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 Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with repressed chromatin compartment and reveals transcription dynamics

2019 ◽  
Author(s):  
Alexey A. Gavrilov ◽  
Anastasiya A. Zharikova ◽  
Aleksandra A. Galitsyna ◽  
Artem V. Luzhin ◽  
Natalia M. Rubanova ◽  
...  
Keyword(s):  
Messenger Rna ◽  
K562 Cells ◽  
Biological Processes ◽  
Rna Molecules ◽  
Proximity Ligation ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Genomic Regions ◽  
Kinetics Of ◽  
Inactive Chromatin

AbstractNon-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. We found two microRNAs—MIR3648 and MIR3687 transcribed from the rRNA locus—that are associated with inactive chromatin genome wide. These miRNAs favor bulk heterochromatin over Polycomb-repressed chromatin and interact preferentially with late-replicating genomic regions. 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.

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 Long Non-Coding RNAs in Multiple Myeloma

2019 ◽  
Vol 5 (1) ◽  
pp. 13 ◽  
Author(s):  
Romana Butova ◽  
Petra Vychytilova-Faltejskova ◽  
Adela Souckova ◽  
Sabina Sevcikova ◽  
Roman Hajek
Keyword(s):  
Multiple Myeloma ◽  
Plasma Cells ◽  
Current Knowledge ◽  
Biological Processes ◽  
Cell Distribution ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
New Treatment ◽  
Long Non Coding Rna

Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long non-coding RNA molecules (lncRNA) linked to development and progression of many tumors suggested their important role in tumorigenesis. To date, over 15,000 lncRNA molecules characterized by diversity of function and specificity of cell distribution were identified in the human genome. Due to their involvement in proliferation, apoptosis, metabolism, and differentiation, they have a key role in the biological processes and pathogenesis of many diseases, including MM. This review summarizes current knowledge of non-coding RNAs (ncRNA), especially lncRNAs, and their role in MM pathogenesis. Undeniable involvement of lncRNAs in MM development suggests their potential as biomarkers.

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.

LncRNAs roles in Chemoresistance of Cancer cells

2021 ◽  
Vol 21 ◽  
Author(s):  
Sina Taghvimi ◽  
Sepideh Abbaszadeh ◽  
Fatemeh Bahrami Banan ◽  
Elahe Soltani Fard ◽  
Zeinab Jamali ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Noncoding Rnas ◽  
Signal Pathway ◽  
Tumor Formation ◽  
Minimum Length ◽  
Limiting Factor ◽  
Rna Molecules ◽  
Important Health ◽  
Non Coding Rnas ◽  
Important Health Issue

: Cancer is an important health issue worldwide. Cancer therapy is multifaceted, and drug resistance is still the major limiting factor in treatment of patients with this disease. Although the mechanisms of anticancer drug resistance have been broadly investigated, a massive biological signal pathway of Non-coding RNAs (ncRNAs) involved in this process has not been completely understood. Long noncoding RNAs (lncRNAs) are a kind of transcripts with a minimum length of 200 nucleotides in size which have a limited potential for coding proteins. The roles of these RNA molecules have been evaluated in relation to several pathological processes including tumor formation and progression. Increasing evidence haverecently reported that non-coding RNAs (ncRNAs), particularly long non-coding RNAs have significant roles in many cellular and genomic processes, and because of their potential in regulation specific genes, they are also involved in drug resistance. In this review, we review the literature on the features oflncRNA, their regulation roles in the gene expression related to chemoresistance and the potential of these RNAs as targeted therapies for personalized treatment in cancers.

Noncoding RNAs and Colorectal Cancer:A General Overview

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
Jonathan Souza Sarraf ◽  
Taynah Cascaes Puty ◽  
Emanuely Magno da Silva ◽  
Thais Suellen Ramos Allen ◽  
Yasmim Souza Sarraf ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Practice ◽  
Noncoding Rnas ◽  
Target Prediction ◽  
Small Interfering Rnas ◽  
Noncoding Regions ◽  
Rna Molecules ◽  
Small Noncoding Rnas ◽  
Non Coding Rnas ◽  
Nucleolar Rnas

Background: Colorectal cancer (CRC) is the second most prevalent cancer in the world when nonmelanoma skin cases are not considered. Different epigenetic mechanisms play a role in the development of cancer. Noncoding RNAs (ncRNAs) are RNA molecules transcribed from noncoding regions of the genome. These are divided into sncRNAs (small noncoding RNAs: <200 nucleotides - including miRNAs [microRNAs], siRNAs [small interfering RNAs], piRNAs [piwi-interacting RNAs], snoRNAs [small nucleolar RNAs]) and lncRNAs (long noncoding RNAs: >200 nucleotides – includingcircular RNAs [circRNAs]). NcRNAs can act as oncogenes or as tumor suppressor genes in CRC and are potential biomarkers of diagnosis, with possible clinical implications. Objective: This article aims to make a general review around all types of non-coding RNAs and influence in colorectal cancer, focus in biomarkesof CRC and their possible applications in clinical practice, as well as review their biogenesis and functions. Furthermore, we seek to summarize possible databases available for new searches and studies that require sequence annotation, comparison sequences and target prediction for ncRNAs with the hope ofgathering information that can aid in the process of understanding and translating the use of ncRNAs into clinical practice.

scholarly journals Genome-Wide Identification of Long Non-coding RNAs Responsive to Lasiodiplodia theobromae Infection in Grapevine

