Multiple levels of post-transcriptional control of expression of the poly (A)-binding Protein

Bag, Jnanankur; Bhattacharjee, Rumpa Biswas

doi:10.4161/rna.7.1.10256

Cited by 27 publications

(21 citation statements)

References 78 publications

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“…For example, FAM1 showed significant similarity to the motif for PUMILIO, a family of proteins involved in RNA degradation and inhibition of RNA translation (Spassov and Jurecic, 2003). Also demonstrating significant similarities are motifs for the RNA splicing regulator, epithelial splicing regulatory protein 1 (ESRP1; also known as RBM35a) (Warzecha et al, 2009); the cytoplasmic poly(A) binding protein (PABPC), which mediates ribosome recruitment and translation initiation of target transcripts (Bag and Bhattacharjee, 2010)); and the serine/arginine-rich splicing factor 1 (SRSF1), another regulator of RNA splicing. Thus, CBX7 motifs appear to possess prominent characteristics that overlap those of known RNA binding proteins.…”

Section: Resultsmentioning

confidence: 99%

Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3′ UTRs to Regulate mRNA Expression

et al. 2017

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SUMMARY Interaction networks between chromatin complexes and long noncoding RNAs have become a recurrent theme in epigenetic regulation. However, technical limitations have precluded identification of RNA binding motifs for chromatin-associated proteins. Here we add a denaturation step to UV-crosslink RNA immunoprecipitation (dCLIP), and apply dCLIP to mouse and human chromobox homolog 7 (CBX7), an RNA-binding subunit of Polycomb repressive complex 1 (PRC1). In both species, CBX7 predominantly binds 3’ untranslated regions (UTRs) of messenger RNAs. CBX7 binds with a median RNA “footprint” of 171–183 nucleotides, the small size of which facilitates motif identification by bioinformatics. We find four families of consensus RNA motifs in mouse, and independent analysis of human CBX7 dCLIP data identifies similar motifs. Their mutation abolishes CBX7 binding in vitro. Pharmacological intervention with antisense oligonucleotides paradoxically increases CBX7 binding and enhances gene expression. These data support the utility of dCLIP and reveal an unexpected functional interaction between CBX7 and the 3’UTRs of mRNA.

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Section: Resultsmentioning

confidence: 99%

Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3′ UTRs to Regulate mRNA Expression

et al. 2017

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“…PABPC1 has been mostly known to bind poly(A) tail and is involved in NMD pathway [49]. Several groups report involvement of PABPC1 in protein complexes playing a role in mRNA stability [50], [51]. Thus, PABPC1 could be also involved in RNA metabolism including splicing.…”

Section: Discussionmentioning

confidence: 99%

Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants

Greger

Rung

et al. 2014

PLoS ONE

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Chimeric RNAs originating from two or more different genes are known to exist not only in cancer, but also in normal tissues, where they can play a role in human evolution. However, the exact mechanism of their formation is unknown. Here, we use RNA sequencing data from 462 healthy individuals representing 5 human populations to systematically identify and in depth characterize 81 RNA tandem chimeric transcripts, 13 of which are novel. We observe that 6 out of these 81 chimeras have been regarded as cancer-specific. Moreover, we show that a prevalence of long introns at the fusion breakpoint is associated with the chimeric transcripts formation. We also find that tandem RNA chimeras have lower abundances as compared to their partner genes. Finally, by combining our results with genomic data from the same individuals we uncover intronic genetic variants associated with the chimeric RNA formation. Taken together our findings provide an important insight into the chimeric transcripts formation and open new avenues of research into the role of intronic genetic variants in post-transcriptional processing events.

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“…In the cytoplasm, PABPC1 binds to the 3= poly(A) tail of eukaryotic mRNAs through its RNA recognition motifs (RRMs) and interacts with the N terminus of eukaryotic initiation factor 4G (eIF4G), part of the eIF4F complex associated with the 5= cap structure. The interactions of PABPC1 with RNA and elF4G cause the mRNA to form a closed loop (6)(7)(8)(9), thereby stabilizing the RNA and promoting ribosome recruitment and translation initiation (8,10). Through interaction with eukaryotic release factor 3 (eRF3) and an exon junction complex, PABPC1 is also involved in nonsense-mediated decay (NMD) (11)(12)(13).…”

mentioning

confidence: 99%

Interplay between Polyadenylate-Binding Protein 1 and Kaposi's Sarcoma-Associated Herpesvirus ORF57 in Accumulation of Polyadenylated Nuclear RNA, a Viral Long Noncoding RNA

Massimelli

Majerčiak

Kruhlak

et al. 2013

J Virol

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Polyadenylate-binding protein cytoplasmic 1 (PABPC1) is a cytoplasmic-nuclear shuttling protein important for protein translation initiation and both RNA processing and stability. We report that PABPC1 forms a complex with the Kaposi's sarcomaassociated herpesvirus (KSHV) ORF57 protein, which allows ORF57 to interact with a 9-nucleotide (nt) core element of KSHV polyadenylated nuclear (PAN) RNA, a viral long noncoding RNA (lncRNA), and increase PAN stability. The N-terminal RNA recognition motifs (RRMs) of PABPC1 are necessary for the direct interaction with ORF57. During KSHV lytic infection, the expression of viral ORF57 leads to a substantial decrease in overall PABPC1 expression, along with a shift in the cellular distribution of the remaining PABPC1 to the nucleus. Interestingly, PABPC1 and ORF57 have opposing functions in modulating PAN steady-state accumulation. The suppressive effect of PABPC1 specific to PAN expression is alleviated by small interfering RNA knockdown of PABPC1 or by overexpression of ORF57. Conversely, ectopic PABPC1 reduces ORF57 steady-state protein levels and induces aberrant polyadenylation of PAN and thereby indirectly inhibits ORF57-mediated PAN accumulation. However, E1B-AP5 (heterogeneous nuclear ribonucleoprotein U-like 1), which interacts with a region outside the 9-nt core to stimulate PAN expression, does not interact or even colocalize with ORF57. Unlike PABPC1, the nuclear distribution of E1B-AP5 remains unchanged by viral lytic infection or overexpression of ORF57. Together, these data indicate that PABPC1 is an important cellular target of viral ORF57 to directly upregulate PAN accumulation during viral lytic infection, and the ability of host PABPC1 to disrupt ORF57 expression is a strategic host counterbalancing mechanism.

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Multiple levels of post-transcriptional control of expression of the poly (A)-binding Protein

Cited by 27 publications

References 78 publications

Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3′ UTRs to Regulate mRNA Expression

Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3′ UTRs to Regulate mRNA Expression

Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants

Interplay between Polyadenylate-Binding Protein 1 and Kaposi's Sarcoma-Associated Herpesvirus ORF57 in Accumulation of Polyadenylated Nuclear RNA, a Viral Long Noncoding RNA

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