scholarly journals Orthogonal Proteomics Methods to Unravel the HOTAIR Interactome

2021 ◽  
Author(s):  
Louis Delhaye ◽  
Edith Bruycker ◽  
Pieter-Jan Volders ◽  
Daria Fijalkowska ◽  
Delphine Sutter ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Protein Complexes ◽  
Data Sets ◽  
Cellular Homeostasis ◽  
Comprehensive List ◽  
Orthogonal Methods ◽  
Non Coding Rnas ◽  
Lncrna Hotair

Abstract Accumulating evidence highlights the role of long non-coding RNAs (lncRNA) in cellular homeostasis, and their dysregulation in disease settings. Most lncRNAs function by interacting with proteins or protein complexes. While several orthogonal methods have been developed to identify these proteins, each method has its inherent strengths and limitations. Here, we combine two RNA-centric methods ChIRP-MS and RNA-BioID to obtain a comprehensive list of proteins that interact with the well-known lncRNA HOTAIR. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in various cancers. Although HOTAIR is known to bind with PRC2 and LSD1 protein complexes, only very limited unbiased comprehensive approaches to map its interactome have been performed. Both ChIRP-MS and RNA-BioID data sets show an association of HOTAIR with mitoribosomes, suggesting that HOTAIR has functions independent of its (post-)transcriptional mode-of-action.

scholarly journals The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease

2014 ◽  
Vol 369 (1652) ◽  
pp. 20130507 ◽  
Author(s):  
Thomas C. Roberts ◽  
Kevin V. Morris ◽  
Matthew J. A. Wood
Keyword(s):  
Brain Function ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Protein Coding ◽  
Low Protein ◽  
Regulated Expression ◽  
The Subject ◽  
Non Coding Rnas ◽  
Transcriptional Output

Long non-coding RNAs (lncRNAs) are transcripts with low protein-coding potential that represent a large proportion of the transcriptional output of the cell. Many lncRNAs exhibit features indicative of functionality including tissue-restricted expression, localization to distinct subcellular structures, regulated expression and evolutionary conservation. Some lncRNAs have been shown to associate with chromatin-modifying activities and transcription factors, suggesting that a common mode of action may be to guide protein complexes to target genomic loci. However, the functions (if any) of the vast majority of lncRNA transcripts are currently unknown, and the subject of investigation. Here, we consider the putative role(s) of lncRNAs in neurodevelopment and brain function with an emphasis on the epigenetic regulation of gene expression. Associations of lncRNAs with neurodevelopmental/neuropsychiatric disorders, neurodegeneration and brain cancers are also discussed.

Participant recruitment and data collection through Facebook: the role of personality factors

2017 ◽  
Author(s):  
Sean Chandler Rife ◽  
Kelly L. Cate ◽  
Michal Kosinski ◽  
David Stillwell
Keyword(s):  
Data Collection ◽  
Social Research ◽  
Personality Factors ◽  
The Internet ◽  
Data Sets ◽  
Social Networking Service ◽  
Participant Recruitment ◽  
Conducting Research ◽  
Promising Avenue

As participant recruitment and data collection over the Internet have become more common, numerous observers have expressed concern regarding the validity of research conducted in this fashion. One growing method of conducting research over the Internet involves recruiting participants and administering questionnaires over Facebook, the world’s largest social networking service. If Facebook is to be considered a viable platform for social research, it is necessary to demonstrate that Facebook users are sufficiently heterogeneous and that research conducted through Facebook is likely to produce results that can be generalized to a larger population. The present study examines these questions by comparing demographic and personality data collected over Facebook with data collected through a standalone website, and data collected from college undergraduates at two universities. Results indicate that statistically significant differences exist between Facebook data and the comparison data-sets, but since 80% of analyses exhibited partial η2 < .05, such differences are small or practically nonsignificant in magnitude. We conclude that Facebook is a viable research platform, and that recruiting Facebook users for research purposes is a promising avenue that offers numerous advantages over traditional samples.

The Role of microRNAs in the Viral Infections

2019 ◽  
Vol 24 (39) ◽  
pp. 4659-4667 ◽  
Author(s):  
Mona Fani ◽  
Milad Zandi ◽  
Majid Rezayi ◽  
Nastaran Khodadad ◽  
Hadis Langari ◽  
...  
Keyword(s):  
Viral Infections ◽  
Rna Viruses ◽  
Regulation Of Gene Expression ◽  
Molecular Structures ◽  
Main Function ◽  
Cellular Functions ◽  
Viral Genes ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs) are non-coding RNAs with 19 to 24 nucleotides which are evolutionally conserved. MicroRNAs play a regulatory role in many cellular functions such as immune mechanisms, apoptosis, and tumorigenesis. The main function of miRNAs is the post-transcriptional regulation of gene expression via mRNA degradation or inhibition of translation. In fact, many of them act as an oncogene or tumor suppressor. These molecular structures participate in many physiological and pathological processes of the cell. The virus can also produce them for developing its pathogenic processes. It was initially thought that viruses without nuclear replication cycle such as Poxviridae and RNA viruses can not code miRNA, but recently, it has been proven that RNA viruses can also produce miRNA. The aim of this articles is to describe viral miRNAs biogenesis and their effects on cellular and viral genes.

