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NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions

ABSTRACT: NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions

PROVIDER: PRJNA792503 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17333957_1.fastq.gz	Fastqsanger.gz
	SRR17333958_1.fastq.gz	Fastqsanger.gz
	SRR17333959_1.fastq.gz	Fastqsanger.gz
	SRR17333960_1.fastq.gz	Fastqsanger.gz
	SRR17333960_2.fastq.gz	Fastqsanger.gz

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NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions

Project description:Purpose:Up to 80% of the human genome produces “dark matter” RNAs, most of which are noncapped RNAs (napRNAs). However, determining the functional impacts and metabolism of napRNAs requires the identification of their full-length sequences. Method:Here, by developing a novel method, NAP-seq, to globally profile the full-length sequences of napRNAs at single-nucleotide resolution, we revealed several novel classes of exceptionally structured noncoding RNAs (ncRNAs). Results:We discovered stably expressed linear intron RNAs (sliRNAs), a novel class of snoRNA-intron RNAs (snotrons), a new class of RNAs embedded in miRNA spacers (misRNAs) and thousands of new structured ncRNAs in humans and mice. These new napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we showed that the novel napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Conclusion:Our approach establishes a paradigm for discovering novel classes of ncRNAs with regulatory potency.

2024-02-19 | GSE192632 | GEO

NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions.

Project description:Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.

| S-EPMC10948791 | biostudies-literature

NAP provides neuroprotection against kainic acid-induced cell death

Project description:NAP - neuroprotective peptide demonstrates increase in neuronal survival when injected into the hippocampus of rats in the model of epilepsy Microarray analysis was used to understand the expression of genes following KA treatment and the changes in gene expression following KA+NAP treatment Keywords: stress response KA was injected into the hippocampus of Sprague-Dawley rats. The other group of rats was injected with KA and NAP(10-13M). The third group was injected with NAP only and the last group was injected with PBS as a vehicle. CA3 area of hippocampus was removed 24h later and RNA extraction was done. The samples were subjected to microarray analysis.

2010-04-06 | E-GEOD-10923 | biostudies-arrayexpress

NAP provides neuroprotection against kainic acid-induced cell death

2010-03-01 | GSE10923 | GEO

Full-length Sequencing of Non-capped RNAs Reveals the Heterogeneity of RNA Processing and Novel Classes of Noncoding RNAs

Project description:Purpose:Up to 80% of the human genome gives rise to “dark matter” RNAs that mainly composes of non-capped RNAs (napRNAs). However, determining the functional impacts and metabolisms of the napRNAs requires identification of their full-length sequences. Method:We developed an approach to globally profile the full-length sequences of napRNAs at single-nucleotide resolution Results:We discovered, for the first time, the stable expressed linear intron RNA (sliRNA), a novel class of snoRNA-intron (snotron) RNAs, a new class of RNA embedded in miRNA spacers (misRNA) and thousands of new exceptional structured ncRNAs and repeat-derived ncRNAs (repeatRNA) in humans and mouse. Importantly, these new napRNAs are dynamic changes in response to various stimuli and biological processes, suggesting that they have potential regulatory functions. Furthermore, we show that functional napRNA FS4, discovered by NAP-seq firstly, promotes HepG2 cell proliferation by interacting with DKC1 to maintain the protein stability. Conclusion:Collectively, our approach establishes a paradigm for mapping and annotating novel class of ncRNAs of many living species.

2024-02-19 | GSE228168 | GEO

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

Project description:Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

| PRJNA271946 | ENA

Nucleosome assembly protein-1 (NAP-1) is regulator of histone H1 acetylation

Project description:We identified NAP-1 as regulator of histone H1 acetyation.

2020-10-10 | GSE159294 | GEO

Assessment Of Long Noncoding RNA CCAT1 In Colorectal Cancer Patients

Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal. 2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging. 3. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in precancerous colorectal diseases. 4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.

| 2330122 | ecrin-mdr-crc

MO-OH-Nap and SAHA induce distinct patterns of gene expression in the multiple myeloma cell line U266.

Project description:Tropolones are small organic compounds with metal-directing moieties. Functionally, tropolones inhibit the proliferation of cancer cell lines, possibly through the inhibition of metalloenzymes such as select histone deacetylases (HDACS). Pan-HDAC inhibitors are therapeutically beneficial in the treatment of multiple myeloma albeit with significant side-effects likely owning to their lack of specificity. It was therefore hypothesized that tropolones might have anti-myeloma activities. To this end, a series of novel a-substituted tropolones were evaluated for cytotoxic effects in multiple myeloma cells. While all tested tropolones showed some level of toxicity, MO-OH-Nap had consistently low EC50 values between 1-11 mM in all three cell lines tested and was used for subsequent experiments. MO-OH-Nap was found to induce apoptosis in a concentration-dependent manner. Time course experiments demonstrated that MO-OH-Nap promotes caspase cleavage in a time-frame that was distinct from the pan-HDAC inhibitor SAHA. Furthermore, MO-OH-Nap- and SAHA-treated cells possess unique gene expression patterns, suggesting they promote apoptosis via different mechanisms. In particular, MO-OH-Nap increases the expression of markers associated with endoplasmic reticulum stress and the unfolded protein response. Synergistic cytotoxic effects were observed when cells were treated with the combination of MO-OH-Nap and the proteasome inhibitor bortezomib. However, treatment with MO-OH-Nap did not abrogate the bortezomib-induced increase in aggresomes, consistent with an HDAC6-independent mechanism for the observed synergy. Collectively, these finding support further investigation into the usefulness of a-substituted tropolones as anti-myeloma agents.

2018-01-01 | GSE93099 | GEO

Blastopirellula marina strain:Nap-Phe MGV

Project description:Blastopirellula marina strain:Nap-Phe MGV Genome sequencing and assembly

| PRJNA435595 | ENA