Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome

Ayupe, Ana C.; Tahira, Ana Carolina; Camargo, Luiz Octávio de Lima; Beckedorff, Felipe; Verjovski-Almeida, Sérgio; Reis, Eduardo M.

doi:10.1080/15476286.2015.1062960

Cited by 68 publications

(48 citation statements)

References 85 publications

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“…The biogenesis of ncRNAs is based on their properties, which are similar to those of mRNAs. Many ncRNAs share structural properties with protein-coding mRNAs, such as alternative splicing, 5 -cap modification and 3 -polyadenylation [32,33], sequence conservation [32] and transport of RNA molecules from the nucleus to the cytoplasm [34,35]. On the other hand, some ncRNAs do not share these similarities, highlighting the existence of differences between coding versus non-coding RNAs [36,37].…”

Section: Biogenesismentioning

confidence: 99%

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Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma

DeOcesano-Pereira

Machado

Chudzinski-Tavassi

et al. 2020

IJMS

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Non-coding RNAs (ncRNAs) comprise a diversity of RNA species, which do not have the potential to encode proteins. Non-coding RNAs include two classes of RNAs, namely: short regulatory ncRNAs and long non-coding RNAs (lncRNAs). The short regulatory RNAs, containing up to 200 nucleotides, include small RNAs, such as microRNAs (miRNA), short interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs). The lncRNAs include long antisense RNAs and long intergenic RNAs (lincRNAs). Non-coding RNAs have been implicated as master regulators of several biological processes, their expression being strictly regulated under physiological conditions. In recent years, particularly in the last decade, substantial effort has been made to investigate the function of ncRNAs in several human diseases, including cancer. Glioblastoma is the most common and aggressive type of brain cancer in adults, with deregulated expression of small and long ncRNAs having been implicated in onset, progression, invasiveness, and recurrence of this tumor. The aim of this review is to guide the reader through important aspects of miRNA and lncRNA biology, focusing on the molecular mechanism associated with the progression of this highly malignant cancer type.

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Section: Biogenesismentioning

confidence: 99%

“…Therefore, each type of RNA has specific checkpoints in expression and different biological roles. Many lncRNAs are located exclusively in the nucleus, and others are cytoplasmic or are located in both nucleus and cytoplasm [33].…”

Section: Biogenesismentioning

confidence: 99%

Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma

DeOcesano-Pereira

Machado

Chudzinski-Tavassi

et al. 2020

IJMS

View full text Add to dashboard Cite

show abstract

“…A small proportion (about 15%) of intronic RNAs without 5'-cap insertion is probably less stable because they form intron lariats in the cell. Despite the lack of coding potential, the majority of intronic and antisense lncRNAs reside in the nucleus and cytoplasm, suggesting their new role in the regulation and regulation of cytoplasmic processes (Ayupe et al 2015). Over 80% of known lncRNAs are localized in the nucleus (Kapranov et al 2007), and for lncRNAs, their best-defined function in the nucleus is their role in regulating gene and genome activity at various levels (Schmitz et al 2016).…”

Section: Lncrnas and Their Biogenesismentioning

confidence: 99%

Long Non-coding RNAs in Peripheral Blood Mononuclear Cells Associated with Alzheimer Disease

2019

JSTR

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Noncoding RNAs have been implicated in important roles in cellular processes and in various diseases with the discovery of novel RNAs. Non-coding RNAs are classified as two groups according to their size. Transcripts with a length of 18-25 nucleotides, including microRNAs (miRNAs), which are important classes that can control the expression of many genes are called as short non coding RNAs while RNAs that greater than 200 nucleotides are termed as long non-coding RNAs (lncRNAs). It was found that lncRNAs were able to regulate gene expression at transcriptional, post-transcriptional and epigenetic levels. Recently, many lncRNAs have been shown to regulate amyloid beta (Aβ) production and synaptic loss in neurons in the nervous system in Alzheimer's Disease (AD). AD is a neurodegenerative disease which is most common in elderly, characterized by amyloid beta plaque accumulation outside the cell, neurofibrillary tangles in the cell and neuronal loss in the nervous system. The definitive diagnosis of AD in the clinic can only be made by observing these pathological changes in the brain during postmortem period. Therefore, there is a great need for biomarkers that may allow the disease to be identified especially at an early stage. The lncRNAs, which are thought to contribute to the development of disease, are seen as both targets and tools in new treatment approaches. It is thought that new treatment approaches can be developed by illuminating the functions of all lncRNAs in human genome and it can be used as biomarkers in the early diagnosis of diseases. After the discovery that serum, plasma and mononuclear cells in the blood reflect inflammatory pathogenesis in search for a biomarker to be involved in the diagnosis of AD, studies have focused on peripheral blood. Recent studies have shown that mononuclear cells (PBMC) found in peripheral blood reflect inflammatory and apoptotic mechanisms in AD more in comparison to serum and plasma-based biomarkers.

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“…As it becomes increasingly apparent that these molecules are critical elements of human physiology, we chose here to focus on identifying key lncRNAs in AC biology so that their roles may be further investigated. One subset of lncRNAs known as long intergenic noncoding RNAs (lincRNAs) has been shown to have high‐tissue specificity and evolutionary conservation, as well as developmental specificity, and therefore may play critical roles in cartilage development and homeostasis (Ayupe et al, ; Khalil et al, ; Morris & Mattick, ; Necsulea et al, ; Ulitsky, Shkumatava, Jan, Sive, & Bartel, ; Washietl, Kellis, & Garber, ). We also focus on identification of TFs because as direct regulators of transcription, they are likely to play critical roles in driving AC cellular phenotypes.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome dynamics of long noncoding RNAs and transcription factors demarcate human neonatal, adult, and human mesenchymal stem cell‐derived engineered cartilage

Vail

Somoza

Caplan

et al. 2019

J Tissue Eng Regen Med

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The engineering of a native‐like articular cartilage (AC) is a long‐standing objective that could serve the clinical needs of millions of patients suffering from osteoarthritis and cartilage injury. An incomplete understanding of the developmental stages of AC has contributed to limited success in this endeavor. Using next generation RNA sequencing, we have transcriptionally characterized two critical stages of AC development in humans—that is, immature neonatal and mature adult, as well as tissue‐engineered cartilage derived from culture expanded human mesenchymal stem cells. We identified key transcription factors (TFs) and long noncoding RNAs (lncRNAs) as candidate drivers of the distinct phenotypes of these tissues. AGTR2, SCGB3A1, TFCP2L1, RORC, and TBX4 stand out as key TFs, whose expression may be capable of reprogramming engineered cartilage into a more expandable and neonatal‐like cartilage primed for maturation into biomechanically competent cartilage. We also identified that the transcriptional profiles of many annotated but poorly studied lncRNAs were dramatically different between these cartilages, indicating that lncRNAs may also be playing significant roles in cartilage biology. Key neonatal‐specific lncRNAs identified include AC092818.1, AC099560.1, and KC877982. Collectively, our results suggest that tissue‐engineered cartilage can be optimized for future clinical applications by the specific expression of TFs and lncRNAs.

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Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome

Cited by 68 publications

References 85 publications

Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma

Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma

Long Non-coding RNAs in Peripheral Blood Mononuclear Cells Associated with Alzheimer Disease

Transcriptome dynamics of long noncoding RNAs and transcription factors demarcate human neonatal, adult, and human mesenchymal stem cell‐derived engineered cartilage

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