Understanding the proteome encoded by "non-coding RNAs": new insights into human genome

The emerging role of circular RNAs in cisplatin resistance in ovarian cancer: From molecular mechanism to future potential

Ovarian cancer (OC) is the most common cause of death in female cancers. The prognosis of OC is very poor due to delayed diagnosis and identification of most patients in advanced stages, metastasis, recurrence, and resistance to chemotherapy. As chemotherapy with platinum-based drugs such as cisplatin (DDP) is the main treatment in most OC cases, resistance to DDP is an important obstacle to achieving satisfactory therapeutic efficacy. Consequently, knowing the different molecular mechanisms involved in resistance to DDP is necessary to achieve new therapeutic approaches. According to numerous recent studies, non-coding RNAs (ncRNAs) could regulate proliferation, differentiation, apoptosis, and chemoresistance in many cancers, including OC. Most of these ncRNAs are released by tumor cells into human fluid, allowing them to be used as tools for diagnosis. CircRNAs are ncRNA family members that have a role in the initiation, progression, and chemoresistance regulation of various cancers. In the current study, we investigated the roles of several circRNAs and their signaling pathways on OC progression and also on DDP resistance during chemotherapy.

CircTRIM1 encodes TRIM1-269aa to promote chemoresistance and metastasis of TNBC via enhancing CaM-dependent MARCKS translocation and PI3K/AKT/mTOR activation

Peptides and proteins encoded by noncanonical open reading frames (ORFs) of circRNAs have recently been recognized to play important roles in disease progression, but the biological functions and mechanisms of these peptides and proteins are largely unknown. Here, we identified a potential coding circular RNA, circTRIM1, that was upregulated in doxorubicin-resistant TNBC cells by intersecting transcriptome and translatome RNA-seq data, and its expression was correlated with clinicopathological characteristics and poor prognosis in patients with TNBC. CircTRIM1 possesses a functional IRES element along with an 810 nt ORF that can be translated into a novel endogenously expressed protein termed TRIM1-269aa. Functionally, we demonstrated that TRIM1-269aa, which is involved in the biological functions of circTRIM1, promoted chemoresistance and metastasis in TNBC cells both in vitro and in vivo. In addition, we found that TRIM1-269aa can be packaged into exosomes and transmitted between TNBC cells. Mechanistically, TRIM1-269aa enhanced the interaction between MARCKS and calmodulin, thus promoting the calmodulin-dependent translocation of MARCKS, which further initiated the activation of the PI3K/AKT/mTOR pathway. Overall, circTRIM1, which encodes TRIM1-269aa, promoted TNBC chemoresistance and metastasis by enhancing MARCKS translocation and PI3K/AKT/mTOR activation. Our investigation has yielded novel insights into the roles of protein-coding circRNAs and supported circTRIM1/TRIM1-269aa as a novel promising prognostic and therapeutic target for patients with TNBC.

Novel insights into small open reading frame-encoded micropeptides in hepatocellular carcinoma: A potential breakthrough

Traditionally, non-coding RNAs (ncRNAs) are regarded as a class of RNA transcripts that lack encoding capability; however, advancements in technology have revealed that some ncRNAs contain small open reading frames (sORFs) that are capable of encoding micropeptides of approximately 150 amino acids in length. sORF-encoded micropeptides (SEPs) have emerged as intriguing entities in hepatocellular carcinoma (HCC) research, shedding light on this previously unexplored realm. Recent studies have highlighted the regulatory functions of SEPs in the occurrence and progression of HCC. Some SEPs exhibit inhibitory effects on HCC, but others facilitate its development. This discovery has revolutionized the landscape of HCC research and clinical management. Here, we introduce the concept and characteristics of SEPs, summarize their associations with HCC, and elucidate their carcinogenic mechanisms in HCC metabolism, signaling pathways, cell proliferation, and metastasis. In addition, we propose a step-by-step workflow for the investigation of HCC-associated SEPs. Lastly, we discuss the challenges and prospects of applying SEPs in the diagnosis and treatment of HCC. This review aims to facilitate the discovery, optimization, and clinical application of HCC-related SEPs, inspiring the development of early diagnostic, individualized, and precision therapeutic strategies for HCC.

