Short interfering RNAs (siRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes
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ABSTRACT:
PROVIDER: PRJNA755338 | ENA |
REPOSITORIES: ENA
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Project description:We introduced into subcutaneous fully-differentiated human adipocytes from the same subject short interfering RNAs (siRNAs), thus enabling the study of functional consequences of OLFM2 (siOLFM2; n=3 biological replicates) and PKP2 (siPKP2; n=3) knockdown in these cells. A lipid-based transfection reagent (i.e. Lipofectamine 3000 reagent) was used to provide a transient (72h), convenient, reliable and efficient transfection into in vitro cultured and fully differentiated adipocytes. A non-targeting siRNA was used as control (siCTRL; n=4) for both modifications.
2021-12-28 | GSE182231 | GEO
Project description:Tissue specificity of chalcone synthase short interfering RNAs (CHS siRNAs) that control seed color
| PRJNA999374 | ENA
Project description:We introduced into subcutaneous fully-differentiated human adipocytes from the same subject small hairpin RNAs (shRNAs) against two genes, thus enabling the study of functional consequences of sustained OLFM2 (shOLFM2; n=3 biological replicates) and PKP2 (shPKP2; n=3) knockdown in these cells. The lentiviral-based transfection was used to provide a long-lasting, convenient, reliable and efficient knockdown into in vitro cultured and fully differentiated adipocytes maintained for 6 d after reaching fully differentiation. A non-targeting shRNA was used as control (shCTRL; n=4) and reference for both modifications.
2021-12-28 | GSE182229 | GEO
Project description:Plant TRANS-ACTING SIRNA3 (TAS3)-derived short-interfering RNAs (siRNAs) include tasiR-ARFs, which are functionally conserved in targeting AUXIN RESPONSE FACTOR (ARF) genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sative). Small RNA-seq results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice degradome datasets, and some of these siRNA-target interactions were experimentally confirmed in rice tas3 mutants. Consistent with altered expression of target genes, phenotypic variations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether our study sheds new insights into TAS3 genes in plants and expand our knowledge about rice TAS3 siRNA-target interactions.
2022-01-26 | GSE174453 | GEO
Project description:To explore the downstream genes of PKP2,we performed RNA-seq to screen after overexpression of PKP2 in A549 cells.
2023-08-05 | GSE155759 | GEO
Project description:We previously showed CHS siRNAs levels to be high in immature seed coats of seed with dominant alleles of the I locus that controls seed color (Tuteja et al., Plant Cell 2009; Cho et al., Plos One, 2013) and to be much lower in several other tissues sampled (Zabala et al., BMC Plant Biology 2012). Here, we examined 15 additional small RNA populations by high-throughput sequencing of developing seed coats of various stages from cultivars with the dominant I and i-i alleles that specify yellow seed coats or from spontaneous mutations to pigmented seed coats. The CHS siRNAs were tissue specific and found at high levels of up to 5700 normalized RPMs (reads per millions) in immature seed coats but were less than 6 RPMs in libraries from 21 non-seed coat samples including the embryonic axis, different stages of seedlings cotyledons, vegetative buds, and shoot tips, illustrating the tightly controlled tissue-specific expression of the CHS siRNAs in seed coats.
2025-07-31 | GSE239484 | GEO
Project description:With long-read assemblies, we delineate three origins of short interfering RNAs for chalcone synthase (CHS siRNAs) in Glycine max. Mutations from ii (yellow seed coat with black hilum) to i (fully pigmented) lack either a single antisense CHS1 gene by deletion or the partial 5’ subtilisin fragment-CHS1 gene region by a large inversion mutation. On the other hand, we show that the dominant I allele, with fully yellow seed coats, arose from the i black, wild soybean genome by an inverted duplication that places a partial 5’ DnaJ fragment next to slightly truncated CHS genes. In a direct I to i mutation, the two CHS genes are further truncated, destroying their capacity to produce siRNAs. The two-color saddle pattern of the ik allele arose by an inverted duplication event that places a partial 5’ P450 fragment in front of two inverted repeat CHS genes. Despite the importance of the three different 5’ promoters that abut inverted repeat CHS genes as drivers of precursor expression, the profiles of cognate gene family members for subtilisin, DnaJ, and P450 are not always limited to the seed coat as tightly as CHS siRNAs, implying that transcriptional or processing events for CHS dsRNA or siRNAs differ in other tissues.
2025-07-31 | GSE239923 | GEO
Project description:Lentiviral-mediated small hairpin RNAs (shRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes
| PRJNA755335 | ENA
Project description:Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial cardiac disease associated with ventricular arrhythmias and an increased risk of sudden cardiac death. Currently, there are no approved treatments that address the underlying genetic cause of this disease, representing a significant unmet need. Mutations in Plakophilin-2 (PKP2), encoding a desmosomal protein, account for approximately 40% of ARVC cases and result in reduced gene expression. Methods: Our goal is to examine the feasibility and the efficacy of adeno-associated virus 9 (AAV9)-mediated restoration of PKP2 expression in a cardiac specific knock-out mouse model of Pkp2. Results: We show that a single dose of AAV9:PKP2 gene delivery prevents disease development before the onset of cardiomyopathy and attenuates disease progression after overt cardiomyopathy. Restoration of PKP2 expression leads to a significant extension of lifespan by restoring cellular structures of desmosomes and gap junctions, preventing or halting decline in left ventricular ejection fraction, preventing or reversing dilation of the right ventricle, ameliorating ventricular arrhythmia event frequency and severity, and preventing adverse fibrotic remodeling. RNA sequencing analyses show that restoration of PKP2 expression leads to highly coordinated and durable correction of PKP2-associated transcriptional networks beyond desmosomes, revealing a broad spectrum of biological perturbances behind ARVC disease etiology. Conclusions: We identify fundamental mechanisms of PKP2-associated ARVC beyond disruption of desmosome function. The observed PKP2 dose-function relationship indicates that cardiac-selective AAV9:PKP2 gene therapy may be a promising therapeutic approach to treat ARVC patients with PKP2 mutations.
2024-02-23 | GSE253223 | GEO
Project description:TAS3-derived short-interfering RNAs confer cleavage of mRNAs in rice
| PRJNA729996 | ENA