The lncRNA hsrω regulates arginine dimethylation of human FUS to cause its proteasomal degradation in Drosophila

ERO1A inhibition mitigates neuronal ER stress and ameliorates UBQLN2ALS phenotypes in Drosophila melanogaster

Modulating the ER stress pathway holds therapeutic promise for neurodegenerative diseases; however, identifying optimal targets remains challenging. In this study, we conducted an unbiased screening to systematically search for commonly up-regulated proteins in ER stress-related neurodegenerative conditions, with endoplasmic reticulum oxidoreductase 1 alpha (ERO1A) emerging as a significant hit. Further experiments conducted in the model organism Drosophila melanogaster demonstrated that elevated levels of Drosophila ERO1A (ERO1L) were indeed detrimental to neurons. Conversely, genetic suppression or pharmacological inhibition of ERO1L activity provided neuroprotection under ER stress and extended the lifespan of flies. To translate these findings, we performed a genetic modifier screening and underscored significant neuroprotective effects against UBQLN2ALS pathology. Additionally, administration of the chemical probe inhibitor of ERO1A, known as EN460, enhanced locomotive functions and neuromuscular junction (NMJ) morphology in Drosophila UBQLN2ALS model. Mechanistically, targeting ERO1L during environmental or pathological ER stress mitigated proteotoxic stress by lowering either the PERK or IRE1 branches of the unfolded protein response (UPR). These findings suggest ERO1A as a promising therapeutic target in UBQLN2ALS and other ER stress-related conditions.

FOXP3-regulated lncRNA NONHSAT136151 promotes colorectal cancer progression by disrupting QKI interaction with target mRNAs

The role of lncRNAs in the pathogenesis of cancer, including colorectal cancer (CRC), has repeatedly been demonstrated. However, very few lncRNAs have been well annotated functionally. Our study identified a novel lncRNA upregulated in CRC, NONHSAT136151, which was correlated with clinical progression. In functional assays, NONHSAT136151 significantly enhanced CRC cell proliferation, migration and invasion. Mechanistically, NONHSAT136151 interacted with RNA-binding protein (RBP) QKI (Quaking) to interfere with QKI binding to target mRNAs and regulate their expression. As well, FOXP3 may be causally related to the dysregulation of NONHSAT136151 in CRC cells through its transcriptional activity. In conclusion, our findings identified a novel lncRNA regulated by FOXP3 participates in CRC progression through interacting with QKI, indicating a novel lncRNA-RBP interaction mechanism is involved in CRC pathogenesis.

The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses

The GAGA protein (also known as GAF) is a transcription factor encoded by the Trl gene in D. melanogaster. GAGA is involved in the regulation of transcription of many genes at all stages of fly development and life. Recently, we investigated the participation of GAGA in spermatogenesis and discovered that Trl mutants experience massive degradation of germline cells in the testes. Trl underexpression induces autophagic death of spermatocytes, thereby leading to reduced testis size. Here, we aimed to determine the role of the transcription factor GAGA in the regulation of ectopic germline cell death. We investigated how Trl underexpression affects gene expression in the testes. We identified 15,993 genes in three biological replicates of our RNA-seq analysis and compared transcript levels between hypomorphic Trl ^R85/Trl ³⁶² and Oregon testes. A total of 2,437 differentially expressed genes were found, including 1,686 upregulated and 751 downregulated genes. At the transcriptional level, we detected the development of cellular stress in the Trl-mutant testes: downregulation of the genes normally expressed in the testes (indicating slowed or abrogated spermatocyte differentiation) and increased expression of metabolic and proteolysis-related genes, including stress response long noncoding RNAs. Nonetheless, in the Flybase Gene Ontology lists of genes related to cell death, autophagy, or stress, there was no enrichment with GAGA-binding sites. Furthermore, we did not identify any specific GAGA-dependent cell death pathway that could regulate spermatocyte death. Thus, our data suggest that GAGA deficiency in male germline cells leads to an imbalance of metabolic processes, impaired mitochondrial function, and cell death due to cellular stress.