Exploring noncoding variants in genetic diseases: from detection to functional insights

Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.

Ribosome profiling: a powerful tool in oncological research

Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.

Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots

Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m6A), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.

Critical roles of non-coding RNAs in lifecycle and biology of Marek's disease herpesvirus

Over the past two decades, numerous non-coding RNAs (ncRNAs) have been identified in different biological systems including virology, especially in large DNA viruses such as herpesviruses. As a representative oncogenic alphaherpesvirus, Marek's disease virus (MDV) causes an important immunosuppressive and rapid-onset neoplastic disease of poultry, namely Marek's disease (MD). Vaccinations can efficiently prevent the onset of MD lymphomas and other clinical disease, often heralded as the first successful example of vaccination-based control of cancer. MDV infection is also an excellent model for research into virally-induced tumorigenesis. Recently, great progress has been made in understanding the functions of ncRNAs in MD biology. Herein, we give a review of the discovery and identification of MDV-encoded viral miRNAs, focusing on the genomics, expression profiles, and emerging critical roles of MDV-1 miRNAs as oncogenic miRNAs (oncomiRs) or tumor suppressor genes involved in the induction of MD lymphomas. We also described the involvements of host cellular miRNAs, lincRNAs, and circRNAs participating in MDV life cycle, pathogenesis, and/or tumorigenesis. The prospects, strategies, and new techniques such as the CRISPR/Cas9-based gene editing applicable for further investigation into the ncRNA-mediated regulatory mechanisms in MDV pathogenesis/oncogenesis were also discussed, together with the possibilities of future studies on antiviral therapy and the development of new efficient MD vaccines.

Small Non-Coding RNAs in Human Cancer

Small non-coding RNAs are widespread in the biological world and have been extensively explored over the past decades. Their fundamental roles in human health and disease are increasingly appreciated. Furthermore, a growing number of studies have investigated the functions of small non-coding RNAs in cancer initiation and progression. In this review, we provide an overview of the biogenesis of small non-coding RNAs with a focus on microRNAs, PIWI-interacting RNAs, and a new class of tRNA-derived small RNAs. We discuss their biological functions in human cancer and highlight their clinical application as molecular biomarkers or therapeutic targets.

Visually predicting microRNA-regulated tumor metastasis by intracellularly 3D counting of fluorescent spots based on in situ growth of DNA flares

INTRODUCTION

MicroRNAs (miRNAs) have been revealed to be critical genetic regulators in various physiological processes and thus quantitative information on the expression level of critical miRNAs has important implications for the initiation and development of human diseases, including cancers.

OBJECTIVES

We herein develop three-dimensionally (3D) counting of intracellular fluorescent spots for accurately evaluating microRNA-21 (miRNA-21) expression in individual HeLa cells based on stimuli-activated in situ growth of optical DNA flares, grid-patterned DNA-protein hybrids (GDPHs).

METHODS

Target miRNA is sequence-specifically detected down to 10 pM owing to efficient signal amplification. Within living cells, GDPH flares are nuclease resistant and discrete objects with retarded mobility, enabling the screening of intracellular location and distribution of miRNAs and realizing in situ counting of target species with a high accuracy.

RESULTS

The quantitative results of intracellular miRNAs by 3D fluorescence counts are consistent with qPCR gold standard assay, exhibiting the superiority over 2D counts. By screening the expression of intracellular miR-21 that can down-regulate the programmed cell death 4 (PDCD4) protein, the proliferation and migration of HeLa cells, including artificially-regulated ones, were well estimated, thus enabling the prediction of cancer metastasis in murine tumor models.

CONCLUSION

The experiments in vitro, ex vivo and in vivo demonstrate that GDPH-based 3D fluorescence counts at the single cell level provide a valuable molecular tool for understanding biological function of miRNAs and especially for recognizing aggressive CTCs, offering a design blueprint for further expansion of DNA structural nanotechnology in predicting distant metastasis and prevention of tumor recurrence after primary resection.

