scholarly journals Paternal chronic folate supplementation induced the transgenerational inheritance of acquired developmental and metabolic changes in chickens

2019 ◽  
Vol 286 (1910) ◽  
pp. 20191653 ◽  
Author(s):  
Shengru Wu ◽  
Wei Guo ◽  
Xinyi Li ◽  
Yanli Liu ◽  
Yulong Li ◽  
...  
Keyword(s):  
Glucose Metabolism ◽  
Messenger Rna ◽  
Metabolic Changes ◽  
Micro Rna ◽  
Differentially Expressed ◽  
Folate Supplementation ◽  
Non Coding Rna ◽  
Differentially Expressed Mirnas ◽  
Long Non Coding Rna ◽  
Competitive Endogenous Rna

Increasing evidence indicates that paternal diet can result in metabolic changes in offspring, but the definite mechanism remains unclear in birds. Here, we fed breeder cocks five different diets containing 0, 0.25, 1.25, 2.50 and 5.00 mg kg −1 folate throughout life. Paternal folate supplementation (FS) was beneficial to the growth and organ development of broiler offspring. Most importantly, the lipid and glucose metabolism of breeder cocks and broiler offspring were affected by paternal FS, according to biochemical and metabolomic analyses. We further employed global analyses of hepatic and spermatozoal messenger RNA (mRNA), long non-coding RNA (lncRNA) and micro RNA (miRNA). Some key genes involved in the glycolysis or gluconeogenesis pathway and the PPAR signalling pathway, including PEPCK , ANGPTL4 and THRSP , were regulated by differentially expressed hepatic and spermatozoal miRNAs and lncRNAs in breeder cocks and broiler offspring. Moreover, the expression of ANGPTL4 could also be regulated by differentially expressed miRNAs and lncRNAs in spermatozoa via competitive endogenous RNA (ceRNA) mechanisms. Overall, this model suggests that paternal folate could transgenerationally regulate lipid and glucose metabolism in broiler offspring and the epigenetic transmission may involve altered spermatozoal miRNAs and lncRNAs.

scholarly journals LINC01018 and SMIM25 sponged miR-182-5p in endometriosis revealed by the ceRNA network construction

2020 ◽  
Vol 34 ◽  
pp. 205873842097630
Author(s):  
Li Jiang ◽  
Mengmeng Zhang ◽  
Sixue Wang ◽  
Yuzhen Xiao ◽  
Jingni Wu ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Cerna Network ◽  
Non Coding Rna ◽  
Differentially Expressed Mirnas ◽  
Long Non Coding Rna

The current study intended to explore the interaction of the long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) under the background of competitive endogenous RNA (ceRNA) network in endometriosis (EMs). The differentially expressed miRNAs (DEmiRs), differentially expressed lncRNA (DELs), and differentially expressed genes (DEGs) between EMs ectopic (EC) and eutopic (EU) endometrium based on three RNA-sequencing datasets (GSE105765, GSE121406, and GSE105764) were identified, which were used for the construction of ceRNA network. Then, DEGs in the ceRNA network were performed with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) analysis. Besides, the DEmiRs in the ceRNA network were validated in GSE124010. And the target DELs and DEGs of verified DEmiRs were validated in GSE86534. The correlation of verified DEmiRs, DEGs, and DELs was explored. Moreover, gene set enrichment analysis (GSEA) was applied to investigate the function of verified DEmiRs, DEGs, and DELs. Overall, 1352 DEGs and 595 DELs from GSE105764, along with 27 overlapped DEmiRs between GSE105765 and GSE121406, were obtained. Subsequently, a ceRNA network, including 11 upregulated and 16 downregulated DEmiRs, 7 upregulated and 13 downregulated DELs, 48 upregulated and 46 downregulated DEGs, was constructed. The GO and KEGG pathway analysis showed that this ceRNA network probably was associated with inflammation-related pathways. Furthermore, hsa-miR-182-5p and its target DELs (LINC01018 and SMIM25) and DEGs (BNC2, CHL1, HMCN1, PRDM16) were successfully verified in the validation analysis. Besides, hsa-miR-182-5p was significantly negatively correlated with these target DELs and DEGs. The GSEA analysis implied that high expression of LINC01018, SMIM25, and CHL1, and low expression of hsa-miR-182-5p would activate inflammation-related pathways in endometriosis EU samples. LINC01018 and SMIM25 might sponge hsa-miR-182-5p to upregulate downstream genes such as CHL1 to promote the development of endometriosis.

