scholarly journals Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 205 ◽  
Author(s):  
Olga A. Postnikova ◽  
Igor B. Rogozin ◽  
William Samuel ◽  
German Nudelman ◽  
Vladimir N. Babenko ◽  
...  
Keyword(s):  
Retinal Pigment Epithelium ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Non Coding Rna ◽  
Small Set ◽  
Flexible Adaptation ◽  
Non Coding Rnas ◽  
Whole Genome Alignment ◽  
Long Non Coding Rna

Currently, several long non-coding RNAs (lncRNAs) (TUG1, MALAT1, MEG3 and others) have been discovered to regulate normal visual function and may potentially contribute to dysfunction of the retina. We decided to extend these analyses of lncRNA genes to the retinal pigment epithelium (RPE) to determine whether there is conservation of RPE-expressed lncRNA between human and bovine genomes. We reconstructed bovine RPE lncRNAs based on genome-guided assembly. Next, we predicted homologous human transcripts based on whole genome alignment. We found a small set of conserved lncRNAs that could be involved in signature RPE functions that are conserved across mammals. However, the fraction of conserved lncRNAs in the overall pool of lncRNA found in RPE appeared to be very small (less than 5%), perhaps reflecting a fast and flexible adaptation of the mammalian eye to various environmental conditions.

scholarly journals Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2006
Author(s):  
Hongyu Liu ◽  
Ibrar Muhammad Khan ◽  
Huiqun Yin ◽  
Xinqi Zhou ◽  
Muhammad Rizwan ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Age Groups ◽  
Adherens Junction ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Rna Interaction ◽  
Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

scholarly journals The Impact of miRNAs in Health and Disease of Retinal Pigment Epithelium

2021 ◽  
Vol 8 ◽  
Author(s):  
Daniela Intartaglia ◽  
Giuliana Giamundo ◽  
Ivan Conte
Keyword(s):  
Retinal Pigment Epithelium ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Fine Tuning ◽  
Molecular Networks ◽  
Therapeutic Approaches ◽  
Pathological Conditions ◽  
Health And Disease ◽  
Non Coding Rnas ◽  
The Impact

MicroRNAs (miRNAs), a class of non-coding RNAs, are essential key players in the control of biological processes in both physiological and pathological conditions. miRNAs play important roles in fine tuning the expression of many genes, which often have roles in common molecular networks. miRNA dysregulation thus renders cells vulnerable to aberrant fluctuations in genes, resulting in degenerative diseases. The retinal pigment epithelium (RPE) is a monolayer of polarized pigmented epithelial cells that resides between the light-sensitive photoreceptors (PR) and the choriocapillaris. The demanding physiological functions of RPE cells require precise gene regulation for the maintenance of retinal homeostasis under stress conditions and the preservation of vision. Thus far, our understanding of how miRNAs function in the homeostasis and maintenance of the RPE has been poorly addressed, and advancing our knowledge is central to harnessing their potential as therapeutic agents to counteract visual impairment. This review focuses on the emerging roles of miRNAs in the function and health of the RPE and on the future exploration of miRNA-based therapeutic approaches to counteract blinding diseases.

scholarly journals NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants

2020 ◽  
Vol 49 (D1) ◽  
pp. D165-D171
Author(s):  
Lianhe Zhao ◽  
Jiajia Wang ◽  
Yanyan Li ◽  
Tingrui Song ◽  
Yang Wu ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Transcript Level ◽  
Tissue Expression ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
The Relationship ◽  
Long Non Coding Rna ◽  
Predicted Function

Abstract NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.

scholarly journals Long Non-Coding RNA Expression Profiling in Aging Rats with Erectile Dysfunction

2015 ◽  
Vol 37 (4) ◽  
pp. 1513-1526 ◽  
Author(s):  
Lianjun Pan ◽  
Jiehua Ma ◽  
Feng Pan ◽  
Dan Zhao ◽  
Jianping Gao
Keyword(s):  
Erectile Dysfunction ◽  
Expression Profiles ◽  
Critical Role ◽  
Altered Expression ◽  
Aged People ◽  
Age Related ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Rna Expression Profiling ◽  
Long Non Coding Rna

Background/Aims: Erectile dysfunction (ED) in aged people remains a topic of interest to andrological physicians. Long non-coding RNAs (lncRNAs), which form the largest group of non-coding RNAs, have been shown to regulate various biological processes. The function of lncRNAs in age-related erectile dysfunction (A-ED) pathogenesis remains poorly understood. Methods: This study aims to assess the differential expression profiles of mRNAs and lncRNAs between A-ED and normal control (NC) samples. Using a second-generation lncRNA microarray, we detected a total of 8,744 lncRNAs and 13,585 coding transcripts. Results: We identified 608 up-regulated and 406 down-regulated lncRNAs in A-ED compared with NC samples, by setting a filter of fold-change >2.0. Gene Ontology and pathway analysis revealed that a muscle contraction disorder induced by abnormal ion channels might play a critical role in the pathogenesis of A-ED. Conclusion: Our results show significantly altered expression profiles of lncRNAs and mRNAs between A-ED and NC. This study may provide information for further research on A-ED and may be helpful for finding a new therapeutic target for A-ED.

scholarly journals Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium

2014 ◽  
Vol 13s5 ◽  
pp. CIN.S14074 ◽  
Author(s):  
Heuy-Ching Wang ◽  
Whitney A. Greene ◽  
Ramesh R. Kaini ◽  
Jane Shen-Gunther ◽  
Hung-I H Chen ◽  
...  
Keyword(s):  
Retinal Pigment Epithelium ◽  
Mirna Expression ◽  
Cell Cycle Progression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Ips Cells ◽  
Differentially Expressed ◽  
Induced Pluripotent