New Insights into the Importance of Long Non-Coding RNAs in Lung Cancer: Future Clinical Approaches

In mammals, a large part of the gene expression products come from the non-coding ribonucleotide sequences of the protein. These short and long sequences are within the range of tens to hundreds of nucleotides, encompassing more than 200 RNA molecules, and their function is known as the molecular structure of long non-coding RNA (lncRNA). LncRNA molecules are unique nucleotides that have a substantial role in epigenetic regulation, transcription, and post-transcriptional modifications in different ways. According to the results of recent studies, lncRNAs have been shown to assume various roles, including tumor suppression or oncogenic functions in common types of cancer such as lung and breast cancer. These non-coding RNAs (ncRNAs) play a pivotal role in activating transcription factors, managing the ribonucleoproteins, the framework for collecting co-proteins, intermittent processing regulations, chromatin status alterations, and maintaining the control within the cell. Cutting-edge technologies have been introduced to disclose several types of lncRNAs within the nucleus and the cytoplasm, which have accomplished important achievements that are applicable in medicine. Due to these efforts, various data centers have been created to facilitate and modify scientific information related to these molecules, including detection, classification, biological evolution, gene status, spatial structure, status, and location of these small molecules. In the present study, we attempt to present the impacts of these ncRNAs on lung cancer with an emphasis on their mechanisms and functions.

The use of ribosome-nascent chain complex-seq to reveal the translated mRNA profile and the role of ASN1 in resistance to Verticillium wilt in cotton

We combined traditional mRNA-seq and RNC-seq together to reveal post-transcriptional regulation events impacting gene expression and interactions between the serious fungal pathogen Verticillium dahliae and a susceptible host, Gossypium hirsutum TM-1. After screening the differentially expressed and translated genes, V. dahliae infection was observed to influence gene transcription and translation in its host. Interestingly, the asparagine synthase (ASN1) gene transcripts increased significantly with the increase of infection time, while the rate of ASN1 protein accumulation in host TM-1 was distinctly lower than that in resistant hosts. We knocked down the ASN1 gene in resistant plants (ZZM2), and found that Verticillium-resistance was significantly reduced upon knockdown of ASN1. Our study revealed both transcriptional and post-transcriptional regulation of gene expression in TM-1 cotton plants infected by V. dahliae, and showed that ASN1 functions in the V. dahliae resistance process. These insights support breeding of disease resistance in cotton.

Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues

Small open reading frame encoded peptides (SEPs), also called microproteins, play a vital role in biological processes. Plenty of their open reading frames are located within the non-coding RNA (ncRNA) range. Recent research has demonstrated that ncRNA-encoded polypeptides have essential functions and exist ubiquitously in various tissues. To better understand the role of microproteins, especially ncRNA-encoded proteins, expressed in different tissues, we profiled the proteomic characterization of five mouse tissues by mass spectrometry, including bottom-up, top-down, and de novo sequencing strategies. Bottom-up and top-down with database-dependent searches identified 811 microproteins in the OpenProt database. De novo sequencing identified 290 microproteins, including 12 ncRNA-encoded microproteins that were not found in current databases. In this study, we discovered 1,074 microproteins in total, including 270 ncRNA-encoded microproteins. From the annotation of these microproteins, we found that the brain contains the largest number of neuropeptides, while the spleen contains the most immunoassociated microproteins. This suggests that microproteins in different tissues have tissue-specific functions. These unannotated ncRNA-coded microproteins have predicted domains, such as the macrophage migration inhibitory factor domain and the Prefoldin domain. These results expand the mouse proteome and provide insight into the molecular biology of mouse tissues.

Autoactivation of Translation Causes the Bloom of Prorocentrum donghaiense in Harmful Algal Blooms

Harmful algal blooms (HABs) are symptomatic of ecosystem imbalance, leading to major worldwide marine natural disasters, and seriously threaten the human health. Some HAB algae's exceptional genome size prohibited the genomic investigations on molecular mechanisms, for example, Prorocentrum. This study performed translatome sequencing (RNC-seq) for Prorocentrum donghaiense to assemble the translatome reference sequences on appropriate cost to enable the global molecular study at translatome and proteome levels. By analyzing the translatome and proteome of P. donghaiense in phosphor-rich, phosphor-deficient, and phosphor-restored media, we found massive up-regulation of energy and material production pathways in phosphor-rich conditions that enables autoactivation of translation, which is the key to its exponential growth in HABs. To break down the autoactivation, we demonstrated that mild translation delay using very low concentrations of cycloheximide efficiently controls the blooming without harming other aquatic organisms and humans. Our result provides a novel hint for controlling HABs and demonstrated the RNC-seq as an economic strategy on investigating functions of organisms with large and unknown genomes.