LncRNA-IRAR-mediated regulation of insulin receptor transcripts in Drosophila melanogaster during nutritional stress

The insulin signalling pathway plays a crucial role in regulating the metabolism of sugars, fats and proteins in cells, thereby affecting the growth, metabolism, reproduction and ageing of organisms. However, little is known about the functions of long non-coding RNAs (lncRNAs) in the regulation of insulin receptors under stress conditions in insects. In this study, we showed that insulin receptor-associated lncRNA (IRAR) regulates insulin receptor transcripts in response to nutritional stress in Drosophila melanogaster. Genome editing by CRISPR-Cas9 showed reduced sensitivity of IRAR mutants to environmental nutritional changes. In contrast, the sensitivity of mutants overexpressing tubulin-gal4 > IRAR increased under low nutrition. The pupation and eclosion timings in IRAR mutants were significantly delayed with an increase in insulin concentration compared with that in the w1118 group. In addition, the expression pattern of IRAR was almost consistent with that of the four transcripts of the insulin receptor from the embryonic period to the adult period. RNA immunoprecipitation assay showed the direct regulation of insulin receptor transcripts by IRAR to the through FOXO binding under nutritional stress. To our knowledge, this is the first study that describes a model of lncRNA-mediated development regulation through insulin receptor transcripts.

Nuclear RNA transcript levels modulate nucleocytoplasmic distribution of ALS/FTD-associated protein FUS

Fused in Sarcoma (FUS) is a nuclear RNA/DNA binding protein that mislocalizes to the cytoplasm in the neurodegenerative diseases ALS and FTD. Despite the existence of FUS pathogenic mutations that result in nuclear import defects, a subset of ALS/FTD patients display cytoplasmic accumulation of wild-type FUS, although the underlying mechanism is unclear. Here we confirm that transcriptional inhibition, specifically of RNA polymerase II (RNAP II), induces FUS cytoplasmic translocation, but we show that several other stresses do not. We found unexpectedly that the epitope specificity of different FUS antibodies significantly affects the apparent FUS nucleocytoplasmic ratio as determined by immunofluorescence, explaining inconsistent observations in previous studies. Significantly, depletion of the nuclear mRNA export factor NXF1 or RNA exosome cofactor MTR4 promotes FUS nuclear retention, even when transcription is repressed, while mislocalization was independent of the nuclear protein export factor CRM1 and import factor TNPO1. Finally, we report that levels of nascent RNAP II transcripts, including those known to bind FUS, are reduced in sporadic ALS iPS cells, linking possible aberrant transcriptional control and FUS cytoplasmic mislocalization. Our findings thus reveal that factors that influence accumulation of nuclear RNAP II transcripts modulate FUS nucleocytoplasmic homeostasis, and provide evidence that reduced RNAP II transcription can contribute to FUS mislocalization to the cytoplasm in ALS.

Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis

Long non-coding RNAs (lncRNAs) are highly expressed and can modulate multiple cellular processes including transcription, splicing, translation, and many diverse signaling events. LncRNAs can act as sponges for miRNAs, RNA and DNA binding proteins, functioning as competitive endogenous RNAs. The contribution of lncRNAs to microbial pathogenesis is largely neglected in eukaryotic pathogens despite the abundance of RNA sequencing datasets encompassing conditions of stress, gene deletions and conditions that mimic the host environment. The human fungal pathogen Cryptococcus neoformans encodes 6975 (84%) protein-coding and 1359 (16%) non-protein-coding RNAs, of which 1182 (14.2%) are lncRNAs defined by a threshold of greater than 200 nucleotides in length. Here, we discuss the current state of knowledge in C. neoformans lncRNA biology. Utilizing existing RNA seq datasets, we examine trends in lncRNA expression and discuss potential implications for pathogenesis.