The purpose of this study is to characterize the microRNA (miRNA) expression profiles of induced pluripotent stem (iPS) cells and retinal pigment epithelium (RPE) derived from induced pluripotent stem cells (iPS-RPE). MiRNAs have been demonstrated to play critical roles in both maintaining pluripotency and facilitating differentiation. Gene expression networks accountable for maintenance and induction of pluripotency are linked and share components with those networks implicated in oncogenesis. Therefore, we hypothesize that miRNA expression profiling will distinguish iPS cells from their iPS-RPE progeny. To identify and analyze differentially expressed miRNAs, RPE was derived from iPS using a spontaneous differentiation method. MiRNA microarray analysis identified 155 probes that were statistically differentially expressed between iPS and iPS-RPE cells. Up-regulated miRNAs including miR-181c and miR-129–5p may play a role in promoting differentiation, while down-regulated miRNAs such as miR-367, miR-18b, and miR-20b are implicated in cell proliferation. Subsequent miRNA-target and network analysis revealed that these miRNAs are involved in cellular development, cell cycle progression, cell death, and survival. A systematic interrogation of temporal and spatial expression of iPS-RPE miRNAs and their associated target mRNAs will provide new insights into the molecular mechanisms of carcinogenesis, eye differentiation and development.

scholarly journals Potential Biomarkers for Therapeutic Monitoring and Clinical Outcome in Breast Cancer

2021 ◽  
Author(s):  
Yuki Yamamoto ◽  
Sabrina La Salvia ◽  
Sahoo Susmita ◽  
Hidetoshi Tahara
Keyword(s):  
Expression Profiles ◽  
Therapeutic Targets ◽  
Transfer Rna ◽  
Therapeutic Monitoring ◽  
Transfer Rnas ◽  
Non Coding Rna ◽  
Tumor Tissues ◽  
Non Coding Rnas ◽  
Long Non Coding Rna ◽  
Potential Biomarkers

Non-coding RNAs are a species of RNA that are not translated to proteins. These include transfer RNAs and ribosomal RNAs, microRNAs, transfer RNA-derived fragments, and long non-coding RNA. It is known that expression levels of some non-coding RNAs included microRNAs are altered in cancer cells or tumor tissues. Moreover, expression profiles of such non-coding RNAs correlate between tissues and body fluids. Therefore, several non-coding RNAs are being used as diagnostic/prognosis biomarkers or therapeutic targets in cancer. In this chapter, we review about representative non-coding RNAs and introduce especially microRNA as diagnosis/prognosis biomarkers and therapeutic targets.

scholarly journals A General Computational Framework for Prediction of Disease-associated Non-coding RNAs

2019 ◽  
Vol 35 (2) ◽  
Author(s):  
Duc-Hau Le
Keyword(s):  
Computational Methods ◽  
Computational Models ◽  
Base Pairs ◽  
Computational Framework ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Small Set ◽  
Computational Aspects ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Since last decade, we have been witnessing the raise of non-coding RNAs (ncRNAs) in biomedical research. Many ncRNAs have been identified and classified into different classes based on their length in number of base pairs (bp). In parallel, our understanding about functions of ncRNAs is gradually increased. However, only small set among tens of thousands of ncRNAs have been well studied about their functions and their roles in development of diseases. This raises a pressing need to develop computational methods to associate diseases and ncRNAs. Two most widely studied ncRNAs are microRNA (miRNA) and long non-coding RNA (lncRNA), since miRNAs are the regulators of most protein-coding genes and lncRNAs are the most ubiquitously found in mammalian. To date, many computational methods have been also proposed for prediction of disease-associated miRNAs and lncRNAs, and recently comprehensively reviewed. However, in the previous reviews, these computational methods were described separately, thus this limits our understanding about their underlying computational aspects. Therefore, in this study, we propose a general computational framework for prediction of disease-associated ncRNAs. The framework demonstrates a whole computational process from data preparation to computational models.

scholarly journals Expression Profiles of Long Non-Coding RNA GAS5 and MicroRNA-222 in Younger AML Patients

Diagnostics ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 86
Author(s):  
Djordje Pavlovic ◽  
Natasa Tosic ◽  
Branka Zukic ◽  
Zlatko Pravdic ◽  
Nada Suvajdzic Vukovic ◽  
...  
Keyword(s):  
Malignant Disease ◽  
Expression Profiles ◽  
Normal Karyotype ◽  
Expression Level ◽  
Healthy Controls ◽  
Non Coding Rna ◽  
Micro Rnas ◽  
Non Coding Rnas ◽  
New Biomarkers ◽  
Long Non Coding Rna

Acute myeloid leukemia (AML) is a heterogeneous malignant disease both on clinical and genetic levels. AML has poor prognosis and, therefore, there is a constant need to find new prognostic markers, as well as markers that can be used as targets for innovative therapeutics. Recently, the search for new biomarkers has turned researchers’ attention towards non-coding RNAs, especially long non-coding RNAs (lncRNAs) and micro RNAs (miRNAs). We investigated the expression level of growth arrest-specific transcript 5 (GAS5) lncRNA in 94 younger AML patients, and also the expression level of miR-222 in a cohort of 39 AML patients with normal karyotype (AML-NK), in order to examine their prognostic potential. Our results showed that GAS5 expression level in AML patients was lower compared to healthy controls. Lower GAS5 expression on diagnosis was related to an adverse prognosis. In the AML-NK group patients had higher expression of miR-222 compared to healthy controls. A synergistic effect of GAS5low/miR-222high status on disease prognosis was not established. This is the first study focused on examining the GAS5 and miR-222 expression pattern in AML patients. Its initial findings indicate the need for further investigation of these two non-coding RNAs, their potential roles in leukemogenesis, and the prognosis of AML patients.

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