MicroRNAs as Biomarker for Breast Cancer

2020 ◽  
Vol 20 (10) ◽  
pp. 1597-1610 ◽  
Author(s):  
Taru Aggarwal ◽  
Ridhima Wadhwa ◽  
Riya Gupta ◽  
Keshav Raj Paudel ◽  
Trudi Collet ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Association Studies ◽  
Large Family ◽  
Breast Cancer Diagnosis ◽  
Cell Multiplication ◽  
Cell Physiology ◽  
Gene Transcript ◽  
Genome Wide Association Studies ◽  
Non Coding Rnas

Regardless of advances in detection and treatment, breast cancer affects about 1.5 million women all over the world. Since the last decade, genome-wide association studies (GWAS) have been extensively conducted for breast cancer to define the role of miRNA as a tool for diagnosis, prognosis and therapeutics. MicroRNAs are small, non-coding RNAs that are associated with the regulation of key cellular processes such as cell multiplication, differentiation, and death. They cause a disturbance in the cell physiology by interfering directly with the translation and stability of a targeted gene transcript. MicroRNAs (miRNAs) constitute a large family of non-coding RNAs, which regulate target gene expression and protein levels that affect several human diseases and are suggested as the novel markers or therapeutic targets, including breast cancer. MicroRNA (miRNA) alterations are not only associated with metastasis, tumor genesis but also used as biomarkers for breast cancer diagnosis or prognosis. These are explained in detail in the following review. This review will also provide an impetus to study the role of microRNAs in breast cancer.

Emerging role of non-coding RNAs in response of cancer cells to radiotherapy

2021 ◽  
Vol 218 ◽  
pp. 153327
Author(s):  
Kaveh Ebahimzadeh ◽  
Hamed Shoorei ◽  
Seyed Ali Mousavinejad ◽  
Farhad Tondro Anamag ◽  
Marcel E. Dinger ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Non Coding Rnas

scholarly journals The Gene Regulatory Roles of Herbal Extracts on the Growth, Immune System, and Reproduction of Fish

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2167
Author(s):  
Ehsan Ahmadifar ◽  
Hamideh Pourmohammadi Fallah ◽  
Morteza Yousefi ◽  
Mahmoud A. O. Dawood ◽  
Seyed Hossein Hoseinifar ◽  
...  
Keyword(s):  
Immune System ◽  
Mode Of Action ◽  
Medicinal Herbs ◽  
Environmental Stressors ◽  
Fish Diet ◽  
Sustainable Aquaculture ◽  
Herbal Supplements ◽  
Aquatic Animals ◽  
Gene Regulatory

The crucial need for safe and healthy aquatic animals obligates researchers in aquaculture to investigate alternative and beneficial additives. Medicinal herbals and their extracts are compromised with diverse effects on the performances of aquatic animals. These compounds can affect growth performance and stimulate the immune system when used in fish diet. In addition, the use of medicinal herbs and their extracts can reduce oxidative stress induced by several stressors during fish culture. Correspondingly, aquatic animals could gain increased resistance against infectious pathogens and environmental stressors. Nevertheless, the exact mode of action where these additives can affect aquatic animals’ performances is still not well documented. Understanding the mechanistic role of herbal supplements and their derivatives is a vital tool to develop further the strategies and application of these additives for feasible and sustainable aquaculture. Gene-related studies have clarified the detailed information on the herbal supplements’ mode of action when administered orally in aquafeed. Several review articles have presented the potential roles of medicinal herbs on the performances of aquatic animals. However, this review article discusses the outputs of studies conducted on aquatic animals fed dietary, medicinal herbs, focusing on the gene expression related to growth and immune performances. Furthermore, a particular focus is directed to the expected influence of herbal supplements on the reproduction of aquatic animals.

The expression profile and role of non-coding RNAs in obesity

2021 ◽  
Vol 892 ◽  
pp. 173809
Author(s):  
Soudeh Ghafouri-Fard ◽  
Mohammad Taheri
Keyword(s):  
Expression Profile ◽  
Non Coding Rnas

scholarly journals Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunzhen Cheng ◽  
Fan Liu ◽  
Na Tian ◽  
Raphael Anue Mensah ◽  
Xueli Sun ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Acid Metabolism ◽  
Function Analysis ◽  
Regulatory Role ◽  
Novel Genes ◽  
Root Transcriptome ◽  
Qrt Pcr ◽  
Non Coding Rnas ◽  
Infection Stage

AbstractFusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.

Assessment of the role of non-coding RNAs in the pathophysiology of Parkinson's disease

2021 ◽  
Vol 896 ◽  
pp. 173914
Author(s):  
Omidvar Rezaei ◽  
Saeedeh Nateghinia ◽  
Mehrdad A. Estiar ◽  
Mohammad Taheri ◽  
Soudeh Ghafouri-Fard
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Non Coding Rnas
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