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Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes

ABSTRACT: The human genome encodes a multitude of different noncoding transcripts that have been tra-ditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple func-tional transcripts that warrant future studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE221958 | GEO | 2023/02/20

REPOSITORIES: GEO

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Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-coding Genes II

Project description:Human genome encodes a multitude of different non-coding transcripts that have been traditionally separated based on their lengths into long or small non-coding RNAs. The vast majority of both long and short non-coding transcripts are not annotated and their functions, mechanisms of action and biological relevance remain unknown. However, based on the functional understanding of the known classes of long and small non-coding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Still, direct evidence of functionality is lacking for most non-coding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we have developed a high-throughput assay to test functionality of sncRNAs based on overexpressing them in human cells. Surprisingly, we found that a significant fraction (> 40%) unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small non-coding transcriptome can harbor multiple functional transcripts that warrant future studies.

2023-02-20 | GSE221956 | GEO

Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-coding Genes I

2023-02-20 | GSE221954 | GEO

Identification of new snoRNAs in human muscle cells

Project description:Small non-coding RNAs (sncRNAs) represent an important class of regulatory RNAs involved in the regulation of transcription, RNA splicing or translation. Among these sncRNAs, small nucleolar RNAs (snoRNAs) mostly originate from intron splicing in humans and are central to posttranscriptional regulation of gene expression. Yet, the characterization of the complete repertoire of sncRNAs in a given cellular context and the functional annotation of the human transcriptome are far from complete. Here, we report the large-scale identification of sncRNAs in the size range of 50 to 200 nucleotides, without a priori on their biogenesis, structure and genomic origin, in the context of normal human muscle cells. We provided a complete set of experimental validation of novel candidate snoRNAs by evaluating the prerequisites for their biogenesis and functionality, leading to their validation as genuine snoRNAs. Interestingly, we also found intergenic snoRNAs, which we showed are in fact integrated into candidate introns of unannotated transcripts or degraded by the Nonsense Mediated Decay pathway. Hence, intergenic snoRNAs represent a new type of landmark for the identification of new transcripts that have gone undetected because of low abundance or degradation after the release of the snoRNA.

2021-09-28 | GSE178649 | GEO

Small non-coding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

Project description:Small non-coding RNAs (sncRNAs) are generated from different genomic loci and have important roles in biological processes, such as cell proliferation and regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNAs, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small interfering RNAs), piRNAs and plant specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all these diverse sncRNAs. A novel web server, sRNAtools (https://bioinformatics.sc.cn/sRNAtools), is presented that can be used in conjunction with high-throughput sequencing to discover, profile and functionally annotate sncRNAs, including miRNAs, isomiRs, piRNAs, tRFs, tRNAs, snRNAs, snoRNAs, rRNAs, phasiRNAs, and plant specific 24-nt siRNAs for 21 species. In this study, sRNAtools has been used in sncRNA profiling in poplar wood tissues, which identified many wood related sncRNAs expression patterns.We believe that sRNAtools will greatly benefit the scientific community as an integrated tool to study sncRNAs.

2019-11-15 | GSE139897 | GEO

Genome-wide and Cell-type Selective Profiling of In Vivo Small Noncoding RNA:Target RNA Interactions by Chimeric RNA Sequencing

Project description:Small noncoding RNAs (sncRNAs) can regulate biological processes by impacting posttranscriptional gene expression through repressing the levels and translation of targeted transcripts. Despite clear biological importance of sncRNAs, developed approaches to unambiguously define sncRNA:target RNA interactions in a genome-wide manner remain challenging and have not been widely adopted. We present CIMERA-seq, a robust strategy that incorporates covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of the in vivo interactions by sequencing the resulting chimeric RNAs. Modifications are incorporated that increase the capacity for processing low abundance samples and which permit cell-type selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome wide and cell-type selective CIMERA-seq enhances researchers’ ability to study the role of sncRNAs in mediating post-transcriptional gene regulation in diverse model systems and tissue types.

