scholarly journals Long Non-coding RNA H19 Regulates Porcine Satellite Cell Differentiation Through miR-140-5p/SOX4 and DBN1

2020 ◽  
Vol 8 ◽  
Author(s):  
Jingxuan Li ◽  
Tao Su ◽  
Cheng Zou ◽  
Wenzhe Luo ◽  
Gaoli Shi ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Myogenic Differentiation ◽  
Molecular Model ◽  
Cdna Libraries ◽  
Non Coding Rna ◽  
Interaction Experiment ◽  
The One ◽  
Transcription Factor 4 ◽  
Long Non Coding Rna ◽  
Regulatory Models

The H19 gene promotes skeletal muscle differentiation in mice, but the regulatory models and mechanisms of myogenesis regulated by H19 are largely unknown in pigs. Therefore, the regulatory modes of H19 in the differentiation of porcine skeletal muscle satellite cells (PSCs) need to be determined. We observed that H19 gene silencing could decrease the expressions of the myogenin (MYOG) gene, myogenic differentiation (MYOD), and myosin heavy chain (MYHC) in PSCs. Therefore, we constructed and sequenced 12 cDNA libraries of PSCs after knockdown of H19 at two differentiation time points to analyze the transcriptome differences. A total of 11,419 differentially expressed genes (DEGs) were identified. Among these DEGs, we found through bioinformatics analysis and protein interaction experiment that SRY-box transcription factor 4 (SOX4) and Drebrin 1 (DBN1) were the key genes in H19-regulated PSC differentiation. Functional analysis shows that SOX4 and DBN1 promote PSC differentiation. Mechanistically, H19 regulates PSC differentiation through two different pathways. On the one hand, H19 functions as a molecular sponge of miR-140-5p, which inhibits the differentiation of PSCs, thereby modulating the derepression of SOX4. On the other hand, H19 regulates PSC differentiation through directly binding with DBN1. Furthermore, MYOD binds to the promoters of H19 and DBN1. The knockdown of MYOD inhibits the expression of H19 and DBN1. We determined the function of H19 and provided a molecular model to elucidate H19’s role in regulating PSC differentiation.

scholarly journals Long Non-Coding RNA Myoparr Regulates GDF5 Expression in Denervated Mouse Skeletal Muscle

2019 ◽  
Vol 5 (2) ◽  
pp. 33 ◽  
Author(s):  
Keisuke Hitachi ◽  
Masashi Nakatani ◽  
Kunihiro Tsuchida
Keyword(s):  
Skeletal Muscle ◽  
Muscle Atrophy ◽  
Myogenic Differentiation ◽  
Bmp Signaling ◽  
Skeletal Muscle Atrophy ◽  
Secretory Proteins ◽  
Non Coding Rna ◽  
Denervated Muscles ◽  
Long Non Coding Rna

Skeletal muscle is a highly plastic tissue and decreased skeletal muscle mass (muscle atrophy) results in deteriorated motor function and perturbed body homeostasis. Myogenin promoter-associated long non-coding RNA (lncRNA) Myoparr promotes skeletal muscle atrophy caused by surgical denervation; however, the precise molecular mechanism remains unclear. Here, we examined the downstream genes of Myoparr during muscle atrophy following denervation of tibialis anterior (TA) muscles in C57BL/6J mice. Myoparr knockdown affected the expression of 848 genes. Sixty-five of the genes differentially regulated by Myoparr knockdown coded secretory proteins. Among these 65 genes identified in Myoparr-depleted skeletal muscles after denervation, we focused on the increased expression of growth/differentiation factor 5 (GDF5), an inhibitor of muscle atrophy. Myoparr knockdown led to activated bone morphogenetic protein (BMP) signaling in denervated muscles, as indicated by the increased levels of phosphorylated Smad1/5/8. Our detailed evaluation of downstream genes of Myoparr also revealed that Myoparr regulated differential gene expression between myogenic differentiation and muscle atrophy. This is the first report demonstrating the in vivo role of Myoparr in regulating BMP signaling in denervated muscles. Therefore, lncRNAs that have inhibitory activity on BMP signaling may be putative therapeutic targets for skeletal muscle atrophy.

scholarly journals IIMLP: integrated information-entropy-based method for LncRNA prediction

2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Junyi Li ◽  
Huinian Li ◽  
Xiao Ye ◽  
Li Zhang ◽  
Qingzhe Xu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
Information Entropy ◽  
Area Under The Curve ◽  
Prediction Method ◽  
Machine Learning Algorithms ◽  
Reading Frame ◽  
Non Coding Rna ◽  
The One ◽  
Long Non Coding Rna

Abstract Background The prediction of long non-coding RNA (lncRNA) has attracted great attention from researchers, as more and more evidence indicate that various complex human diseases are closely related to lncRNAs. In the era of bio-med big data, in addition to the prediction of lncRNAs by biological experimental methods, many computational methods based on machine learning have been proposed to make better use of the sequence resources of lncRNAs. Results We developed the lncRNA prediction method by integrating information-entropy-based features and machine learning algorithms. We calculate generalized topological entropy and generate 6 novel features for lncRNA sequences. By employing these 6 features and other features such as open reading frame, we apply supporting vector machine, XGBoost and random forest algorithms to distinguish human lncRNAs. We compare our method with the one which has more K-mer features and results show that our method has higher area under the curve up to 99.7905%. Conclusions We develop an accurate and efficient method which has novel information entropy features to analyze and classify lncRNAs. Our method is also extendable for research on the other functional elements in DNA sequences.

