scholarly journals Molecular Mechanisms and Function Prediction of Long Noncoding RNA

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Handong Ma ◽  
Yun Hao ◽  
Xinran Dong ◽  
Qingtian Gong ◽  
Jingqi Chen ◽  
...  
Keyword(s):  
Computational Methods ◽  
Genetic Information ◽  
Noncoding Rna ◽  
Recent Progress ◽  
Molecular Mechanisms ◽  
Noncoding Rnas ◽  
Whole Genome ◽  
Biological Functions ◽  
Large Numbers ◽  
And Function

The central dogma of gene expression considers RNA as the carrier of genetic information from DNA to protein. However, it has become more and more clear that RNA plays more important roles than simply being the information carrier. Recently, whole genome transcriptomic analyses have identified large numbers of dynamically expressed long noncoding RNAs (lncRNAs), many of which are involved in a variety of biological functions. Even so, the functions and molecular mechanisms of most lncRNAs still remain elusive. Therefore, it is necessary to develop computational methods to predict the function of lncRNAs in order to accelerate the study of lncRNAs. Here, we review the recent progress in the identification of lncRNAs, the molecular functions and mechanisms of lncRNAs, and the computational methods for predicting the function of lncRNAs.

GAMYB TF modulates bHLH142 and is homeostatically regulated by TDR TF during rice anther tapetal and pollen development

2021 ◽  
Author(s):  
Swee-Suak Ko ◽  
Min-Jeng Li ◽  
Yi-Cheng Ho ◽  
Chun-Ping Yu ◽  
Ting-Ting Yang ◽  
...  
Keyword(s):  
Pollen Development ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Specific Binding ◽  
Biological Functions ◽  
Altered Expression ◽  
Regulatory Pathways ◽  
E Box ◽  
And Function ◽  
Different Tissues

Abstract GAMYB, UDT1, TIP2/bHLH142, TDR, and EAT1/DTD are important transcription factors (TFs) that play a crucial role during rice pollen development. This study demonstrates that bHLH142 acts downstream of UDT1 and GAMYB and works as a “hub” in these two pollen pathways. We show that GAMYB modulates bHLH142 expression through specific binding to the MYB motif of bHLH142 promoter during early stage of pollen development; while TDR acts as a transcriptional repressor of the GAMYB modulation of bHLH142 by binding to the E-box close to the MYB motif on the promoter. The altered expression of TFs highlights the importance that a tight, precise, and coordinated regulation among these TFs is essential for normal pollen development. Most notably, this study illustrates the regulatory pathways of GAMYB and UDT1 that rely on bHLH142 in a direct and an indirect manner, respectively, and function in different tissues with distinct biological functions during pollen development. This study advances our understanding of the molecular mechanisms of rice pollen development.

scholarly journals Biological functions and clinical significance of long noncoding RNAs in bladder cancer

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yan Zhang ◽  
Xianwu Chen ◽  
Juntao Lin ◽  
Xiaodong Jin
Keyword(s):  
Bladder Cancer ◽  
Clinical Significance ◽  
Noncoding Rna ◽  
Epithelial Mesenchymal Transition ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Research Progress ◽  
High Morbidity ◽  
Biological Functions ◽  
Mesenchymal Transition

AbstractBladder cancer (BCa) is one of the 10 most common cancers with high morbidity and mortality worldwide. Long noncoding RNAs (lncRNAs), a large class of noncoding RNA transcripts, consist of more than 200 nucleotides and play a significant role in the regulation of molecular interactions and cellular pathways during the occurrence and development of various cancers. In recent years, with the rapid advancement of high-throughput gene sequencing technology, several differentially expressed lncRNAs have been discovered in BCa, and their functions have been proven to have an impact on BCa development, such as cell growth and proliferation, metastasis, epithelial-mesenchymal transition (EMT), angiogenesis, and drug-resistance. Furthermore, evidence suggests that lncRNAs are significantly associated with BCa patients’ clinicopathological characteristics, especially tumor grade, TNM stage, and clinical progression stage. In addition, lncRNAs have the potential to more accurately predict BCa patient prognosis, suggesting their potential as diagnostic and prognostic biomarkers for BCa patients in the future. In this review, we briefly summarize and discuss recent research progress on BCa-associated lncRNAs, while focusing on their biological functions and mechanisms, clinical significance, and targeted therapy in BCa oncogenesis and malignant progression.

scholarly journals Long noncoding RNA: a dazzling dancer in tumor immune microenvironment