2019 ◽  
Vol 15 ◽  
pp. 117693431984136 ◽  
Author(s):  
Qikai Xing ◽  
Wei Zhang ◽  
Mei Liu ◽  
Lingxian Li ◽  
Xinghong Li ◽  
...  
Keyword(s):  
Biological Processes ◽  
Rna Seq ◽  
Lasiodiplodia Theobromae ◽  
Rna Molecules ◽  
Grapevine Trunk Diseases ◽  
Genome Wide ◽  
Botryosphaeria Dieback ◽  
Trunk Diseases ◽  
Non Coding Rnas ◽  
Insight Into

Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are longer than 200 nucleotides and do not encode proteins. Numerous lncRNAs have recently emerged as important regulators of many biological processes in animals and plants, including responses to environmental stress and pathogens. Botryosphaeria dieback is one of the more severe grapevine trunk diseases worldwide. However, how lncRNAs function during Botryosphaeriaceae infection is largely unknown. We performed high-throughput RNA-sequencing (RNA-seq) of susceptible and more tolerant grapevine cultivars infected with Lasiodiplodia theobromae. Overall, we predicted 1826 novel candidate lncRNAs, including long intergenic non-coding RNAs (lincRNAs) and natural antisense transcripts (lncNATs). The data reveal the functions of a set of lncRNAs that were differentially expressed between the resistant cultivar Merlot and the susceptible cultivar Cabernet Franc. Several lncRNAs were predicted to be precursors for grape microRNAs involved in the L theobromae infection. These results provide new insight into the lncRNAs of grapevine that are involved in the response to L theobromae infection.

scholarly journals Increased hippocampal excitability in miR-324-null mice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dan J. Hayman ◽  
Tamara Modebadze ◽  
Sarah Charlton ◽  
Kat Cheung ◽  
Jamie Soul ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Target Genes ◽  
Translational Repression ◽  
Rna Molecules ◽  
Rna Transcripts ◽  
Gene Transcripts ◽  
Non Coding Rnas ◽  
Interictal Discharges ◽  
The Brain

AbstractMicroRNAs are non-coding RNAs that act to downregulate the expression of target genes by translational repression and degradation of messenger RNA molecules. Individual microRNAs have the ability to specifically target a wide array of gene transcripts, therefore allowing each microRNA to play key roles in multiple biological pathways. miR-324 is a microRNA predicted to target thousands of RNA transcripts and is expressed far more highly in the brain than in any other tissue, suggesting that it may play a role in one or multiple neurological pathways. Here we present data from the first global miR-324-null mice, in which increased excitability and interictal discharges were identified in vitro in the hippocampus. RNA sequencing was used to identify differentially expressed genes in miR-324-null mice which may contribute to this increased hippocampal excitability, and 3′UTR luciferase assays and western blotting revealed that two of these, Suox and Cd300lf, are novel direct targets of miR-324. Characterisation of microRNAs that produce an effect on neurological activity, such as miR-324, and identification of the pathways they regulate will allow a better understanding of the processes involved in normal neurological function and in turn may present novel pharmaceutical targets in treating neurological disease.

scholarly journals Non-coding RNAs: New therapeutic targets and opportunities for hepatocellular carcinoma

2016 ◽  
Vol 2 (1) ◽  
pp. 5
Author(s):  
Yu Cuiyun ◽  
Qian Ning ◽  
Zhi-Ping Li ◽  
Wen Huang ◽  
Jia Yu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Open Reading Frame ◽  
Regulation Mechanism ◽  
Biological Processes ◽  
Biological Functions ◽  
Protein Coding ◽  
Reading Frame ◽  
Rna Molecules ◽  
Non Coding Rnas ◽  
Diagnosis Therapy

<p align="left">Non-coding RNAs (ncRNA) are RNA molecules without protein coding functions owing to the lack of an open reading frame (ORF). Based on the length, ncRNAs can be divided into long and short ncRNAs; short ncRNAs include miRNAs and piRNAs. Hepatocellular carcinoma (HCC) is among the most frequent forms of cancer worldwide and its incidence is increasing rapidly. Studies have found that ncRNAs are likely to play a crucial role in a variety of biological processes including the pathogenesis and progression of HCC. In this review, we summarized the regulation mechanism and biological functions of ncRNAs in HCC with respect to its application in HCC diagnosis, therapy and prognosis.</p>

scholarly journals Emerging Role of MiR-192-5p in Human Diseases

2021 ◽  
Vol 12 ◽  
Author(s):  
Fu-jia Ren ◽  
Yao Yao ◽  
Xiao-yu Cai ◽  
Guo-ying Fang
Keyword(s):  
Target Genes ◽  
Noncoding Rnas ◽  
Human Diseases ◽  
Circular Rnas ◽  
Biological Processes ◽  
Transcriptional Expression ◽  
Diagnosis And Prognosis ◽  
Infection Disease ◽  
Non Coding Rnas

MicroRNAs (miRNAs) are a type of small non-coding RNAs that play an essential role in numerous biological processes by regulating the post-transcriptional expression of target genes. Recent studies have demonstrated that miR-192-5p, a member of the miR-192 family, partakes in several human diseases, especially various cancers, including cancers of the lung, liver, and breast. Importantly, the levels of miR-192-5p are abundant in biofluids, including the serum and urine, and the exosomal levels of miR-192-5p in circulation can aid in the diagnosis and prognosis of various diseases, such as chronic hepatitis B (CHB) infection disease. Notably, recent studies suggest that miR-192-5p is regulated by long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). However, there are no comprehensive overviews on the role of miR-192-5p in human diseases. This review discusses the significant studies on the role of miR-192-5p in various human diseases, with special emphasis on the diseases of the respiratory and digestive systems.

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