Human satellite-III non-coding RNAs modulate heat-shock-induced transcriptional repression

Goenka, Anshika; Sengupta, Suman; Pandey, Rajesh; Parihar, Rashmi; Mohanta, Girish C.; Mukerji, Mitali; Ganesh, Subramaniam

doi:10.1242/jcs.189803

Cited by 62 publications

(89 citation statements)

References 60 publications

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“…Expression of arcRNAs and sequestration of specific RBPs in nuclear bodies contribute to the regulation of gene expression under stress conditions, oncogenic transformation and disease [44][45][46] . So far, all known arcRNAs are long noncoding RNAs (lncRNAs).…”

Section: Discussionmentioning

confidence: 99%

SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly

Königs

Machado

Arnold

et al. 2020

Nat Struct Mol Biol

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Results SRSF7 overexpression induces auto-regulation.To investigate the mechanisms of SRSF7 homeostasis, we generated cell lines SRSF7 is an essential RNA-binding protein whose misexpression promotes cancer. Here, we describe how SRSF7 maintains its protein homeostasis in murine P19 cells using an intricate negative feedback mechanism. SRSF7 binding to its premessenger RNA promotes inclusion of a poison cassette exon and transcript degradation via nonsense-mediated decay (NMD). However, elevated SRSF7 levels inhibit NMD and promote translation of two protein halves, termed Split-ORFs, from the bicistronic SRSF7-PCE transcript. The first half acts as dominant-negative isoform suppressing poison cassette exon inclusion and instead promoting the retention of flanking introns containing repeated SRSF7 binding sites. Massive SRSF7 binding to these sites and its oligomerization promote the assembly of large nuclear bodies, which sequester SRSF7 transcripts at their transcription site, preventing their export and restoring normal SRSF7 protein levels. We further show that hundreds of human and mouse NMD targets, especially RNA-binding proteins, encode potential Split-ORFs, some of which are expressed under specific cellular conditions. SRSF7 binding promotes splicing of NMD-sensitive and -resistant SRSF7 isoforms. To understand the mechanism of SRSF7 auto-regulation, we examined the binding of SRSF7 protein to SRSF7 transcripts using individual-nucleotide resolution ultraviolet (UV) crosslinking and immunoprecipitation (iCLIP). We used normalized significant crosslink events (X-links, false discovery rate (FDR) < 0.05) from SRSF3 and SRSF7 iCLIP datasets of P19 cell lines without OE 8 . Similar to SRSF3, which promotes the inclusion of the PCE in SRSF7 transcripts 17 , SRSF7 showed enriched crosslinks in an extended region encompassing the PCE, its flanking introns 3a and 3b, and exons 3, 4 and 5 ( Fig. 1d). Quantification revealed that SRSF7 binds ~50-fold more to SRSF7 transcripts than SRSF3 ( Supplementary Table 1), indicating that SRSF7 has an unusual preference for its own transcripts.RNA-seq followed by quantification of junction reads revealed that SRSF7 OE promotes inclusion of either the complete PCE (460 nucleotides (nt)) or a partial PCE (107 nt) in SRSF7 transcripts ( Fig. 1e). Additionally, both PCE-flanking introns (3a and 3b) and intron 5 displayed increased read coverage, indicating that they are partly retained upon SRSF7 OE. Semiquantitative reverse transcription PCR and sequencing confirmed that SRSF7 OE caused the appearance of transcripts containing the entire PCE (SRSF7-PCE, orange asterisk), the partial PCE (SRSF7-PCE 1/4 , yellow asterisk) or the PCE in combination with both flanking introns (SRSF7-I3a+b, red asterisk) or with only intron 3b (SRSF7-I3b, green asterisk; Fig. 1f and Extended Data Fig. 1b,c). Identical isoforms were detected for endogenous and SRSF7-GFP reporter transcripts, indicating that auto-regulation operates similarly on both.All these transcripts contain PTCs and should be s...

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Section: Discussionmentioning

confidence: 99%

SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly

Königs

Machado

Arnold

et al. 2020

Nat Struct Mol Biol

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“…NSBs are protein-RNA complexes that form in response to stress-induced transcription of satellite III (SatIII) repeats from pericentromeric heterochromatin 50 . The resultant SatIII transcripts act as scaffolds that recruit various RBPs, notably the transcription factor HSF1 and the hnRNP SAFB, to NSBs, resulting in the appearance of several nuclear granules that dissipate following stressor removal 42,42,50 . Despite a well-characterized mechanism of formation, the functions of NSBs have remained enigmatic.…”

