scholarly journals Platforms for Investigating LncRNA Functions

2018 ◽  
Vol 23 (6) ◽  
pp. 493-506 ◽  
Author(s):  
John Lalith Charles Richard ◽  
Pieter Johan Adam Eichhorn
Keyword(s):  
Next Generation Sequencing ◽  
Dosage Compensation ◽  
Messenger Rna ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Biological Processes ◽  
Protein Kinetics ◽  
Heterogeneous Nature ◽  
Eukaryotic Genomes ◽  
Generation Sequencing

Prior to the sequencing of the human genome, it was presumed that most of the DNA coded for proteins. However, with the advent of next-generation sequencing, it has now been recognized that most complex eukaryotic genomes are in fact transcribed into noncoding RNAs (ncRNAs), including a family of transcripts referred to as long noncoding RNAs (lncRNAs). LncRNAs have been implicated in many biological processes ranging from housekeeping functions such as transcription to more specialized functions such as dosage compensation or genomic imprinting, among others. Interestingly, lncRNAs are not limited to a defined set of functions but can regulate varied activities such as messenger RNA degradation, translation, and protein kinetics or function as RNA decoys or scaffolds. Although still in its infancy, research into the biology of lncRNAs has demonstrated the importance of lncRNAs in development and disease. However, the specific mechanisms through which these lncRNAs act remain poorly defined. Focused research into a small number of these lncRNAs has provided important clues into the heterogeneous nature of this family of ncRNAs. Due to the complex diversity of lncRNA function, in this review, we provide an update on the platforms available for investigators to aid in the identification of lncRNA function.

MicroRNAs: Key Regulators in Lung Cancer

MicroRNA ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Younes El Founini ◽  
Imane Chaoui ◽  
Hind Dehbi ◽  
Mohammed El Mzibri ◽  
Roger Abounader ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Messenger Rna ◽  
Recent Literature ◽  
Immune Surveillance ◽  
Rna Stability ◽  
Noncoding Rnas ◽  
Therapy Resistance ◽  
Biological Processes ◽  
Genome Wide ◽  
Stable Forms

: Noncoding RNAs have emerged as key regulators of the genome upon gene expression profiling and genome-wide sequencing. Among these noncoding RNAs, microRNAs are short noncoding RNAs that regulate a plethora of functions, biological processes and human diseases by targeting the messenger RNA stability through 3’UTR binding, leading to either mRNA cleavage or translation repression, depending on microRNA-mRNA complementarity degree. Additionally, strong evidence has suggested that dysregulation of miRNAs contribute to the etiology and progression of human cancers, such as lung cancer, the most common and deadliest cancer worldwide. Indeed, by acting as oncogenes or tumor suppressors, microRNAs control all aspects of lung cancer malignancy, including cell proliferation, survival, migration, invasion, angiogenesis, cancer stem cells, immune-surveillance escape, and therapy resistance; and their expressions are often associated with clinical parameters. Moreover, several deregulated microRNAs in lung cancer are carried by exosomes, microvesicles and secreted in body fluids, mainly the circulation where they conserve their stable forms. Subsequently, seminal efforts have been focused on extracellular microRNAs levels as noninvasive diagnostic and prognostic biomarkers in lung cancer. In this review, focusing on recent literature, we summarize the deregulation, mechanisms of action, functions and highlight clinical applications of miRNAs for better management and design of future lung cancer targeted therapies.

scholarly journals Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

2020 ◽  
Vol 48 (12) ◽  
pp. 6699-6714 ◽  
Author(s):  
Alexey A Gavrilov ◽  
Anastasiya A Zharikova ◽  
Aleksandra A Galitsyna ◽  
Artem V Luzhin ◽  
Natalia M Rubanova ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Noncoding Rnas ◽  
K562 Cells ◽  
Biological Processes ◽  
Intron Splicing ◽  
Rna Molecules ◽  
Proximity Ligation ◽  
Data Support ◽  
Non Coding Rnas ◽  
Kinetics Of

