Identification of differentially expressed long non-coding RNAs and messenger RNAs involved with muscle development in Dazu black goats through RNA sequencing

2022 ◽  
pp. 1-9
Author(s):  
Chao-Nan Huang ◽  
Cheng-Li Liu ◽  
Shi-Qi Zeng ◽  
Chang-Bao Liu ◽  
Wei-Jiang Si ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Muscle Development ◽  
Differentially Expressed ◽  
Messenger Rnas ◽  
Non Coding Rnas

scholarly journals Temporal transcriptomic changes in long non-coding RNAs and messenger RNAs involved in the host immune and metabolic response during Toxoplasma gondii lytic cycle

2022 ◽  
Vol 15 (1) ◽  
Author(s):  
Sha-Sha Wang ◽  
Chun-Xue Zhou ◽  
Hany M. Elsheikha ◽  
Jun-Jun He ◽  
Feng-Cai Zou ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Rna Sequencing ◽  
Lytic Cycle ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Sequencing Analysis ◽  
Messenger Rnas ◽  
Receptor Signaling ◽  
Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) are important regulators of various biological and pathological processes, in particular the inflammatory response by modulating the transcriptional control of inflammatory genes. However, the role of lncRNAs in regulating the immune and inflammatory responses during infection with the protozoan parasite Toxoplasma gondii remains largely unknown. Methods We performed a longitudinal RNA sequencing analysis of human foreskin fibroblast (HFF) cells infected by T. gondii to identify differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs), and dysregulated pathways over the course of T. gondii lytic cycle. The transcriptome data were validated by qRT-PCR. Results RNA sequencing revealed significant transcriptional changes in the infected HFFs. A total of 697, 1234, 1499, 873, 1466, 561, 676 and 716 differentially expressed lncRNAs (DElncRNAs), and 636, 1266, 1843, 2303, 3022, 1757, 3088 and 2531 differentially expressed mRNAs (DEmRNAs) were identified at 1.5, 3, 6, 9, 12, 24, 36 and 48 h post-infection, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DElncRNAs and DEmRNAs revealed that T. gondii infection altered the expression of genes involved in the regulation of host immune response (e.g., cytokine–cytokine receptor interaction), receptor signaling (e.g., NOD-like receptor signaling pathway), disease (e.g., Alzheimer's disease), and metabolism (e.g., fatty acid degradation). Conclusions These results provide novel information for further research on the role of lncRNAs in immune regulation of T. gondii infection. Graphical Abstract

scholarly journals Comprehensive analysis of differentially expressed profiles of long non-coding RNAs and messenger RNAs in kaolin-induced hydrocephalus

Gene ◽  
2019 ◽  
Vol 697 ◽  
pp. 184-193 ◽  
Author(s):  
Yan-Hui Shi ◽  
Xin-Wei He ◽  
Feng-Di Liu ◽  
Yi-Sheng Liu ◽  
Yue Hu ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Messenger Rnas ◽  
Non Coding Rnas

scholarly journals Identification of Differentially Expressed lncRNAs and mRNAs in Children with Acquired Aplastic Anemia by RNA Sequencing

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Shuanglong Lu ◽  
Xiaoxiao Song ◽  
Jing Chen ◽  
Xiaohong Qiao
Keyword(s):  
Aplastic Anemia ◽  
Rna Sequencing ◽  
Future Study ◽  
Literature Search ◽  
Noncoding Rnas ◽  
Potential Functions ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
Messenger Rnas ◽  
Blood Samples

Background. The effects of long noncoding RNAs (lncRNAs) and their related messenger RNAs (mRNAs) remain unknown in children with acquired aplastic anemia (AA). The aim of this study is to screen key lncRNAs and mRNAs and investigate their potential roles in the pathology of acquired AA in children. Methods. RNA sequencing was performed to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between blood samples of acquired AA children and healthy controls. cis-regulation, trans-regulation, competing endogenous (Ce) regulation networks of DElncRNAs and DEmRNAs were constructed. A literature search was performed to identify immune- or hematopoietic-related DElncRNA-DEmRNA pairs, and qPCR was conducted to validate the expression of the immune- or hematopoietic-related DElncRNA and DEmRNA. Results. 60 DElncRNAs and 364 DEmRNAs were identified. 13 DElncRNAs were predicted to have 15 cis-regulated target DEmRNAs, 16 DElncRNAs might have 28 trans-regulated DEmRNAs, and 2 DElncRNAs might have 9 Ce-regulated DEmRNAs. After literature screen and qPCR validation, 6 immune- or hematopoietic-related DElncRNA-DEmRNA pairs in the networks above were identified as key RNAs in the pathology of acquired AA. Conclusion. This study revealed key lncRNAs in children with acquired AA and proposed their potential functions by predicting their target mRNAs, which lay the foundation for future study of potential effects of lncRNAs in children with acquired AA.