2020 ◽  
Vol 39 (1) ◽  
Author(s):  
Yalu Zhang ◽  
Qiaofei Liu ◽  
Quan Liao
Keyword(s):  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Immune Escape ◽  
Noncoding Rnas ◽  
Pathological Process ◽  
Cellular Functions ◽  
Immune Microenvironment ◽  
Protein Coding ◽  
Functional Roles ◽  
Tumor Immune Microenvironment

Abstract Long noncoding RNAs (lncRNAs) are a class of endogenous, non-protein coding RNAs that are highly linked to various cellular functions and pathological process. Emerging evidence indicates that lncRNAs participate in crosstalk between tumor and stroma, and reprogramming of tumor immune microenvironment (TIME). TIME possesses distinct populations of myeloid cells and lymphocytes to influence the immune escape of cancer, the response to immunotherapy, and the survival of patients. However, hitherto, a comprehensive review aiming at relationship between lncRNAs and TIME is missing. In this review, we focus on the functional roles and molecular mechanisms of lncRNAs within the TIME. Furthermore, we discussed the potential immunotherapeutic strategies based on lncRNAs and their limitations.

Insight into long noncoding RNA–miRNA–mRNA axes in myocardial ischemia-reperfusion injury: the implications for mechanism and therapy

Epigenomics ◽  
2019 ◽  
Vol 11 (15) ◽  
pp. 1733-1748 ◽  
Author(s):  
Wei Xiong ◽  
Yan Qu ◽  
Hongmei Chen ◽  
Jinqiao Qian
Keyword(s):  
Myocardial Ischemia ◽  
Reperfusion Injury ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Noncoding Rnas ◽  
Myocardial Ischemia Reperfusion Injury ◽  
Myocardial Ischemia Reperfusion ◽  
Insight Into

Emerging evidence has demonstrated that regulatory noncoding RNAs (ncRNAs), such as long noncoding RNAs (lncRNAs) and miRNAs, play crucial roles in the initiation and progress of myocardial ischemia-reperfusion injury (MIRI), which is associated with autophagy, apoptosis and necrosis of cardiomyocytes, as well as oxidative stress, inflammation and mitochondrial dysfunction. LncRNAs serve as a precursor or host of miRNAs and directly/indirectly affecting miRNAs via competitive binding or sponge effects. Simultaneously, miRNAs post-transcriptionally regulate the expression of genes by targeting various mRNA sequences due to their imperfect pairing with mRNAs. This review summarizes the potential regulatory role of lncRNA–miRNA–mRNA axes in MIRI and related molecular mechanisms of cardiac disorders, also provides insight into the potential therapies for MIRI-induced diseases.

scholarly journals LncRNA DANCR functions as a competing endogenous RNA to regulate RAB1A expression by sponging miR-634 in glioma

2018 ◽  
Vol 38 (1) ◽  
Author(s):  
Dawei Xu ◽  
Jian Yu ◽  
Guojun Gao ◽  
Guangjian Lu ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Cell Lines ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Glioma Cells ◽  
Tumor Grade ◽  
Underlying Mechanism ◽  
Luciferase Reporter ◽  
Biological Functions ◽  
Advanced Tumor ◽  
Rna Immunoprecipitation

Long noncoding RNA (lncRNA) differentiation antagonizing nonprotein coding RNA (DANCR) plays important regulatory roles in many solid tumors. However, the effect of DANCR in glioma progression and underlying molecular mechanisms were not entirely explored. In the present study, we determined the expression of DANCR in glioma tissues and cell lines using qRT-PCR and further defined the biological functions. Furthermore, we used luciferase reporter assay, Western blot, and RNA immunoprecipitation (RIP) to explore the underlying mechanism. Our results showed that DANCR was significantly up-regulated in glioma tissues and cell lines (U251, U118, LN229, and U87MG). High DANCR expression was correlated with advanced tumor grade. Inhibition of DANCR suppressed the glioma cells proliferation and induced cells arrested in the G0/G1 phase. In addition, we verified that DANCR could directly interact with miR-634 in glioma cells and this interaction resulted in the inhibition of downstream of RAB1A expression. The present study demonstrated that DANCR/miR-634/RAB1A axis plays crucial roles in the progression of glioma, and DANCR might potentially serve as a therapeutic target for the treatment of glioma patients.

scholarly journals Human Long Noncoding RNA Interactome: Detection, Characterization and Function

2020 ◽  
Vol 21 (3) ◽  
pp. 1027 ◽  
Author(s):  
Kazimierczyk ◽  
Kasprowicz ◽  
Kasprzyk ◽  
Wrzesinski
Keyword(s):  
Noncoding Rna ◽  
Potential Role ◽  
Integrated Analysis ◽  
Biological Functions ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
New Generation ◽  
Cellular Components ◽  
Proteins And Peptides

