The Association of MEG3 LncRNA with Nuclear Speckles in Living Cells

Overview

Journal Cells

Publisher MDPI

Specialties Biochemistry
Biophysics
Cell Biology
Molecular Biology

Date 2022 Jun 24

PMID 35741072

Authors

Sarah E Hasenson

Ella Alkalay

Mohammad K Atrash

Alon Boocholez

Julianna Gershbaum

Hodaya Hochberg-Laufer

Yaron Shav-Tal

Affiliations

Soon will be listed here.

Abstract

Nuclear speckles are nuclear bodies containing RNA-binding proteins as well as RNAs including long non-coding RNAs (lncRNAs). Maternally expressed gene 3 (MEG3) is a nuclear retained lncRNA found to associate with nuclear speckles. To understand the association dynamics of MEG3 lncRNA with nuclear speckles in living cells, we generated a fluorescently tagged MEG3 transcript that could be detected in real time. Under regular conditions, transient association of MEG3 with nuclear speckles was observed, including a nucleoplasmic fraction. Transcription or splicing inactivation conditions, known to affect nuclear speckle structure, showed prominent and increased association of MEG3 lncRNA with the nuclear speckles, specifically forming a ring-like structure around the nuclear speckles. This contrasted with metastasis-associated lung adenocarcinoma (MALAT1) lncRNA that is normally highly associated with nuclear speckles, which was released and dispersed in the nucleoplasm. Under normal conditions, MEG3 dynamically associated with the periphery of the nuclear speckles, but under transcription or splicing inhibition, MEG3 could also enter the center of the nuclear speckle. Altogether, using live-cell imaging approaches, we find that MEG3 lncRNA is a transient resident of nuclear speckles and that its association with this nuclear body is modulated by the levels of transcription and splicing activities in the cell.

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References

Bernard D, Prasanth K, Tripathi V, Colasse S, Nakamura T, Xuan Z . A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010; 29(18):3082-93. PMC: 2944070. DOI: 10.1038/emboj.2010.199. View

Carter K, Bowman D, Carrington W, Fogarty K, McNeil J, Fay F . A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science. 1993; 259(5099):1330-5. DOI: 10.1126/science.8446902. View

Tian Z, Guo X, Zhao Y, Fang Y . Decreased expression of long non-coding RNA MEG3 acts as a potential predictor biomarker in progression and poor prognosis of osteosarcoma. Int J Clin Exp Pathol. 2016; 8(11):15138-42. PMC: 4713643. View

Zhang X, Rice K, Wang Y, Chen W, Zhong Y, Nakayama Y . Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. Endocrinology. 2009; 151(3):939-47. PMC: 2840681. DOI: 10.1210/en.2009-0657. View

Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy S, Phair R . In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol. 2007; 14(9):796-806. PMC: 4942130. DOI: 10.1038/nsmb1280. View

Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S . Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J. 2017; 36(10):1447-1462. PMC: 5430218. DOI: 10.15252/embj.201695848. View

Thiry M . The interchromatin granules. Histol Histopathol. 1995; 10(4):1035-45. View

Shav-Tal Y, Darzacq X, Shenoy S, Fusco D, Janicki S, Spector D . Dynamics of single mRNPs in nuclei of living cells. Science. 2004; 304(5678):1797-800. PMC: 4765737. DOI: 10.1126/science.1099754. View

Sun Q, Hao Q, Prasanth K . Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet. 2017; 34(2):142-157. PMC: 6002860. DOI: 10.1016/j.tig.2017.11.005. View

10.

Mor A, Suliman S, Ben-Yishay R, Yunger S, Brody Y, Shav-Tal Y . Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat Cell Biol. 2010; 12(6):543-52. DOI: 10.1038/ncb2056. View

11.

Mao Y, Zhang B, Spector D . Biogenesis and function of nuclear bodies. Trends Genet. 2011; 27(8):295-306. PMC: 3144265. DOI: 10.1016/j.tig.2011.05.006. View

12.

OKeefe R, Mayeda A, Sadowski C, Krainer A, Spector D . Disruption of pre-mRNA splicing in vivo results in reorganization of splicing factors. J Cell Biol. 1994; 124(3):249-60. PMC: 2119927. DOI: 10.1083/jcb.124.3.249. View

13.

Clemson C, Hutchinson J, Sara S, Ensminger A, Fox A, Chess A . An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell. 2009; 33(6):717-26. PMC: 2696186. DOI: 10.1016/j.molcel.2009.01.026. View

14.

Cmarko D, Verschure P, Martin T, Dahmus M, Krause S, Fu X . Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol Biol Cell. 1999; 10(1):211-23. PMC: 25164. DOI: 10.1091/mbc.10.1.211. View

15.

Smith K, Hall L, Lawrence J . Nuclear hubs built on RNAs and clustered organization of the genome. Curr Opin Cell Biol. 2020; 64:67-76. PMC: 7371543. DOI: 10.1016/j.ceb.2020.02.015. View

16.

Murphy S, Wylie A, Coveler K, Cotter P, Papenhausen P, Sutton V . Epigenetic detection of human chromosome 14 uniparental disomy. Hum Mutat. 2003; 22(1):92-7. DOI: 10.1002/humu.10237. View

17.

Ilik I, Malszycki M, Lubke A, Schade C, Meierhofer D, Aktas T . SON and SRRM2 are essential for nuclear speckle formation. Elife. 2020; 9. PMC: 7671692. DOI: 10.7554/eLife.60579. View

18.

Hall L, Smith K, Byron M, Lawrence J . Molecular anatomy of a speckle. Anat Rec A Discov Mol Cell Evol Biol. 2006; 288(7):664-75. PMC: 2563428. DOI: 10.1002/ar.a.20336. View

19.

Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M . Pharmacological inhibition of the spliceosome subunit SF3b triggers exon junction complex-independent nonsense-mediated decay. J Cell Sci. 2017; 130(9):1519-1531. DOI: 10.1242/jcs.202200. View

20.

Sunwoo H, Dinger M, Wilusz J, Amaral P, Mattick J, Spector D . MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2008; 19(3):347-59. PMC: 2661813. DOI: 10.1101/gr.087775.108. View