scholarly journals Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma

2021 ◽  
Vol 12 ◽  
Author(s):  
An-Cheng Qin ◽  
Yi Qian ◽  
Yu-Yuan Ma ◽  
Yong Jiang ◽  
Wei-Feng Qian
Keyword(s):  
Thyroid Carcinoma ◽  
Anaplastic Thyroid Carcinoma ◽  
Differentially Expressed ◽  
Loss Of Function ◽  
Non Coding Rna ◽  
Polymerase Chain ◽  
Underlying Mechanisms ◽  
Pathway Analyses ◽  
Long Non Coding Rna ◽  
Competitive Endogenous Rna

Anaplastic thyroid carcinoma (ATC) is one of the most aggressive human malignancies with poor prognosis. However, the underlying mechanisms of ATC remain to be elucidated. Recently, increasing studies have focused on competitive endogenous RNA (ceRNA) to discover valuable biomarkers for the diagnosis of ATC. The present study identified 705 differentially expressed mRNAs and 47 differentially expressed lncRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also conducted. Additionally, an lncRNA/miRNA/mRNA network was constructed which included 1103 regulatory relations. The upregulation of RP11-395G23.3 in ATC cells was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). In the loss of function assays, results suggested silencing of RP11-395G23.3 inhibited cell proliferation and induced cell apoptosis. Mechanically, RP11-395G23.3 could increase ROR1 via sponging miR-124-3p as a ceRNA. Moreover, ROR1 expression was decreased with the downregulation of RP11-395G23.3, but was rescued by the co-transfection of the miR-124-3p inhibitor in ATC cells. Our research suggested that the RP11-395G23.3/miR-124-3p/ROR1 axis potentially acted as a potential target for the diagnosis of ATC.

scholarly journals Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongwei Yan ◽  
Qi Liu ◽  
Jieming Jiang ◽  
Xufang Shen ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Sex Determination ◽  
High Throughput Sequencing ◽  
Sex Differentiation ◽  
Mature Mirnas ◽  
Takifugu Rubripes ◽  
Sequencing Technology ◽  
Non Coding Rna ◽  
Differentially Expressed Mirnas ◽  
Tiger Pufferfish ◽  
Long Non Coding Rna

AbstractAlthough sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.

scholarly journals Integrative Analysis of lncRNAs, miRNAs, and mRNA-Associated ceRNA Network in an Atopic Dermatitis Recurrence Model

2018 ◽  
Vol 19 (10) ◽  
pp. 3263 ◽  
Author(s):  
Xiaoyu Wang ◽  
Kaifan Bao ◽  
Peng Wu ◽  
Xi Yu ◽  
Can Wang ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Messenger Rna ◽  
Integrative Analysis ◽  
Ample Evidence ◽  
Cerna Network ◽  
Non Coding Rna ◽  
Recurrence Model ◽  
Non Coding Rnas ◽  
Remission Phase ◽  
Long Non Coding Rna

Atopic dermatitis (AD) is a prevalent inflammatory skin disease characterized by its chronic nature and relapse. Ample evidence suggests that non-coding RNAs play a major role in AD pathogenesis. However, the mechanism remains unknown, particularly in AD recurrence. Dynamic morphological and cytokine changes were measured throughout the whole course of an FITC-induced AD recurrence murine model. Microarray assay and integrative analysis were performed to comprehensively explore long non-coding RNA (lncRNA), messenger RNA (mRNA), and microRNA (miRNA) networks. Our results showed that an AD recurrence model was established. Overall, 5766 lncRNAs, 4025 mRNAs, and 202 miRNAs changed after elicitation, whereas, 419 lncRNAs, 349 mRNAs, and more notably, only 23 miRNAs, were dysregulated in the remission phase. Gene ontology (GO) and KEGG pathway enrichment analyses were used to investigate the potential functions of the dysregulated genes. The altered regulation of seven miRNAs and seven lncRNAs were validated in different stages of the model. The competing endogenous RNA (ceRNA) network inferred that lncRNA humanlincRNA0490+ could compete for miR-155-5p binding, through which it might affect Pkiα expression. Altogether, our findings have provided a novel perspective on the potential roles of non-coding RNAs in AD, and suggest that specific non-coding RNAs could be new therapeutic targets against AD recurrence.