2024-07-11 | GSE263988 | GEO

HIV-1 RNAs are not part of the Argonaute 2 associated RNA interference pathway in macrophages

Project description:MiRNAs and other small noncoding RNAs (sncRNAs) are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs) have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi) pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte-derived macrophages (MDM). The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP), which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM) were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs. PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified, suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages.

2015-07-14 | GSE70851 | GEO

microRNA profiling by array of Sinorhizobium meliloti grown under heat, cold, acidic, basic, oxidative and salt stress in time course.

Project description:Identification and expression profiling of stress induced (heat and cold shock, acidic, basic, oxidative and saline stress) and non stress induced (Logarithmic and stationary phase) sRNAs by oligonucleotide microarray: In these microarray hybridizations, signals derived from fractions composed of small (<200 nt) and long (>200 nt) RNAs were compared. This strategy allowed for identifying sequence regions predominantly present in the small RNA fraction excluding sequence regions that were also represented in the long RNA fraction at a considerable level. Applying a cut-off of ? 8 to the ratio of signals derived from the small RNA to signals from the long RNA fraction were determined as putative small noncoding RNAs.

2011-03-08 | E-MTAB-204 | biostudies-arrayexpress

Circulating microRNA and 5’ tRNA halves signatures of genotype-by-age interactions in the longlived Ames dwarf mouse.

Project description:Recent evidence demonstrates that serum levels of specific small noncoding RNAs (sncRNAs) including miRNAs and 5’ tRNA halves significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 43 miRNAs and 19 5’ tRNA halves during aging [Genotype-by-Age interaction (GbA)]. GbA miRNAs showed four distinct expression patterns and significant over-targeting of transcripts involved in age-related processes. Functional enrichment analysis of putative miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs and 5’-tRNA halves modulated by age in the long-lived Ames mouse.

2018-05-27 | GSE69274 | GEO

The long noncoding RNA neuroLNC modulates neurotransmitter release interacting with a neurodegeneration-associated protein

Project description:The roles of long noncoding RNAs (lncRNAs) in synaptic transmission and neuronal development are emerging. Here we applied an integrated bioinformatic/biological screening strategy to identify lncRNAs that regulate synaptic vesicle release. We identified neuroLNC, a conserved neuron-specific nuclear lncRNA that modulates synaptic vesicle release, presynaptic calcium influx, neurite elongation and neuronal migration. In neurons neuroLNC interacts with a neurodegeneration-associated protein and tunes a set of presynaptic transcripts implicated in neurotransmitter release.

2020-05-26 | PXD013434 | Pride

University of Washington CSF biomarker study for Parkinson disease

Project description:<p>There is a clear need to develop biomarkers for Parkinson disease (PD) diagnosis and monitoring disease progression. In this study we evaluated cerebrospinal fluid (CSF) proteins, which are known to be critically involved in PD or identified in our preliminary profiling studies, aptamers, and RNAs as potential PD biomarkers. Access to subjects for this study was via the Pacific Northwest Udall Center (PANUC) and the Alzheimer's Disease Research Center (ADRC) at the University of Washington and Oregon Health and Sciences University (OHSU). Using CSF samples from 30 well-characterized patients with PD and 30 age-, sex-matched healthy controls, we prepared RNA seq libraries and performed deep sequencing of all RNA species, including small and long RNA, mRNAs, noncoding RNAs and differentially spliced transcripts. We then tried several methods for RNAseq data analysis to optimize our analysis pipeline. We identified a total of 3381 transcripts corresponding to 182 long intergenic RNAs (LincRNAs), 11 microRNAs (miRNAs), 2861 protein-coding transcripts, 200 pseudogenes and 127 antisense RNAs; some of them were differentially expressed between PD and control groups. Selected differentially expressed RNAs have been validated in the same set of CSF samples using real-time PCR (RT-PCR). Further validations in independent, larger cohorts of samples are still ongoing. Our results obtained so far suggested that CSF proteins and RNAs could be used as good indexes for PD diagnosis and disease severity/progression. This study is a part of the NIDDS-funded Parkinson's Disease Biomarkers Program (PDBP).</p>

| phs000901 | dbGaP

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