Multifaceted roles of YEATS domain-containing proteins and novel links to neurological diseases

The so-called Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain-containing proteins, hereafter referred to as YD proteins, take control over the transcription by multiple steps of regulation either involving epigenetic remodelling of chromatin or guiding the processivity of RNA polymerase II to facilitate elongation-coupled mRNA 3' processing. Interestingly, an increasing amount of evidence suggest a wider repertoire of YD protein's functions spanning from non-coding RNA regulation, RNA-binding proteins networking, post-translational regulation of a few signalling transduction proteins and the spindle pole formation. However, such a large set of non-canonical roles is still poorly characterized. Notably, four paralogous of human YEATS domain family members, namely eleven-nineteen-leukaemia (ENL), ALL1-fused gene from chromosome 9 protein (AF9), YEATS2 and glioma amplified sequence 41 (GAS41), have a strong link to cancer yet new findings also highlight a potential novel role in neurological diseases. Here, in an attempt to more comprehensively understand the complexity of four YD proteins and to gain more insight into the novel functions they may accomplish in the neurons, we summarized the YD protein's networks, systematically searched and reviewed the YD genetic variants associated with neurodevelopmental disorders and finally interrogated the model organism Drosophila melanogaster.

The distal arthrogryposis-linked p.R63C variant promotes the stability and nuclear accumulation of TNNT3

Background

Distal arthrogryposis (DA) is comprised of a group of rare developmental disorders in muscle, characterized by multiple congenital contractures of the distal limbs. Fast skeletal muscle troponin‐T (TNNT3) protein is abundantly expressed in skeletal muscle and plays an important role in DA. Missense variants in TNNT3 are associated with DA, but few studies have fully clarified its pathogenic role.

Methods

Sanger sequencing was performed in three generation of a Chinese family with DA. To determine how the p.R63C variant contributed to DA, we identified a variant in TNNT3 (NM_006757.4): c.187C>T (p.R63C). And then we investigated the effects of the arginine to cysteine substitution on the distribution pattern and the half‐life of TNNT3 protein.

Results

The protein levels of TNNT3 in affected family members were 0.8‐fold higher than that without the disorder. TNNT3 protein could be degraded by the ubiquitin‐proteasome complex, and the p.R63C variant did not change TNNT3 nuclear localization, but significantly prolonged its half‐life from 2.5 to 7 h, to promote its accumulation in the nucleus.

Conclusion

The p.R63C variant increased the stability of TNNT3 and promoted nuclear accumulation, which suggested its role in DA.

A Survey of Current Resources to Study lncRNA-Protein Interactions

Phenotypes are driven by regulated gene expression, which in turn are mediated by complex interactions between diverse biological molecules. Protein-DNA interactions such as histone and transcription factor binding are well studied, along with RNA-RNA interactions in short RNA silencing of genes. In contrast, lncRNA-protein interaction (LPI) mechanisms are comparatively unknown, likely directed by the difficulties in studying LPI. However, LPI are emerging as key interactions in epigenetic mechanisms, playing a role in development and disease. Their importance is further highlighted by their conservation across kingdoms. Hence, interest in LPI research is increasing. We therefore review the current state of the art in lncRNA-protein interactions. We specifically surveyed recent computational methods and databases which researchers can exploit for LPI investigation. We discovered that algorithm development is heavily reliant on a few generic databases containing curated LPI information. Additionally, these databases house information at gene-level as opposed to transcript-level annotations. We show that early methods predict LPI using molecular docking, have limited scope and are slow, creating a data processing bottleneck. Recently, machine learning has become the strategy of choice in LPI prediction, likely due to the rapid growth in machine learning infrastructure and expertise. While many of these methods have notable limitations, machine learning is expected to be the basis of modern LPI prediction algorithms.