scholarly journals Long-non Coding RNAs Related to Fat Deposition in Pigs Included lncRNA Corresponding to Human MALAT1

2021 ◽  
Author(s):  
Katarzyna Piórkowska ◽  
Kacper Żukowski ◽  
Katarzyna Ropka-Molik ◽  
Mirosław Tyra
Keyword(s):  
Regulatory Elements ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Sequencing Method ◽  
Non Coding Rnas ◽  
Potential Interactions ◽  
Long Non Coding Rna ◽  
Generation Sequencing

Obesity is a problem in the last decades since the development of different technologies forced the submission of a faster pace of life, resulting in nutrition style changes. In turn, domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied the next-generation sequencing method to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), included long-non coding RNA molecules. The Freiburg RNA tool was applied to recognise predicting hybridisation energy of RNA-RNA interactions. The results indicated several long non-coding RNAs (lncRNAs) whose expression was significantly positively or negatively associated with fat deposition. lncRNAs play an essential role in regulating gene expression by sponging miRNA, binding transcripts, facilitating translation, or coding other smaller RNA regulatory elements. In the pig fat tissue of obese group, increased expression of lncRNAs corresponding to human MALAT1 was observed that previously recognised in the obesity-related context. Moreover, hybridisation energy analyses pinpointed numerous potential interactions between identified differentially expressed lncRNAs, and obesity-related genes and miRNAs expressed in AT.

scholarly journals Aberrant expression of long non-coding RNA in thyroid neoplasms

2019 ◽  
pp. 17-25
Author(s):  
В.Д. Якушина ◽  
А.С. Танас ◽  
А.В. Лавров
Keyword(s):  
Thyroid Cancer ◽  
Signaling Pathway ◽  
In Silico ◽  
Thyroid Nodules ◽  
Differentially Expressed ◽  
Follicular Variant ◽  
Aberrant Expression ◽  
Lncrna Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Актуальность. Длинные некодирующие РНК (днРНК) при раке щитовидной железы плохо изучены; не известны днРНК, общие и специфичные для фолликулярного и классического вариантов папиллярного рака, не установлены днРНК, аберрантно экспрессированные при других основных субтипах злокачественных новообразований щитовидной железы, а также при доброкачественных новообразованиях. Цель исследования - определить днРНК, аберрантно экспрессированные при фолликулярной аденоме (ФА), фолликулярном раке (ФРЩЖ), фолликулярном и классическом вариантах папиллярного рака (ПРЩЖ), анапластическом раке (АРЩЖ) щитовидной железы. Методы. Проанализирована экспрессия днРНК по данным исследований на микрочипах (8 независимых экспериментов, доступных в GEO) и секвенирования РНК (PRJEB11591 и TCGA-THCA). Исследованы 246 образцов нормальной ткани щитовидной железы, 26 - ФА, 30 - ФРЩЖ, 181 - фолликулярного варианта ПРЩЖ, 481 - классического варианта ПРЩЖ и 49 - АРЩЖ. Для классического и фолликулярного вариантов ПРЩЖ выполнена валидация дифференциальной экспрессии in silico. Потенциальные биологические функции были оценены в результате анализа обогащения коэкспрессированных генов. Результаты. Определены днРНК, дифференциально экспрессированные при ФА, ФРЩЖ, фолликулярном и классическом вариантах ПРЩЖ и АРЩЖ. Выявлены 8 днРНК, экспрессия которых изменена во всех субтипах новообразований щитовидной железы, 22 - общих для ПРЩЖ, 32 - специфичных для классического варианта ПРЩЖ, 1 - специфичная для фолликулярного варианта ПРЩЖ, и 177 - специфичных для АРЩЖ. Статистически значимо дифференциально экспрессированных днРНК в ФРЩ по сравнению с ФА не выявлено. Ранее известные онкогенные и супрессорные днРНК NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, RMST впервые обнаружены в новообразованиях щитовидной железы. Выявленные днРНК предположительно вовлечены в клеточную адгезию, организацию экстрацеллюлярного матрикса, образование эндодермы, регуляцию клеточного цикла и митоза, полярности клеток, сигнальные пути VEGF и WNT. Выводы. Установлены общие и специфичные паттерны экспрессии днРНК в доброкачественных и злокачественных новообразованиях щитовидной железы. Background. Long non-coding RNA (lncRNA) in thyroid cancer are poorly investigated; no lncRNAs common and specific for the follicular and classical variants of papillary cancer, as well as no lncRNAs aberrantly expressed in benign nodules or other subtypes of thyroid cancer are established. The objective of the study is to determine long noncoding RNAs aberrantly expressed in follicular adenoma (FA), follicular carcinoma (FTC), follicular and classical variants of papillary carcinoma (PTC), anaplastic carcinoma (ATC). Methods. lncRNA expression was analyzed in dataset of Microarray (8 independent experiments available in GEO) and RNA-seq studies (PRJEB11591 and TCGA-THCA). In total, 246 samples of normal thyroid tissue, 26 FAs, 30 FTCs, 181 follicular variant PTCs, 481 classic variant PTCs and 49 ATCs were examined. In silico validation was performed. Potential biological functions were assessed by enrichment analysis of coexpressed genes. Results. LncRNAs differentially expressed in FA, FTC, follicular, and classical variants of PTC, and ATC are identified. There are 8 lncRNAs common for all investigated thyroid nodules, 22 common for PTC, 32 specific for classical PTC, 1 specific for follicular variant of PTC, and 177 specific for ATC. No lncRNA significantly differentially expressed in FTC compared to FA is identified. The previously described oncogenic and suppressor lncRNAs NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, RMST are detected in thyroid carcinomas for the first time. Identified lncRNA are putatively involved in cell adhesion, extracellular matrix organization, endoderm formation, VEGF signaling pathway, WNT signaling pathway and cell polarity, cell cycle and mitosis. Conclusion. The general and specific patterns of lncRNA expression in benign and malignant thyroid nodules are established.

