Novel Approaches to Profile Functional Long Noncoding RNAs Associated with Stem Cell Pluripotency

Overview

Journal Curr Genomics

Publisher Bentham Science Publishers

Date 2020 Jul 14

PMID 32655297

Citations 2

Authors

Yanbo Zhu

Zi Yan

Ze Tang

Wei Li

Affiliations

Soon will be listed here.

Abstract

The pluripotent state of stem cells depends on the complicated network orchestrated by thousands of factors and genes. Long noncoding RNAs (lncRNAs) are a class of RNA longer than 200 nt without a protein-coding function. Single-cell sequencing studies have identified hundreds of lncRNAs with dynamic changes in somatic cell reprogramming. Accumulating evidence suggests that they participate in the initiation of reprogramming, maintenance of pluripotency, and developmental processes by cis and/or trans mechanisms. In particular, they may interact with proteins, RNAs, and chromatin modifier complexes to form an intricate pluripotency-associated network. In this review, we focus on recent progress in approaches to profiling functional lncRNAs in somatic cell reprogramming and cell differentiation.

Citing Articles

LncRNA Osilr9 coordinates promoter DNA demethylation and the intrachromosomal loop structure required for maintaining stem cell pluripotency.

Zhu Y, Yan Z, Fu C, Wen X, Jia L, Zhou L Mol Ther. 2022; 31(6):1791-1806.

PMID: 36523163 PMC: 10278046. DOI: 10.1016/j.ymthe.2022.12.010.

Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture.

Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L J Cell Biol. 2022; 221(4).

PMID: 35171230 PMC: 8855478. DOI: 10.1083/jcb.202009134.

References

Zhao J, Ohsumi T, Kung J, Ogawa Y, Grau D, Sarma K . Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell. 2010; 40(6):939-53. PMC: 3021903. DOI: 10.1016/j.molcel.2010.12.011. View

Lopez-Leon M, Outeiro T, Goya R . Cell reprogramming: Therapeutic potential and the promise of rejuvenation for the aging brain. Ageing Res Rev. 2017; 40:168-181. DOI: 10.1016/j.arr.2017.09.002. View

Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B . MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 2015; 6:7743. PMC: 4525211. DOI: 10.1038/ncomms8743. View

. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57-74. PMC: 3439153. DOI: 10.1038/nature11247. View

Cui C, Shu W, Li P . Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications. Front Cell Dev Biol. 2016; 4:89. PMC: 5011256. DOI: 10.3389/fcell.2016.00089. View

Di Baldassarre A, Cimetta E, Bollini S, Gaggi G, Ghinassi B . Human-Induced Pluripotent Stem Cell Technology and Cardiomyocyte Generation: Progress and Clinical Applications. Cells. 2018; 7(6). PMC: 6025241. DOI: 10.3390/cells7060048. View

Chakraborty D, Kappei D, Theis M, Nitzsche A, Ding L, Paszkowski-Rogacz M . Combined RNAi and localization for functionally dissecting long noncoding RNAs. Nat Methods. 2012; 9(4):360-2. DOI: 10.1038/nmeth.1894. View

Yan L, Yang M, Guo H, Yang L, Wu J, Li R . Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013; 20(9):1131-9. DOI: 10.1038/nsmb.2660. View

Dinger M, Amaral P, Mercer T, Pang K, Bruce S, Gardiner B . Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008; 18(9):1433-45. PMC: 2527704. DOI: 10.1101/gr.078378.108. View

10.

Wang K, Chang H . Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011; 43(6):904-14. PMC: 3199020. DOI: 10.1016/j.molcel.2011.08.018. View

11.

Kim H, Kim J . A guide to genome engineering with programmable nucleases. Nat Rev Genet. 2014; 15(5):321-34. DOI: 10.1038/nrg3686. View

12.

Pan Q, Shai O, Lee L, Frey B, Blencowe B . Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008; 40(12):1413-5. DOI: 10.1038/ng.259. View

13.

Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X . Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell. 2010; 6(5):468-78. PMC: 2954317. DOI: 10.1016/j.stem.2010.03.015. View

14.

Yu C, Kuo H . The Trans-Spliced Long Noncoding RNA tsRMST Impedes Human Embryonic Stem Cell Differentiation Through WNT5A-Mediated Inhibition of the Epithelial-to-Mesenchymal Transition. Stem Cells. 2016; 34(8):2052-62. DOI: 10.1002/stem.2386. View

15.

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View

16.

Zhang S, Wang Y, Jia L, Wen X, Du Z, Wang C . Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing. Genome Res. 2019; 29(9):1521-1532. PMC: 6724666. DOI: 10.1101/gr.244996.118. View

17.

Clark M, Mercer T, Bussotti G, Leonardi T, Haynes K, Crawford J . Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods. 2015; 12(4):339-42. DOI: 10.1038/nmeth.3321. View

18.

Sherstyuk V, Medvedev S, Zakian S . Noncoding RNAs in the Regulation of Pluripotency and Reprogramming. Stem Cell Rev Rep. 2017; 14(1):58-70. DOI: 10.1007/s12015-017-9782-9. View

19.

Gu T, Guo F, Yang H, Wu H, Xu G, Liu W . The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature. 2011; 477(7366):606-10. DOI: 10.1038/nature10443. View

20.

Engreitz J, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C . The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013; 341(6147):1237973. PMC: 3778663. DOI: 10.1126/science.1237973. View