1,653
Views
15
CrossRef citations to date
0
Altmetric
Research Paper

Identification and epigenetic analysis of divergent long non-coding RNAs in multilineage differentiation of human Neural Progenitor Cells

, , , , , , , & show all
Pages 13-24 | Received 13 Nov 2018, Accepted 17 Nov 2018, Published online: 27 Dec 2018

References

  • Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online. 2014;16:11. PubMed PMID: 25276098; PubMed Central PMCID: PMC4177375.
  • Jia H, Osak M, Bogu GK, et al. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. Rna. 2010 Aug;16(8):1478–1487. PubMed PMID: 20587619; PubMed Central PMCID: PMC2905748.
  • Luo S, Lu JY, Liu L, et al. Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells. Cell Stem Cell. 2016 May 5;18(5):637–652. PubMed PMID: 26996597.
  • Katayama S, Tomaru Y, Kasukawa T, et al. Antisense transcription in the mammalian transcriptome. Science. 2005 Sep 2;309(5740):1564–1566. PubMed PMID: 16141073.
  • Sigova AA, Mullen AC, Molinie B, et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2876–2881. PubMed PMID: 23382218; PubMed Central PMCID: PMC3581948.
  • Magistri M, Faghihi MA, St Laurent G 3rd, et al. Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet. 2012 Aug;28(8):389–396. PubMed PMID: 22541732; PubMed Central PMCID: PMC3768148.
  • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915–1927. PubMed PMID: 21890647; PubMed Central PMCID: PMC3185964.
  • Bonaguidi MA, Wheeler MA, Shapiro JS, et al. In vivo clonal analysis reveals self-renewing and multipotent adult neural stem cell characteristics. Cell. 2011 Jun 24;145(7):1142–1155. PubMed PMID: 21664664; PubMed Central PMCID: PMC3124562.
  • Dinger ME, Amaral PP, Mercer TR, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008 Sep;18(9):1433–1445. PubMed PMID: 18562676; PubMed Central PMCID: PMC2527704.
  • D’Haene E, Jacobs EZ, Volders PJ, et al. Identification of long non-coding RNAs involved in neuronal development and intellectual disability. Sci Rep. 2016 Jun20;6:28396. PubMed PMID: 27319317; PubMed Central PMCID: PMC4913242.
  • Ramos AD, Andersen RE, Liu SJ, et al. The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell. 2015 Apr 2;16(4):439–447. PubMed PMID: 25800779; PubMed Central PMCID: PMC4388801.
  • He D, Wang J, Lu Y, et al. lncRNA functional networks in oligodendrocytes reveal stage-specific myelination control by an lncOL1/Suz12 complex in the CNS. Neuron. 2017 Jan 18;93(2):362–378. PubMed PMID: 28041882; PubMed Central PMCID: PMC5600615.
  • Dong X, Chen K, Cuevas-Diaz Duran R, et al. Comprehensive identification of long non-coding RNAs in purified cell types from the brain reveals functional LncRNA in OPC fate determination. PLoS Genet. 2015 Dec;11(12):e1005669. PubMed PMID: 26683846; PubMed Central PMCID: PMC4980008.
  • Mercer TR, Qureshi IA, Gokhan S, et al. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci. 2010 Feb5;11:14.. PubMed PMID: 20137068; PubMed Central PMCID: PMC2829031.
  • Zhang Y, Sloan SA, Clarke LE, et al. Purification and characterization of progenitor and mature human astrocytes reveals transcriptional and functional differences with mouse. Neuron. 2016 Jan 6;89(1):37–53. PubMed PMID: 26687838; PubMed Central PMCID: PMC4707064.
  • Agostini M, Romeo F, Inoue S, et al. Metabolic reprogramming during neuronal differentiation. Cell Death Differ. 2016 Sep 1;23(9):1502–1514. PubMed PMID: 27058317; PubMed Central PMCID: PMC5072427.
  • Magistri M, Khoury N, Mazza EM, et al. A comparative transcriptomic analysis of astrocytes differentiation from human neural progenitor cells. Eur J Neurosci. 2016 Nov;44(10):2858–2870. PubMed PMID: 27564458; PubMed Central PMCID: PMC5118072.