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish

Simple Summary

Noncoding RNAs (ncRNAs) regulate a variety of fundamental life processes such as development, physiology, metabolism and circadian rhythmicity. RNA-sequencing (RNA-seq) technology has facilitated the sequencing of the whole transcriptome, thereby capturing and quantifying the dynamism of transcriptome-wide RNA expression profiles. However, much remains unrevealed in the huge noncoding RNA datasets that require further bioinformatic analysis. In this study, we applied six bioinformatic tools to investigate coding potentials of approximately 21,000 lncRNAs. A total of 313 lncRNAs are predicted to be coded by all the six tools. Our findings provide insights into the regulatory roles of lncRNAs and set the stage for the functional investigation of these lncRNAs and their encoded micropeptides.

Abstract

Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify 2730–6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted by all the six bioinformatic tools. We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses. These predicted zebrafish coding lncRNAs set the stage for further experimental studies.

Long noncoding RNA AANCR modulates innate antiviral responses by blocking miR-210-dependent MITA downregulation in teleost fish, Miichthys miiuy

Viral infection induces the initiation of antiviral effectors and cytokines which are critical mediators of innate antiviral responses. The critical molecular determinants are responsible for triggering an appropriate immune response. Long noncoding RNAs (lncRNAs) have emerged as new gene modulators involved in various biological processes, while how lncRNAs operate in lower vertebrates are still unknown. Here, we discover a long noncoding RNA, termed antiviral-associated long noncoding RNA (AANCR), as a novel regulator for innate antiviral responses in teleost fish. The results indicate that fish MITA plays an essential role in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus (SCRV) production. miR-210 reduces MITA expression and suppress MITA-mediated antiviral responses, which may help viruses evade host antiviral responses. Further, AANCR functions as a competing endogenous RNA (ceRNA) for miR-210 to control protein abundance of MITA, thereby inhibiting SCRV replication and promoting antiviral responses. Our data not only shed new light on understanding the function role of lncRNA in biological processes in teleost fish, but confirmed the hypothesis that ceRNA networks exist widely in vertebrates.

LncRNA TTTY15 knockdown alleviates H2O2-stimulated myocardial cell injury by regulating the miR-98-5p/CRP pathway

Acute myocardial infarction (AMI) can lead to myocardial injury, and long non-coding RNA (lncRNA) has been found to play an important regulatory role in the process of myocardial injury. However, the role and potential mechanisms of lncRNA testis-specific transcript Y-linked 15 (TTTY15) in AMI-induced myocardial injury has not been fully elucidated. Hydrogen peroxide (H₂O₂)-induced AMI cell model was built and AMI mice model were constructed. Relative expression levels of TTTY15, miR-98-5p and C-reactive protein (CRP) were determined by quantitative real-time PCR (qRT-PCR). Cell counting kit 8 (CCK8) assay, flow cytometry and enzyme-linked immunosorbent assay (ELISA) were employed to assess cell viability, apoptosis, inflammatory response and oxidative stress. Western blot (WB) analysis was used to assess the protein expression levels. The mechanism of TTTY15 was confirmed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Our results revealed that TTTY15 was upregulated and miR-98-5p was downregulated in AMI patients and H₂O₂-stimulated myocardial cells. Knockdown of TTTY15 could alleviate H₂O₂-stimulated myocardial cell injury in vitro and AMI progression in vivo. Bioinformatics analysis and the rescue experiments confirmed that TTTY15 positively regulated H₂O₂-induced myocardial cell injury via regulating CRP by sponging miR-98-5p. Our research proposed that lncRNA TTTY15 promoted myocardial cell injury by regulating the miR-98-5p/CRP axis, suggesting that TTTY15 might be a potential target for alleviating AMI-caused myocardial cell injury.