The Role of Tumor-related LncRNA PART1 in cancer

2021 ◽  
Vol 27 ◽  
Author(s):  
Jinlan Chen ◽  
Enqing Meng ◽  
Yexiang Lin ◽  
Yujie Shen ◽  
Chengyu Hu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Malignant Tumors ◽  
Migration And Invasion ◽  
Signal Pathways ◽  
Toll Like Receptor ◽  
Non Coding Rna ◽  
Regulated Expression ◽  
The One ◽  
Long Non Coding Rna

Background: As we all know, long non-coding RNA (lncRNA) affects tumor progression, which has caused a great upsurge in recent years. It can also affect the growth, migration, and invasion of tumors. When we refer to the abnormal expression of lncRNA, we will find it associated with malignant tumors. In addition, lncRNA has been proved to be a key targeted gene for the treatment of some diseases. PART1, a member of lncRNA, has been reported as a regulator in the process of tumor occurrence and development. This study aims to reveal the biological functions, specific mechanisms, and clinical significance of PART1 in various tumor cells. Methods: Through the careful search of PUBMED, the mechanisms of the effect of PART1 on tumorigenesis and development are summarized. Results: On the one hand, the up-regulated expression of PART1 plays a tumor-promoting role in tumors, including lung cancer, prostate cancer, bladder cancer and so on. On the other hand, PART1 is down-regulated in gastric cancer, glioma and other tumors to play a tumor inhibitory role. In addition, PART1 regulates tumor growth mainly by targeting microRNA such as miR-635, directly regulating the expression of proteins such as FUS/EZH2, affecting signal pathways such as the Toll-like receptor pathway, or regulating immune cells. Conclusion: PART1 is closely related to tumors by regulating a variety of molecular mechanisms. In addition, PART1 can be used as a clinical marker for the early diagnosis of tumors and plays an important role in tumor-targeted therapy.

A novel long non-coding RNA, lncKBTBD10, involved in bovine skeletal muscle myogenesis

2018 ◽  
Vol 55 (1) ◽  
pp. 25-35 ◽  
Author(s):  
Mingming Chen ◽  
Xin Li ◽  
Xiaojuan Zhang ◽  
Yan Li ◽  
Junxing Zhang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Non Coding Rna ◽  
Bovine Skeletal Muscle ◽  
Long Non Coding Rna

scholarly journals Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita

2020 ◽  
Vol 21 (3) ◽  
pp. 911 ◽  
Author(s):  
Fan Yang ◽  
Dan Zhao ◽  
Haiyan Fan ◽  
Xiaofeng Zhu ◽  
Yuanyuan Wang ◽  
...  
Keyword(s):  
Meloidogyne Incognita ◽  
High Throughput Sequencing ◽  
Molecular Model ◽  
Plant Immunity ◽  
Biocontrol Bacteria ◽  
Non Coding Rna ◽  
Regulation Network ◽  
Non Coding Rnas ◽  
Molecular Functions ◽  
Long Non Coding Rna

Root-knot nematodes (RKNs) severely affect plants growth and productivity, and several commercial biocontrol bacteria can improve plants resistance to RKNs. Pseudomonas putida Sneb821 isolate was found to induce tomatoes resistance against Meloidogyne incognita. However, the molecular functions behind induced resistance remains unclear. Long non-coding RNA (lncRNA) is considered to be a new component that regulates the molecular functions of plant immunity. We found lncRNA was involved in Sneb821-induced tomato resistance to M. incognita. Compared with tomato inoculated with M. incognita, high-throughput sequencing showed that 43 lncRNAs were upregulated, while 35 lncRNAs were downregulated in tomatoes previously inoculated with Sneb821. A regulation network of lncRNAs was constructed, and the results indicated that 12 lncRNAs were found to act as sponges of their corresponding miRNAs. By using qRT-PCR and the overexpression vector pBI121, we found the expression of lncRNA44664 correlated with miR396/GRFs (growth-regulating factors) and lncRNA48734 was correlated with miR156/SPL (squamosal promoter-binding protein-like) transcription factors. These observations provided a novel molecular model in biocontrol bacteria-induced tomato resistance to M. incognita.

scholarly journals 3882A heart-enriched antisense long non-coding RNA regulates the balance between cardiac and skeletal muscle triadin

2017 ◽  
Vol 38 (suppl_1) ◽  
Author(s):  
L. Zhang ◽  
A. Salgado-Somoza ◽  
M. Vausort ◽  
P. Leszek ◽  
Y. Devaux ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaohua Yu ◽  
Yong Zhang ◽  
Tingting Li ◽  
Zhao Ma ◽  
Haixue Jia ◽  
...  
Keyword(s):  
Myogenic Differentiation ◽  
Non Coding Rna ◽  
Long Non Coding Rna
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