Insight Into Spinocerebellar Ataxia Type 31 (SCA31) From Drosophila Model

Spinocerebellar ataxia type 31 (SCA31) is a progressive neurodegenerative disease characterized by degeneration of Purkinje cells in the cerebellum. Its genetic cause is a 2.5- to 3.8-kb-long complex pentanucleotide repeat insertion containing (TGGAA)n, (TAGAA)n, (TAAAA)n, and (TAAAATAGAA)n located in an intron shared by two different genes: brain expressed associated with NEDD4-1 (BEAN1) and thymidine kinase 2 (TK2). Among these repeat sequences, (TGGAA)n repeat was the only sequence segregating with SCA31, which strongly suggests its pathogenicity. In SCA31 patient brains, the mutant BEAN1 transcript containing expanded UGGAA repeats (UGGAA_exp) was found to form abnormal RNA structures called RNA foci in cerebellar Purkinje cell nuclei. In addition, the deposition of pentapeptide repeat (PPR) proteins, poly(Trp-Asn-Gly-Met-Glu), translated from UGGAA_exp RNA, was detected in the cytoplasm of Purkinje cells. To uncover the pathogenesis of UGGAA_exp in SCA31, we generated Drosophila models of SCA31 expressing UGGAA_exp RNA. The toxicity of UGGAA_exp depended on its length and expression level, which was accompanied by the accumulation of RNA foci and translation of repeat-associated PPR proteins in Drosophila, consistent with the observation in SCA31 patient brains. We also revealed that TDP-43, FUS, and hnRNPA2B1, motor neuron disease–linked RNA-binding proteins bound to UGGAA_exp RNA, act as RNA chaperones to regulate the formation of RNA foci and repeat-associated translation. Further research on the role of RNA-binding proteins as RNA chaperones may also provide a novel therapeutic strategy for other microsatellite repeat expansion diseases besides SCA31.

Long noncoding RNA-dependent methylation of nonhistone proteins

In the last decade, an intriguing new paradigm of regulation has emerged in which some transcripts longer than 200 nucleotides and no coding potential, long noncoding RNA (lncRNAs), exhibit the capability to control posttranslational modifications of nonhistone proteins in both invertebrates and vertebrates. The extent of such a regulation is still largely unknown. We performed a systematic review to identify and evaluate the potential impact of lncRNA-dependent methylation of nonhistone proteins. Collectively, these lncRNAs primarily act as scaffolds upon which methyltransferases (MTases) and targets are brought in proximity. In this manner, the N-MTase activity of EZH2, protein arginine-MTase 1/4/5, and SMYD2 is exploited to modulate the stability or the compartmentalization of several nonhistone proteins with roles in cell signaling, gene expression, and RNA processing. Moreover, these lncRNAs can indirectly affect the methylation of nonhistone proteins by transcriptional or posttranscriptional regulation of MTases. Strikingly, the lncRNAs/MTases/nonhistone proteins networking seem to be relevant to carcinogenesis and neurological disorders. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

The long non-coding RNA MIR31HG regulates the senescence associated secretory phenotype

Oncogene-induced senescence provides a barrier against malignant transformation. However, it can also promote cancer through the secretion of a plethora of factors released by senescent cells, called the senescence associated secretory phenotype (SASP). We have previously shown that in proliferating cells, nuclear lncRNA MIR31HG inhibits p16/CDKN2A expression through interaction with polycomb repressor complexes and that during BRAF-induced senescence, MIR31HG is overexpressed and translocates to the cytoplasm. Here, we show that MIR31HG regulates the expression and secretion of a subset of SASP components during BRAF-induced senescence. The SASP secreted from senescent cells depleted for MIR31HG fails to induce paracrine invasion without affecting the growth inhibitory effect. Mechanistically, MIR31HG interacts with YBX1 facilitating its phosphorylation at serine 102 (p-YBX1^S102) by the kinase RSK. p-YBX1^S102 induces IL1A translation which activates the transcription of the other SASP mRNAs. Our results suggest a dual role for MIR31HG in senescence depending on its localization and points to the lncRNA as a potential therapeutic target in the treatment of senescence-related pathologies.

