvora

Keyword(s):

Exon Junction Complex ◽

Core Component ◽

Exon Junction ◽

Complex Core

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The exon junction complex core factor eIF4A3 is a key regulator of HPV16 gene expression

Bioscience Reports ◽

10.1042/bsr20203488 ◽

2021 ◽

Vol 41 (4) ◽

Author(s):

Koceila Meznad ◽

Philippe Paget-Bailly ◽

Elise Jacquin ◽

Anne Peigney ◽

François Aubin ◽

...

Keyword(s):

Gene Expression ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Exon Junction Complex ◽

Eukaryotic Translation ◽

Protein Levels ◽

Exon Junction ◽

Complex Core ◽

Eukaryotic Translation Initiation ◽

E6 And E7

Abstract High-risk human papillomavirus (hrHPVs), particularly HPV16 and HPV18, are the etiologic factors of ano-genital cancers and some head and neck squamous cell carcinomas (HNSCCs). Viral E6 and E7 oncoproteins, controlled at both transcriptional and post-transcriptional levels, drive hrHPVs-induced carcinogenesis. In the present study, we investigated the implication of the DEAD-box helicase eukaryotic translation initiation factor 4A3 (eIF4A3,) an Exon Junction Complex factor, in the regulation of HPV16 gene expression. Our data revealed that the depletion of the factor eIF4A3 up-regulated E7 oncoprotein levels. We also showed that the inhibition of the nonsense-mediated RNA decay (NMD) pathway, resulted in the up-regulation of E7 at both RNA and protein levels. We therefore proposed that HPV16 transcripts might present different susceptibilities to NMD and that this pathway could play a key role in the levels of expression of these viral oncoproteins during the development of HPV-related cancers.

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CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex

10.1101/811018 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jennifer V. Gerbracht ◽

Volker Boehm ◽

Thiago Britto-Borges ◽

Sebastian Kallabis ◽

Janica L. Wiederstein ◽

...

Keyword(s):

Exon Junction Complex ◽

Core Component ◽

Mrna Isoforms ◽

Nonsense Mediated Decay ◽

Exon Junction ◽

Endonucleolytic Cleavage ◽

Core Proteins ◽

Messenger Ribonucleoprotein ◽

Cytoplasmic Processes

AbstractThe exon junction complex (EJC) is an essential constituent and regulator of spliced messenger ribonucleoprotein particles (mRNPs) in metazoans. As a core component of the EJC, CASC3 was described to be pivotal for EJC-dependent nuclear and cytoplasmic processes. However, recent evidence suggests that CASC3 functions differently from other EJC core proteins. Here, we have established human CASC3 knockout cell lines to elucidate the cellular role of CASC3. In the knockout cells, overall EJC composition and EJC-dependent splicing are unchanged. A transcriptome-wide analysis reveals that hundreds of mRNA isoforms targeted by nonsense-mediated decay (NMD) are upregulated. Mechanistically, recruiting CASC3 to reporter mRNAs by direct tethering or via binding to the EJC stimulates mRNA decay and endonucleolytic cleavage at the termination codon. Building on existing EJC-NMD models, we propose that CASC3 equips the EJC with the ability to communicate with the NMD machinery in the cytoplasm. Collectively, our results characterize CASC3 as a peripheral EJC protein that tailors the transcriptome by promoting the degradation of EJC-dependent NMD substrates.

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Roles of the exon junction complex components in the central nervous system: a mini review

Reviews in the Neurosciences ◽

10.1515/revneuro-2017-0113 ◽

2018 ◽

Vol 29 (8) ◽

pp. 817-824 ◽

Cited By ~ 4

Author(s):

Katarzyna Bartkowska ◽

Beata Tepper ◽

Kris Turlejski ◽

Ruzanna L. Djavadian

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Protein Translation ◽

Adult Brain ◽

Initiation Factor ◽

Exon Junction Complex ◽

Exon Junction ◽

Core Proteins ◽

Zygote Development ◽

The Central Nervous System

Abstract The exon junction complex (EJC) consists of four core proteins: Magoh, RNA-binding motif 8A (Rbm8a, also known as Y14), eukaryotic initiation factor 4A3 (eIF4A3, also known as DDX48), and metastatic lymph node 51 (MLN51, also known as Casc3 or Barentsz), which are involved in the regulation of many processes occurring between gene transcription and protein translation. Its main role is to assemble into spliceosomes at the exon-exon junction of mRNA during splicing. It is, therefore, a range of functions concerning post-splicing events such as mRNA translocation, translation, and nonsense-mediated mRNA decay (NMD). Apart from this, proteins of the EJC control the splicing of specific pre-mRNAs, for example, splicing of the mapk transcript. Recent studies support essential functions of EJC proteins in oocytes and, after fertilization, in all stages of zygote development, as well as the growth of the embryo, including the development of the nervous system. During the development of the central nervous system (CNS), the EJC controls mitosis, regulating both symmetric and asymmetric cell divisions. Reduced levels of EJC components cause microcephaly. In the adult brain, Y14 and eIF4A3 appear to be involved in synaptic plasticity and in learning and memory. In this review, we focus on the involvement of EJC components in brain development and its functioning under normal conditions.

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The Exon Junction Complex Core Represses Caner-specific Mature mRNA Re-splicing: A Potential Key Role in Terminating Splicing

10.1101/2021.04.01.438154 ◽

2021 ◽

Author(s):

Yuta Otani ◽

Toshiki Kameyama ◽

Akila Mayeda

Keyword(s):

Cancer Cells ◽

Control Factor ◽

Exon Junction Complex ◽

Core Component ◽

Normal Cells ◽

Knock Down ◽

Exon Junction ◽

Mature Mrna ◽

Complex Core ◽

Specific Mrna

AbstractUsing the TSG101 pre-mRNA, we previously discovered cancer-specific re-splicing of mature mRNA that generates aberrant transcripts/proteins. The fact that mRNA is aberrantly re-spliced in various cancer cells implies there must be an important mechanism to prevent deleterious re-splicing on the spliced mRNA in normal cells. We thus postulated that the mRNA re-splicing is controlled by specific repressors and we searched for repressor candidates by siRNA-based screening for mRNA re-splicing activity. We found that knock-down of EIF4A3, which is a core component of the exon junction complex (EJC), significantly promoted mRNA re-splicing. Remarkably, we could recapitulate cancer-specific mRNA re-splicing in normal cells by knock-down of any of the core EJC proteins, EIF4A3, MAGOH or RBM8A (Y14), implicating the EJC core as the repressor of mRNA re-splicing often observed in cancer cells. We propose that the EJC core is a critical mRNA quality control factor to prevent over-splicing of mature mRNA.

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