Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells

Guo, Chunjie; Ma, Xu-Kai; Xing, Yu-Hang; Zheng, C.; Xu, Yaohui; Shan, Lin; Zhang, Jun; Wang, Shaohua; Wang, Yangming; Carmichael, Gordon G.; Yang, Li; Chen, Lingling

doi:10.1016/j.cell.2020.03.006

Cited by 229 publications

(177 citation statements)

References 80 publications

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“…However, lncRNAs are among least well-understood ncRNAs. This is probably due to the variety of regulatory mechanisms that they could affect [16], but also to their rapid evolution, and consequently, to the absence of recognisable homologs for most of the lncRNAs even in evolutionarily close species [17,18] and to the divergent subcellular location and function of certain conserved lncRNAs [19]. LncRNAs regulate the expression of adjacent genes (cis-acting regulation) or genes located at other genomic locations, even on different chromosomes (trans-acting) [16].…”

Section: Introductionmentioning

confidence: 99%

“…In fish, although functional studies remain highly limited, several publications reported the modulation of lncRNAs after different stimuli and/or conditions with a special focus on the immune system [19]. Because lncRNAs can alter the expression of their adjacent genes, the functionality of those lncRNAs identified in fish is usually predicted based on the function of their neighbouring protein-coding genes [22].…”

Section: Introductionmentioning

confidence: 99%

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Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass (Dicentrarchus labrax L.)

Pereiro

Lama

Moreira

et al. 2020

Biology

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Long noncoding RNAs (lncRNAs) are being increasingly recognised as key modulators of various biological mechanisms, including the immune response. Although investigations in teleosts are still lagging behind those conducted in mammals, current research indicates that lncRNAs play a pivotal role in the response of fish to a variety of pathogens. During the last several years, interest in lncRNAs has increased considerably, and a small but notable number of publications have reported the modulation of the lncRNA profile in some fish species after pathogen challenge. This study was the first to identify lncRNAs in the commercial species European sea bass. A total of 12,158 potential lncRNAs were detected in the head kidney and brain. We found that some lncRNAs were not common for both tissues, and these lncRNAs were located near coding genes that are primarily involved in tissue-specific processes, reflecting a degree of cellular specialisation in the synthesis of lncRNAs. Moreover, lncRNA modulation was analysed in both tissues at 24 and 72 h after infection with nodavirus. Enrichment analysis of the neighbouring coding genes of the modulated lncRNAs revealed many terms related to the immune response and viral infectivity but also related to the stress response. An integrated analysis of the lncRNAs and coding genes showed a strong correlation between the expression of the lncRNAs and their flanking coding genes. Our study represents the first systematic identification of lncRNAs in European sea bass and provides evidence regarding the involvement of these lncRNAs in the response to nodavirus.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass (Dicentrarchus labrax L.)

Pereiro

Lama

Moreira

et al. 2020

Biology

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“…On the other hand, do homologous lncRNAs across species always have the same function? Through systematic high-throughput analysis of sequence and positionally conserved lncRNAs across species, Guo et al [ 119 ] discovered the distinct subcellular localization and function of the lncRNA FAST (FOXD3 anti-sense transcript 1) in human and mouse embryonic stem cells (ESCs). In human ESCs, FAST is mainly expressed in the cytoplasm, where it blocks the interaction of the ubiquitin ligase β-TrCP (transducin repeats-containing protein) with phosphorylated β-catenin, leading to the prevention of β-catenin degradation, activation of WNT signaling, and maintenance of pluripotency.…”

Section: Evolutionary Conservation and Tissue Specificity Of Lncrnmentioning

confidence: 99%

Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Zhao

Teng

Yao

et al. 2020

Cancers

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Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded abundant information about lncRNA functions and underlying mechanisms, albeit with many discrepancies. In this review, we elaborate on the challenges in ascribing functions to lncRNAs based on the features of lncRNAs, including the genomic location, copy number, domain structure, subcellular localization, stability, evolution, and expression pattern. We also describe a framework for the investigation of lncRNA functions and mechanisms of action. Rigorous characterization of cancer-implicated lncRNAs is critical for the identification of bona fide anticancer targets.

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“…Moreover, lncRNAs have great significance in regulating the fate of stem cells, such as maintaining cellular pluripotency [ 9 ]. By carrying out high-throughput sequencing analysis of RNA derived from the nucleus and cytoplasm of embryonic stem cells (ESCs), Guo et al [ 10 ] found that there were significant differences in the processing and subcellular localization of lncRNAs between human and mouse ESCs, which led to different biological functions of lncRNAs in the regulation of cellular pluripotency. Recent studies have shown that lncRNAs also play a pivotal regulatory role in the differentiation and development of germ cells.…”

Section: Introductionmentioning

confidence: 99%

Analysis of lncRNA Expression Profile during the Formation of Male Germ Cells in Chickens

Gao

Zhang

Jin

et al. 2020

Animals

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Germ cells have an irreplaceable role in transmitting genetic information from one generation to the next, and also play an important role in sex differentiation in poultry, while little is known about epigenetic factors that regulate germ cell differentiation. In this study, RNA-seq was used to detect the expression profiles of long non-coding RNAs (lncRNAs) during the differentiation of chicken embryonic stem cells (ESCs) into spermatogonial stem cells (SSCs). The results showed that a total of 296, 280 and 357 differentially expressed lncRNAs (DELs) were screened in ESCs vs. PGCs, ESCs vs. SSCs and PGCs vs. SSCs, respectively. Gene Ontology (GO) and KEGG enrichment analysis showed that DELs in the three cell groups were mainly enriched in autophagy, Wnt/β-catenin, TGF-β, Notch and ErbB and signaling pathways. The co-expression network of 37 candidate DELs and their target genes enriched in the biological function of germ cell development showed that XLOC_612026, XLOC_612029, XLOC_240662, XLOC_362463, XLOC_023952, XLOC_674549, XLOC_160716, ALDBGALG0000001810, ALDBGALG0000002986, XLOC_657380674549, XLOC_022100 and XLOC_657380 were the key lncRNAs in the process of male germ cell formation and, moreover, the function of these DELs may be related to the interaction of their target genes. Our findings preliminarily excavated the key lncRNAs and signaling pathways in the process of male chicken germ cell formation, which could be helpful to construct the gene regulatory network of germ cell development, and also provide new ideas for further optimizing the induction efficiency of germ cells in vitro.

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Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells

Cited by 229 publications

References 80 publications

Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass (Dicentrarchus labrax L.)

Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass (Dicentrarchus labrax L.)

Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Analysis of lncRNA Expression Profile during the Formation of Male Germ Cells in Chickens

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