LncRNA
            <i>SOX1‐OT</i>
            V1 acts as a decoy of HDAC10 to promote SOX1‐dependent hESC neuronal differentiation

Xi, Jiajie; Xu, Yanxin; Guo, Zhenming; Li, Jianguo; Wu, Yukang; Sun, Qiaoyi; Wang, Yuxi; Chen, Mengxia; Zhu, Shifeng; Bian, Shan

doi:10.15252/embr.202153015

Cited by 14 publications

(9 citation statements)

References 54 publications

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“…For individual lncRNAs, Gas5 and Sox1/2ot , which are linked to the regulation of pluripotency and specific linage differentiation ( Knauss et al, 2018 ; Tu et al, 2018 ; Xi et al, 2022 ), were able to recruit many functional factors, such as Ago and Srsf family proteins ( Figure 3B ). Consistent with multi-faceted roles reported previously ( Plath et al, 2003 ; Fang et al, 2004 ; Patil et al, 2016 ), Xist lncRNA could guide the regulation of gene expression through coupling with a variety of proteins including the key components of PRC and m 6 A machineries ( Figure 3B ).…”

Section: Resultsmentioning

confidence: 99%

Dynamic Transcriptome Profiling Reveals LncRNA-Centred Regulatory Networks in the Modulation of Pluripotency

Wang

Zhang

Yuan

et al. 2022

Front. Cell Dev. Biol.

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Long noncoding RNAs (lncRNAs) have emerged as vital regulators of gene expression during embryonic stem cell (ESC) self-renewal and differentiation. Here, we systemically analyzed the differentially regulated lncRNAs during ESC-derived cardiomyocyte (CM) differentiation. We established a perspicuous profile of lncRNA expression at four critical developmental stages and found that the differentially expressed lncRNAs were grouped into six distinct clusters. The cluster with specific expression in ESC enriches the largest number of lncRNAs. Investigation of lncRNA-protein interaction network revealed that they are not only controlled by classic key transcription factors, but also modulated by epigenetic and epitranscriptomic factors including N6-methyladenosine (m6A) effector machineries. A detailed inspection revealed that 28 out of 385 lncRNAs were modified by methylation as well as directly recruited by the nuclear m6A reader protein Ythdc1. Unlike other 27 non-coding transcripts, the ESC-specific lncRNA Gm2379, located in both nucleus and cytoplasm, becomes dramatically upregulated in response to the depletion of m6A or Ythdc1. Consistent with the role of m6A in cell fate regulation, depletion of Gm2379 results in dysregulated expressions of pluripotent genes and crucial genes required for the formation of three germ layers. Collectively, our study provides a foundation for understanding the dynamic regulation of lncRNA transcriptomes during ESC differentiation and identifies the interplay between epitranscriptomic modification and key lncRNAs in the regulation of cell fate decision.

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Section: Resultsmentioning

confidence: 99%

Dynamic Transcriptome Profiling Reveals LncRNA-Centred Regulatory Networks in the Modulation of Pluripotency

Wang

Zhang

Yuan

et al. 2022

Front. Cell Dev. Biol.

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“…In the following, we discuss hypothetical scenarios, in which RUS recruits regulatory functions to chromosomal target loci. It is also possible that RUS sequesters the factors in competition with other interactors, which would have opposite effects on gene regulation compared with recruitment scenarios ( Xi et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

LncRNA RUS shapes the gene expression program towards neurogenesis

Schneider

Müller

et al. 2022

Life Sci. Alliance

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The evolution of brain complexity correlates with an increased expression of long, noncoding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for “RNA upstream of Slitrk3.” The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.

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Section: Discussionmentioning

confidence: 99%

LncRNA RUS shapes the gene expression program towards neurogenesis

Schneider

Müller

et al. 2022

Preprint

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The evolution of brain complexity correlates with an increased expression of long, non-coding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for 'RNA upstream of Slitrk3'. The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases along with neuronal markers during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner

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LncRNA SOX1‐OT V1 acts as a decoy of HDAC10 to promote SOX1‐dependent hESC neuronal differentiation

Cited by 14 publications

References 54 publications

Dynamic Transcriptome Profiling Reveals LncRNA-Centred Regulatory Networks in the Modulation of Pluripotency

Dynamic Transcriptome Profiling Reveals LncRNA-Centred Regulatory Networks in the Modulation of Pluripotency

LncRNA RUS shapes the gene expression program towards neurogenesis

LncRNA RUS shapes the gene expression program towards neurogenesis

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