Xist localization and function: new insights from multiple levels

Cerase, Andrea; Pintacuda, Greta; Tattermusch, Anna; Avner, Philip

doi:10.1186/s13059-015-0733-y

Cited by 162 publications

(140 citation statements)

References 92 publications

(174 reference statements)

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“…1A,B). A recent study has suggested that XCI processes are affected by chromosomal topology and the nuclear locality, and are not established uniformly throughout chromosomes (Cerase et al, 2015). Therefore, we expected that different insertion sites of the two reporter genes might provide different monitoring results depending on the time of development and tissues involved.…”

Section: Results and Discussion Live-cell Imaging Of Xcrmentioning

confidence: 97%

Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells

et al. 2016

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Pluripotent stem cells can be classified into two distinct states, naïve and primed, which show different degrees of potency. One difficulty in stem cell research is the inability to distinguish these states in live cells. Studies on female mice have shown that reactivation of inactive X chromosomes occurs in the naïve state, while one of the X chromosomes is inactivated in the primed state. Therefore, we aimed to distinguish the two states by monitoring X chromosome reactivation. Thus far, X chromosome reactivation has been analysed using fixed cells; here, we inserted different fluorescent reporter gene cassettes (mCherry and eGFP) into each X chromosome. Using these knock-in 'Momiji' mice, we detected X chromosome reactivation accurately in live embryos, and confirmed that the pluripotent states of embryos were stable ex vivo, as represented by embryonic and epiblast stem cells in terms of X chromosome reactivation. Thus, Momiji mice provide a simple and accurate method for identifying stem cell status based on X chromosome reactivation.

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Section: Results and Discussion Live-cell Imaging Of Xcrmentioning

confidence: 97%

Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells

et al. 2016

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“…Interestingly, efficient splicing is more prevalent among lincRNAs that have been shown to have specific functions, such as XIST (Cerase et al 2015), FIRRE (Hacisuleyman et al 2014), and MIAT (Liao et al 2016). Indeed, efficient splicing has been shown to be necessary for some lincRNAs to carry out their function (Marquardt et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

et al. 2016

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While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre-and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters. Surprisingly, we find that H3K9me3-a histone modification typically associated with transcriptional repression-is more enriched at the promoters of active lincRNA loci than at those of active mRNAs. Moreover, H3K9me3-marked lincRNA genes are more tissue-specific. The most discriminant differences between lincRNAs and mRNAs involve splicing. LincRNAs are less efficiently spliced, which cannot be explained by differences in U1 binding or the density of exonic splicing enhancers but may be partially attributed to lower U2AF65 binding and weaker splicing-related motifs. Conversely, the stability of lincRNAs and mRNAs is similar, differing only with regard to the location of stabilizing protein binding sites. Finally, we find that certain transcriptional properties are correlated with higher evolutionary conservation in both DNA and RNA motifs and are enriched in lincRNAs that have been functionally characterized.

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“…• X chromosome silencing by XIST: a 16kB lncRNA (Cerase, et al 2015) human and mouse lncRNAs http://bioinfo.life.hust.edu.cn/lncR NASNP2…”

Section: Declaration Of Interest and Fundingmentioning

confidence: 99%

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

Klinge

2018

Endocrine-Related Cancer

100

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Abstract:The human genome is 'pervasively transcribed' leading to a complex array of noncoding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~ 22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function.LncRNAs fold into structures that interact with DNA, RNA, and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology, and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial, and thyroid.

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Xist localization and function: new insights from multiple levels

Cited by 162 publications

References 92 publications

Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells

Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

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