Abstract Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

scholarly journals Significance of Long Noncoding RNAs in Regenerative Medicine

2017 ◽  
Vol 3 ◽  
pp. 0
Author(s):  
Raheleh Amirkhah
Keyword(s):  
Next Generation Sequencing ◽  
Noncoding Rnas ◽  
Cell Types ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Huge Data ◽  
Paracrine Action ◽  
Different Cell Types ◽  
Generation Sequencing ◽  
Heterogeneous Class

Long noncoding RNAs (lncRNAs) are a heterogeneous class of RNAs with generally longer than 200 nucleotides. It has been proposed that LncRNAs as a piece of paracrine action would control cellular pluripotency, differentiation, maintenance and regulate tissue development, organogenesis and regeneration. Next generation sequencing (RNA-seq) has produced huge data about lncRNAs expression profile in different cell types and condition, but understanding the roles and functions of these novel lncRNAs is poorly understood.

Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiaeThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 767-779 ◽  
Author(s):  
Benjamin R. Harrison ◽  
Oya Yazgan ◽  
Jocelyn E. Krebs
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Messenger Rna ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Small Interfering Rnas ◽  
Ideal System

There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.

scholarly journals Computational Tools for Genome-Wide miRNA Prediction and Study

2012 ◽  
Vol 5 (1) ◽  
pp. 23-30 ◽  
Author(s):  
Tareq B. Malas ◽  
Timothy Ravasi
Keyword(s):  
Messenger Rna ◽  
Biological Processes ◽  
Computational Tools ◽  
Mirna Prediction ◽  
Advantages And Disadvantages ◽  
Non Coding Rna ◽  
Large Numbers ◽  
Genome Wide ◽  
Post Transcriptional Regulation ◽  
Generation Sequencing

MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3'-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages.

scholarly journals Noninvasive characterization of Alzheimer’s disease by circulating, cell-free messenger RNA next-generation sequencing

2020 ◽  
Vol 6 (50) ◽  
pp. eabb1654
Author(s):  
Shusuke Toden ◽  
Jiali Zhuang ◽  
Alexander D. Acosta ◽  
Amy P. Karns ◽  
Neeraj S. Salathia ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Messenger Rna ◽  
Biological Processes ◽  
Molecular Alterations ◽  
Gene Transcripts ◽  
Noninvasive Characterization ◽  
The Brain ◽  
Generation Sequencing

The lack of accessible noninvasive tools to examine the molecular alterations occurring in the brain limits our understanding of the causes and progression of Alzheimer’s disease (AD), as well as the identification of effective therapeutic strategies. Here, we conducted a comprehensive profiling of circulating, cell-free messenger RNA (cf-mRNA) in plasma of 126 patients with AD and 116 healthy controls of similar age. We identified 2591 dysregulated genes in the cf-mRNA of patients with AD, which are enriched in biological processes well known to be associated with AD. Dysregulated genes included brain-specific genes and resembled those identified to be dysregulated in postmortem AD brain tissue. Furthermore, we identified disease-relevant circulating gene transcripts that correlated with the severity of cognitive impairment. These data highlight the potential of high-throughput cf-mRNA sequencing to evaluate AD-related pathophysiological alterations in the brain, leading to precision healthcare solutions that could improve AD patient management.

scholarly journals Complete Genome Sequence of the Model Oleaginous Alga Nannochloropsis gaditana CCMP1894

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Ariel S. Schwartz ◽  
Rob Brown ◽  
Imad Ajjawi ◽  
Jay McCarren ◽  
Suzan Atilla ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Optical Mapping ◽  
Next Generation ◽  
Nannochloropsis Gaditana ◽  
Sequencing Technologies ◽  
Eukaryotic Genomes ◽  
Generation Sequencing

ABSTRACT The model oleaginous alga Nannochloropsis gaditana was completely sequenced using a combination of optical mapping and next-generation sequencing technologies to generate one of the most complete eukaryotic genomes published to date. The assembled genome is 30.7 Mb long.

Sign in / Sign up

Export Citation Format

Share Document