scholarly journals Identification of Non-coding RNA Biomarkers in Stress-induced Depression via Comprehensive Analysis of Competing Endogenous RNA Network

2020 ◽  
Author(s):  
xuanjun liu ◽  
Lan Yan ◽  
Chun Lin ◽  
Yiliang Zhang ◽  
Haofei Miao ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Psychiatric Disease ◽  
Circular Rnas ◽  
Messenger Rnas ◽  
Competing Endogenous Rna ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Promising Perspective

Abstract BackgroundDepression is one of the most common psychiatric disease worldwide. Although the research about the pathogenesis of depression have achieved progress, the detailed effect of non-coding RNAs (ncRNAs) in depression are still not clearly elucidated. This study was aimed to identify non-coding RNA biomarkers in stress-induced depression via comprehensive analysis of competing endogenous RNA networkMethodsIn this present study, we acquired RNA expression from RNA seq expression profile in three mice with depressive-like behaviors using chronic restraint stress paradigm and three C57BL/6J wild-type mice as control mice. ResultsA total of 41 differentially expressed circular RNAs (circRNAs) and 181 differentially expressed messenger RNAs (mRNAs) were up-regulated, and 65 differentially expressed circRNAs and 289 differentially expressed mRNAs were down-regulated, which were selected by a threshold of fold change ≥2 and a p-value < 0.05. Gene Ontology was performed to analyze the biological functions, and we predicted potential signaling pathways based on Kyoto Encyclopedia of Genes and Genomes pathway database. In addition, we constructed a circRNA-microRNA (miRNA)-mRNA regulatory network to further identify non-coding RNAs biomarkers. ConclusionsOur findings provide a promising perspective for further research into molecular mechanisms of depression, and targeting circRNA -mediated competing endogenous RNA (ceRNA) network is a useful strategy to early recognize the depression.

scholarly journals Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun Huang ◽  
Fei Ge ◽  
Xiaoming Ma ◽  
Rongfeng Dai ◽  
Renqing Dingkao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Basis ◽  
Muscle Development ◽  
Expression Profiles ◽  
Economic Benefits ◽  
Production Performance ◽  
Differentially Expressed ◽  
Myoblast Differentiation ◽  
Longissimus Dorsi ◽  
Non Coding Rnas

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

Genome-wide identification and characterization of long non-coding RNAs in Longissimus dorsi skeletal muscle of Shandong black cattle and Luxi cattle

2020 ◽  
Author(s):  
Ruili Liu ◽  
Xianxun Liu ◽  
Kun Yu ◽  
Xuejin Bai ◽  
Yajuan Dong
Keyword(s):  
Skeletal Muscle ◽  
Cell Differentiation ◽  
Muscle Cell ◽  
Muscle Development ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Longissimus Dorsi ◽  
Protein Coding ◽  
Non Coding Rnas

Abstract Background There is increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. Results RNA samples were collected from longissimus dorsi muscle samples of Shandong black cattle and Luxi cattle and libraries were constructed and sequenced. A total of 1415 transcripts (of which 480 were LncRNAs) were differentially expressed (P < 0.05) in the different breeds, and fourteen of these RNAs were randomly selected and validated by qPCR. We found that the most differentially expressed LncRNAs were found on chromosome 9, with 1164 within 50 kb of a protein-coding gene. In addition, Pearson's correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may bind miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds. Conclusions The data obtained in this study were used to predict muscle-related LncRNAs-miRNA-mRNA interaction networks, which can help elucidate the molecular mechanism of cattle muscle development. These results can be used to facilitate livestock breeding and improve livestock production.

scholarly journals Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuanda Lv ◽  
Fengqin Hu ◽  
Yongfeng Zhou ◽  
Feilong Wu ◽  
Brandon S. Gaut
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Transposable Elements ◽  
Rna Sequencing ◽  
Sequence Similarity ◽  
Long Terminal Repeat Retrotransposons ◽  
Differentially Expressed ◽  
Abiotic Stress Response ◽  
Total Rna ◽  
Non Coding Rnas