Section: Discussionmentioning

confidence: 99%

“…qPCR experiments established that our RBM45 siRNAs effectively targeted RBM45, resulting in an approximately 70% decrease in transcript abundance ( Figure S3). As a positive control, we evaluated the effects of SatIII transcript knockdown by siRNA on NSB formation, as prior studies have established that SatIII knockdown abrogates NSB formation 41,42 . siRNA targeting of SatIII reduced transcript levels approximately 80%…”

Section: Rbm45 Associates With Nuclear Stress Bodies (Nsbs)mentioning

confidence: 99%

RBM45 associates with nuclear stress bodies and forms nuclear inclusions during chronic cellular stress and in neurodegenerative diseases

Collins

Bowser

2019

Preprint

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RBM45 is a multifunctional RNA binding protein (RBP) found in cytoplasmic and nuclear inclusions in amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and Alzheimer's disease (AD). While cytoplasmic RBM45 inclusions contain other disease-associated proteins, nuclear RBM45 inclusions are morphologically and biochemically distinct from previously described nuclear inclusion pathology in these diseases. To better understand nuclear RBM45 aggregation and inclusion formation, we evaluated the association of RBM45 with a variety of membraneless nuclear organelles, including nuclear speckles, Cajal bodies, and nuclear gems. Under basal conditions, RBM45 is diffusely distributed throughout the nucleus and does not localize to a specific nuclear organelle. During cellular stress, however, the nuclear RBM45 distribution undergoes an RNA-binding dependent rearrangement wherein RBM45 coalesces into a small number of nuclear puncta. These puncta contain the nuclear stress body (NSB) markers heat shock factor 1 (HSF1) and scaffold attachment factor B (SAFB).During chronic stress, the persistent association of RBM45 with NSBs leads to the formation of large, insoluble nuclear RBM45 inclusions. RBM45 nuclear inclusions persist after stressor removal and NSB disassembly and the inclusions resemble the nuclear RBM45 pathology seen in ALS, FTLD, and AD. We also quantified the cell type-and disease-specific patterns of RBM45 pathology in ALS, FTLD, AD, and non-neurologic disease control subjects. RBM45 nuclear and cytoplasmic inclusions are found in neurons and glia in ALS, FTLD, and AD but not in controls. Across diseases, RBM45 nuclear inclusion pathology occurs more frequently than cytoplasmic RBM45 inclusion pathology and exhibits cell type-specific variation. Collectively, our results define new stress-associated functions of RBM45, a mechanism for its nuclear aggregation and inclusion formation, a role for NSBs in the pathogenesis of diseases such as

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“…The tumor protein p53 was shown to be an interacting part of the nSBs and its interaction with all the components of nSBs was confirmed with STRING‐based protein association network. Using RBP map we checked the in vitro proven study of SRSF1 (ASF) acting as the recruiting partner to SatIII, thereby, mediating the binding of proteins involved in nuclear stress body formation …”

Section: Methodsmentioning

confidence: 99%

Nuclear stress bodies: Interaction of its components in oncogenic regulation

Chatterjee

Sengupta

2019

J of Cellular Biochemistry

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Oncogenesis involves continuous genetic alterations that lead to compromised cellular integrity and immortal cell fate. The cells remain under excessive stress due to endo‐ and exogenous influences. Human Satellite III long noncoding RNA (SatIII lncRNA) is a key regulator of the global cellular stress response, although its function is poorly explained in cancers. The principal regulator of cancer meshwork is tumor protein p53, which if altered may result in chemoresistance. The heat shock factor 1 (HSF1) being a common molecule between the oncogenic control and global cellular stress acts as an oncogene as well as transcribes SatIII upon heat shock. This prompted us to determine the structure of SatIII RNA and establish the association between SatIII‐HSF1‐p53. We determined the most stable structure of SatIII RNA with the least energy of − 115.7 kcal/mol. Also, we observed a possible interaction of p53 with SatIII and HSF1 using support vector machine (SVM) algorithm for predicting RNA‐protein interaction (RPI). Further, we employ the STRING database to understand if p53 is an interacting component of the nuclear stress bodies (nSBs). A precise inference was drawn from molecular docking which confirmed the interaction of SatIII‐HSF1‐p53, where a mutated p53 resulted in an altered DNA‐binding property with the SatIII molecule. This study being first of its kind infers p53 to be a possible integral component of the nSBs, which may regulate cellular stress response during cancer progression in the presence of HSF1 and SatIII. An extended research on the regulations of SatIII and p53 may open new avenues in the field of apoptosis in cancer and the early approach of molecular targeting.

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Human satellite-III non-coding RNAs modulate heat-shock-induced transcriptional repression

Cited by 62 publications

References 60 publications

SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly

SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly

RBM45 associates with nuclear stress bodies and forms nuclear inclusions during chronic cellular stress and in neurodegenerative diseases

Nuclear stress bodies: Interaction of its components in oncogenic regulation

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