The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

scholarly journals Genomic Variants and Multilevel Regulation of ABCA1, ABCG1, and SCARB1 Expression in Atherogenesis

2021 ◽  
Vol 8 (12) ◽  
pp. 170
Author(s):  
Alexandra V. Rozhkova ◽  
Veronika G. Dmitrieva ◽  
Elena V. Nosova ◽  
Alexander D. Dergunov ◽  
Svetlana A. Limborska ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Gene Promoter ◽  
High Density Lipoproteins ◽  
Circular Rnas ◽  
Promoter Regions ◽  
Genomic Variants ◽  
Transcription Activators ◽  
And Function

Atheroprotective properties of human plasma high-density lipoproteins (HDLs) are determined by their involvement in reverse cholesterol transport (RCT) from the macrophage to the liver. ABCA1, ABCG1, and SR-BI cholesterol transporters are involved in cholesterol efflux from macrophages to lipid-free ApoA-I and HDL as a first RCT step. Molecular determinants of RCT efficiency that may possess diagnostic and therapeutic meaning remain largely unknown. This review summarizes the progress in studying the genomic variants of ABCA1, ABCG1, and SCARB1, and the regulation of their function at transcriptional and post-transcriptional levels in atherosclerosis. Defects in the structure and function of ABCA1, ABCG1, and SR-BI are caused by changes in the gene sequence, such as single nucleotide polymorphism or various mutations. In the transcription initiation of transporter genes, in addition to transcription factors, long noncoding RNA (lncRNA), transcription activators, and repressors are also involved. Furthermore, transcription is substantially influenced by the methylation of gene promoter regions. Post-transcriptional regulation involves microRNAs and lncRNAs, including circular RNAs. The potential biomarkers and targets for atheroprotection, based on molecular mechanisms of expression regulation for three transporter genes, are also discussed in this review.

scholarly journals An Arabidopsis long noncoding RNA modulates the transcriptome through interactions with a network of splicing factors

2020 ◽  
Author(s):  
Richard Rigo ◽  
Jérémie Bazin ◽  
Natali Romero-Barrios ◽  
Michaël Moison ◽  
Leandro Lucero ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Root Formation ◽  
Noncoding Rnas ◽  
Dynamic Network ◽  
Splicing Factors ◽  
Genome Wide ◽  
A Minor ◽  
Conserved Core

ABSTRACTAlternative splicing (AS) is a major source of transcriptome and proteome diversity in higher organisms. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through a range of molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRa and b, which affect auxin-driven lateral root formation, can interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyzed the effect of the knockdown and overexpression of ASCO at genome-wide level and found a high number of deregulated and differentially spliced genes, related to flagellin responses and biotic stress. In agreement, roots from ASCO-knocked down plants are more sensitive to flagellin. Surprisingly, only a minor subset of genes overlapped with the AS defects of the nsra/b double mutant. Using biotin-labelled oligonucleotides for RNA-mediated ribonucleoprotein purification, we found that ASCO binds to the highly conserved core spliceosome component PRP8a. ASCO deregulation impairs the recognition of specific flagellin-related transcripts by PRP8a and SmD1b, another spliceosome component, suggesting that ASCO function regulates AS through the interaction with multiple splicing factors. Hence, lncRNAs may interact in a dynamic network with many splicing factors to modulate transcriptome reprogramming in eukaryotes.

scholarly journals Circular RNAs: Biogenesis, Mechanism, and Function in Human Cancers

2019 ◽  
Vol 20 (16) ◽  
pp. 3926 ◽  
Author(s):  
Xing Zhao ◽  
Yujie Cai ◽  
Jianzhen Xu
Keyword(s):  
Noncoding Rna ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cancer Development ◽  
Circular Rnas ◽  
Open Questions ◽  
Circular Configuration ◽  
And Function

CircRNAs are a class of noncoding RNA species with a circular configuration that is formed by either typical spliceosome-mediated or lariat-type splicing. The expression of circRNAs is usually abnormal in many cancers. Several circRNAs have been demonstrated to play important roles in carcinogenesis. In this review, we will first provide an introduction of circRNAs biogenesis, especially the regulation of circRNA by RNA-binding proteins, then we will focus on the recent findings of circRNA molecular mechanisms and functions in cancer development. Finally, some open questions are also discussed.

Long and small noncoding RNAs during oocyte-to-embryo transition in mammals

2017 ◽  
Vol 45 (5) ◽  
pp. 1117-1124 ◽  
Author(s):  
Petr Svoboda
Keyword(s):  
Noncoding Rna ◽  
Transcriptional Control ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Early Embryo ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Major Genome ◽  
Silencing Pathways ◽  
And Function

Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.

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