Abstract Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

scholarly journals Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jinhuan Dou ◽  
Flavio Schenkel ◽  
Lirong Hu ◽  
Adnan Khan ◽  
Muhammad Zahoor Khan ◽  
...  
Keyword(s):  
Heat Stress ◽  
Rna Sequencing ◽  
Adrenal Glands ◽  
Insulin Signalling ◽  
Sequence Similarity ◽  
Mammalian Species ◽  
Differentially Expressed ◽  
Sprague Dawley ◽  
Expression Levels ◽  
Non Coding Rnas

Abstract Background Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by transcriptional regulation. However, no research has been reported on the characterization and functionality of lncRNAs in heat-stressed rats. Results We studied expression levels of lncRNAs in rats during HS, using strand-specific RNA sequencing. Six rats, three in each of Control (22 ± 1 °C) and H120 (42 °C for 120 min) experimental groups, were used to screen for lncRNAs in their liver and adrenal glands. Totally, 4498 and 7627 putative lncRNAs were identified in liver and adrenal glands of the Control and H120 groups, respectively. The majority of lncRNAs were relatively shorter and contained fewer exons than protein-coding transcripts. In total, 482 (174 up-regulated and 308 down-regulated) and 271 (126 up-regulated and 145 down-regulated) differentially-expressed lncRNAs (DElncRNAs, P < 0.05) were identified in the liver and adrenal glands of the Control and H120 groups, respectively. Furthermore, 1274, 121, and 73 target differentially-expressed genes (DEGs) in the liver were predicted to interact with DElncRNAs based on trans−/cis- and sequence similarity regulatory modes. Functional annotation analyses indicated that these DEGs were mostly significantly enriched in insulin signalling, myeloid leukaemia, and glucagon signalling pathways. Similarly, 437, 73 and 41 target DEGs in the adrenal glands were mostly significantly enriched in the cell cycle (trans-prediction) and lysosome pathways (cis-prediction). The DElncRNAs interacting with DEGs that encode heat shock proteins (HSPs) may play an important role in HS response, which include Hsf4, Dnaja1, Dnajb4, Hsph1 and Hspb1 in the liver, and Dnajb13 and Hspb8 in the adrenal glands. The strand-specific RNA sequencing findings were also further verified through RT-qPCR. Conclusions This study is the first to provide a detailed characterization and functional analysis of expression levels of lncRNAs in liver and adrenal glands of heat-stressed rats, which provides basis for further studies on the biological functions of lncRNAs under heat stress in rats and other mammalian species.

scholarly journals Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Jie Liu ◽  
Yan Zhou ◽  
Xin Hu ◽  
Jingchao Yang ◽  
Qiuxia Lei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Muscle Development ◽  
Differentially Expressed ◽  
Chicken Breast ◽  
Regulation Of Transcription ◽  
Rna Seq ◽  
Regulatory Interactions ◽  
Chicken Muscle ◽  
Non Coding Rnas

The developmental complexity of muscle arises from elaborate gene regulation. Long non-coding RNAs (lncRNAs) play critical roles in muscle development through the regulation of transcription and post-transcriptional gene expression. In chickens, previous studies have focused on the lncRNA profile during the embryonic periods, but there are no studies that explore the profile from the embryonic to post-hatching period. Here, we reconstructed 14,793 lncRNA transcripts and identified 2,858 differentially expressed lncRNA transcripts and 4,282 mRNAs from 12-day embryos (E12), 17-day embryos (E17), 1-day post-hatch chicks (D1), 14-day post-hatch chicks (D14), 56-day post-hatch chicks (D56), and 98-day post-hatch chicks (D98), based on our published RNA-seq datasets. We performed co-expression analysis for the differentially expressed lncRNAs and mRNAs, using STEM, and identified two profiles with opposite expression trends: profile 4 with a downregulated pattern and profile 21 with an upregulated pattern. The cis- and trans-regulatory interactions between the lncRNAs and mRNAs were predicted within each profile. Functional analysis of the lncRNA targets showed that lncRNAs in profile 4 contributed to the cell proliferation process, while lncRNAs in profile 21 were mainly involved in metabolism. Our work highlights the lncRNA profiles involved in the development of chicken breast muscle and provides a foundation for further experiments on the role of lncRNAs in the regulation of muscle development.

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