Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Liu, Siling; Wang, Zhengbo; Chen, Dong; Zhang, Bowen; Tian, Ren‐Rong; Wu, Jing; Zhang, Ying; Xu, Ke; Yang, Liu‐Meng; Cheng, Chao; Ma, Jian; Lv, Lei; Zheng, Yong‐Tang; Hu, Xintian; Zhang, Yi; Wang, Xiangting; Li, Jiali

doi:10.1101/gr.217463.116

Cited by 97 publications

(95 citation statements)

References 51 publications

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“…Because expression of lncRNAs involved in X inactivation differs in normal XX and XY cells, this could contribute to sex differences in cancer risk. In addition to the lncRNAs of the XIC, multiple other lncRNAs, located throughout the genome, have been identified as sexbiased in expression [110,124,125]. Functions of lncRNAs include modifying chromatin state and regulating gene expression [126]; thus, differences in even a small number of lncRNAs could have wide ranging effects.…”

Section: Sex Differences In Epigeneticsmentioning

confidence: 99%

Sex differences in cancer mechanisms

et al. 2020

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We now know that cancer is many different diseases, with great variation even within a single histological subtype. With the current emphasis on developing personalized approaches to cancer treatment, it is astonishing that we have not yet systematically incorporated the biology of sex differences into our paradigms for laboratory and clinical cancer research. While some sex differences in cancer arise through the actions of circulating sex hormones, other sex differences are independent of estrogen, testosterone, or progesterone levels. Instead, these differences are the result of sexual differentiation, a process that involves genetic and epigenetic mechanisms, in addition to acute sex hormone actions. Sexual differentiation begins with fertilization and continues beyond menopause. It affects virtually every body system, resulting in marked sex differences in such areas as growth, lifespan, metabolism, and immunity, all of which can impact on cancer progression, treatment response, and survival. These organismal level differences have correlates at the cellular level, and thus, males and females can fundamentally differ in their protections and vulnerabilities to cancer, from cellular transformation through all stages of progression, spread, and response to treatment. Our goal in this review is to cover some of the robust sex differences that exist in core cancer pathways and to make the case for inclusion of sex as a biological variable in all laboratory and clinical cancer research. We finish with a discussion of lab-and clinic-based experimental design that should be used when testing whether sex matters and the appropriate statistical models to apply in data analysis for rigorous evaluations of potential sex effects. It is our goal to facilitate the evaluation of sex differences in cancer in order to improve outcomes for all patients.

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Section: Sex Differences In Epigeneticsmentioning

confidence: 99%

Sex differences in cancer mechanisms

et al. 2020

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“…Given that tissue-specificity can be influenced by cells with common origins, we then investigated the tissue-specificity within tissues related to the nervous system including brain, cerebellum, cortex, olfactory bulb and spinal cord. We found specific expression patterns for 260 lncRNAs in the different samples of the nervous system 28 . Among the nervous system samples, we identified 156 lncRNAs specifically expressed in the cerebellum, 60 in the cortex and 44 in the olfactory-bulb ( Supplementary Table S2); (tau threshold ≥ 0.95).…”

Section: Landscape Of Canine Lncrna Transcriptionmentioning

confidence: 81%

Characterisation and functional predictions of canine long non-coding RNAs

Béguec

Wucher

Lagoutte

et al. 2018

Preprint

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Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and humans through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

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“…On the other hand, 29% of the former were detected only in one cell line compared to 7% of the latter [3]. Highly cell-type-and temporal-specific lncRNA expression patterns have also been shown in vivo [184][185][186][187]. Analyses of patterns of expression of various lncRNAs in mammalian brains based either on in situ hybridization [184] or RNA-seq analysis [185] revealed highly restricted patterns confined to neuroanatomical regions, cell types, or subcellular compartments in a genderdependent fashion.…”

Section: Subtle Effectsmentioning

confidence: 99%

Reverse-genetics studies of lncRNAs—what we have learnt and paths forward

et al. 2020

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Long non-coding RNAs (lncRNAs) represent a major fraction of the transcriptome in multicellular organisms. Although a handful of well-studied lncRNAs are broadly recognized as biologically meaningful, the fraction of such transcripts out of the entire collection of lncRNAs remains a subject of vigorous debate. Here we review the evidence for and against biological functionalities of lncRNAs and attempt to arrive at potential modes of lncRNA functionality that would reconcile the contradictory conclusions. Finally, we discuss different strategies of phenotypic analyses that could be used to investigate such modes of lncRNA functionality.

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Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Cited by 97 publications

References 51 publications

Sex differences in cancer mechanisms

Sex differences in cancer mechanisms

Characterisation and functional predictions of canine long non-coding RNAs

Reverse-genetics studies of lncRNAs—what we have learnt and paths forward

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