  • Dritsoula A, Papaioannou I, Guerra SG, et al. The molecular basis for dysregulated activation of NKX2-5 in vascular remodelling of systemic sclerosis. Arthritis Rheumatol. 2018 Jan 17. DOI:10.1002/art.40419 PubMed PMID: 29342503.
  • Fatima M, Kumari R, Schwamborn JC, et al. Tripartite containing motif 32 modulates proliferation of human neural precursor cells in HIV-1 neurodegeneration. Cell Death Differ. 2016 May;23(5):776–786. PubMed PMID: 26586575; PubMed Central PMCID: PMC4832097.
  • Fatima M, Prajapati B, Saleem K, et al. Novel insights into role of miR-320a-VDAC1 axis in astrocyte-mediated neuronal damage in neuroAIDS. Glia. 2017 Feb;65(2):250–263. PubMed PMID: 27761954.
  • Zheng GQ, Li Y, Gu Y, et al. Beyond water channel: aquaporin-4 in adult neurogenesis. Neurochem Int. 2010 Apr;56(5):651–654. PubMed PMID: 20138100.
  • Kong H, Fan Y, Xie J, et al. AQP4 knockout impairs proliferation, migration and neuronal differentiation of adult neural stem cells. J Cell Sci. 2008 Dec 15;121(Pt 24):4029–4036. PubMed PMID: 19033383.
  • Zhao Y, Sheng HZ, Amini R, et al. Control of hippocampal morphogenesis and neuronal differentiation by the LIM homeobox gene Lhx5. Science. 1999 May 14;284(5417):1155–1158. PubMed PMID: 10325223.
  • Kong H, Sha LL, Fan Y, et al. Requirement of AQP4 for antidepressive efficiency of fluoxetine: implication in adult hippocampal neurogenesis. Neuropsychopharmacol. 2009 Apr;34(5):1263–1276. PubMed PMID: 18923397.
  • Pertea M, Kim D, Pertea GM, et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016 Sep;11(9):1650–1667. PubMed PMID: 27560171; PubMed Central PMCID: PMC5032908.
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357–360. PubMed PMID: 25751142; PubMed Central PMCID: PMC4655817.
  • Ramirez F, Ryan DP, Gruning B, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016 Jul 8;44(W1):W160–5. PubMed PMID: 27079975; PubMed Central PMCID: PMC4987876.
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498–2504. PubMed PMID: 14597658; PubMed Central PMCID: PMC403769.
  • Wu JQ, Habegger L, Noisa P, et al. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254–5259. PubMed PMID: 20194744; PubMed Central PMCID: PMC2841935.
  • Lin M, Pedrosa E, Shah A, et al. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PloS one. 2011;6(9):e23356. PubMed PMID: 21915259; PubMed Central PMCID: PMC3168439.
  • Zhang Y, Chen K, Sloan SA, et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci. 2014 Sep 3;34(36):11929–11947. PubMed PMID: 25186741; PubMed Central PMCID: PMC4152602.
  • Mondal T, Juvvuna PK, Kirkeby A, et al. Sense-antisense lncRNA pair encoded by locus 6p22.3 determines neuroblastoma susceptibility via the USP36-CHD7-SOX9 regulatory axis. Cancer Cell. 2018 Mar 12;33(3):417–434 e7. PubMed PMID: 29533783.
  • Chen Y, Ozturk NC, Zhou FC. DNA methylation program in developing hippocampus and its alteration by alcohol. PloS one. 2013;8(3):e60503. PubMed PMID: 23544149; PubMed Central PMCID: PMC3609790.
  • Chen Y, Damayanti NP, Irudayaraj J, et al. Diversity of two forms of DNA methylation in the brain. Front Genet. 2014;5:46. PubMed PMID: 24653733; PubMed Central PMCID: PMC3948076.
  • Neumann P, Jae N, Knau A, et al. The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2. Nat Commun. 2018 Jan 16;9(1):237. PubMed PMID: 29339785; PubMed Central PMCID: PMC5770451.
  • Labonte B, Engmann O, Purushothaman I, et al. Sex-specific transcriptional signatures in human depression. Nat Med. 2017 Sep;23(9):1102–1111. PubMed PMID: 28825715; PubMed Central PMCID: PMC5734943.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.