scholarly journals Differential long non-coding RNA expression profile and function analysis in primary Sjogren’s syndrome

2021 ◽  
Author(s):  
Xiaochan Chen ◽  
Qi Cheng ◽  
Yan Du ◽  
Lei Liu ◽  
Huaxiang Wu
Keyword(s):  
B Cells ◽  
Primary Sjögren’S Syndrome ◽  
Differentially Expressed ◽  
Expression Level ◽  
Primary Sjogren’S Syndrome ◽  
Primary Sjögren's Syndrome ◽  
Cerna Network ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Healthy Persons

Abstract Background: Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease characterized by abnormal immune cell activation. This study aimed to investigate differentially expressed long non-coding RNA (lncRNA) in peripheral blood mononuclear cells (PBMCs) in patients with pSS to identify lncRNAs that affect pSS pathogenesis. Methods: Total RNA was extrated from PBMCs of 30 patients with pSS and 15 healthy persons. Transcriptome sequencing was used to screen differentially expressed lncRNAs and mRNAs in 8 RNA samples from the discovery cohort. The differentially expressed mRNAs underwent functional enrichment analysis. A protein interaction relationship (PPI) and ceRNA network was constructed. Real-time PCR was used to validate screened lncRNAs in all 45 RNA samples. Results: 1180 lncRNAs and 640 mRNAs were differentially expressed in pSS patients (fold change > 2 in healthy persons). The PPI network was constructed with 640 mRNAs and a ceRNA network with four key lncRNAs (GABPB1-AS1, PSMA3-AS1, LINC00847 and SNHG1). RT-PCR revealed that GABPB1-AS1 and PSMA3-AS1 were significantly upregulated 3.0-and 1.4-fold in the pSS group, respectively. The GABPB1-AS1 expression level was positively correlated with the percentage of B cells and IgG levels. Conclusions: GABPB1-AS1 was significently upregulated in pSS patients, and its expression level is positively correlated with the percentage of B cells and IgG levels. GABPB1-AS1 may be involved in the pathogenesis of pSS.

Sign in / Sign up

Export Citation Format

Share Document