Senescence-associated secretory phenotype (SASP) involves secretion of factors such as pro-inflammatory cytokines. Here the authors show that MIR31HG regulates the expression and secretion of a subset of SASP components that induce paracrine invasion, through interaction with YBX1 and induction of IL1A translation.

Amyotrophic Lateral Sclerosis Genes in Drosophila melanogaster

Amyotrophic lateral sclerosis (ALS) is a devastating adult-onset neurodegenerative disease characterized by the progressive degeneration of upper and lower motoneurons. Most ALS cases are sporadic but approximately 10% of ALS cases are due to inherited mutations in identified genes. ALS-causing mutations were identified in over 30 genes with superoxide dismutase-1 (SOD1), chromosome 9 open reading frame 72 (C9orf72), fused in sarcoma (FUS), and TAR DNA-binding protein (TARDBP, encoding TDP-43) being the most frequent. In the last few decades, Drosophila melanogaster emerged as a versatile model for studying neurodegenerative diseases, including ALS. In this review, we describe the different Drosophila ALS models that have been successfully used to decipher the cellular and molecular pathways associated with SOD1, C9orf72, FUS, and TDP-43. The study of the known fruit fly orthologs of these ALS-related genes yielded significant insights into cellular mechanisms and physiological functions. Moreover, genetic screening in tissue-specific gain-of-function mutants that mimic ALS-associated phenotypes identified disease-modifying genes. Here, we propose a comprehensive review on the Drosophila research focused on four ALS-linked genes that has revealed novel pathogenic mechanisms and identified potential therapeutic targets for future therapy.

Role of Viral Ribonucleoproteins in Human Papillomavirus Type 16 Gene Expression

Human papillomaviruses (HPVs) depend on the cellular RNA-processing machineries including alternative RNA splicing and polyadenylation to coordinate HPV gene expression. HPV RNA processing is controlled by cis-regulatory RNA elements and trans-regulatory factors since the HPV splice sites are suboptimal. The definition of HPV exons and introns may differ between individual HPV mRNA species and is complicated by the fact that many HPV protein-coding sequences overlap. The formation of HPV ribonucleoproteins consisting of HPV pre-mRNAs and multiple cellular RNA-binding proteins may result in the different outcomes of HPV gene expression, which contributes to the HPV life cycle progression and HPV-associated cancer development. In this review, we summarize the regulation of HPV16 gene expression at the level of RNA processing with focus on the interactions between HPV16 pre-mRNAs and cellular RNA-binding factors.

Long Non-Coding RNA-Ribonucleoprotein Networks in the Post-Transcriptional Control of Gene Expression

Although mammals possess roughly the same number of protein-coding genes as worms, it is evident that the non-coding transcriptome content has become far broader and more sophisticated during evolution. Indeed, the vital regulatory importance of both short and long non-coding RNAs (lncRNAs) has been demonstrated during the last two decades. RNA binding proteins (RBPs) represent approximately 7.5% of all proteins and regulate the fate and function of a huge number of transcripts thus contributing to ensure cellular homeostasis. Transcriptomic and proteomic studies revealed that RBP-based complexes often include lncRNAs. This review will describe examples of how lncRNA-RBP networks can virtually control all the post-transcriptional events in the cell.

RNA-binding proteins in tumor progression

RNA-binding protein (RBP) has a highly dynamic spatiotemporal regulation process and important biological functions. They are critical to maintain the transcriptome through post-transcriptionally controlling the processing and transportation of RNA, including regulating RNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation. Alteration of each process will affect the RNA life cycle, produce abnormal protein phenotypes, and thus lead to the occurrence and development of tumors. Here, we summarize RBPs involved in tumor progression and the underlying molecular mechanisms whereby they are regulated and exert their effects. This analysis is an important step towards the comprehensive characterization of post-transcriptional gene regulation involved in tumor progression.