Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA.
Paraspeckles are sub-nuclear domains that are nucleated by long noncoding RNA Neat1. While interaction of protein components of paraspeckles and Neat1 is understood, there is limited information on the interaction of non-structural RNA components with paraspeckles. Here, by varying paraspeckle number and size, we investigate how paraspeckles influence the nuclear organization of their non-structural RNA component Ctn RNA. Our results show that Ctn RNA remains nuclear-retained in the absence of intact paraspeckles, suggesting that they do not regulate nuclear retention of Ctn RNA. In the absence of Neat1, Ctn RNA continues to interact with paraspeckle protein NonO to form residual nuclear foci. In addition, in the absence of Neat1-nucleated paraspeckles, a subset of Ctn RNA localizes to the perinucleolar regions. Concomitant with increase in number of paraspeckles, transcriptional reactivation resulted in increased number of paraspeckle-localized Ctn RNA foci. Similar to Neat1, proteasome inhibition altered the localization of Ctn RNA, where it formed enlarged paraspeckle-like foci. Super-resolution structured illumination microscopic analyses revealed that in paraspeckles, Ctn RNA partially co-localized with Neat1, and displayed a more heterogeneous intra-paraspeckle localization. Collectively, these results show that while paraspeckles do not influence nuclear retention of Ctn RNA, they modulate its intranuclear compartmentalization.
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
Aparna
A
Anantharaman
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
Mahdieh
M
Jadaliha
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
Vidisha
V
Tripathi
RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan.
Shinichi
S
Nakagawa
Institute of Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan.
Tetsuro
T
Hirose
Department of Cell and Developmental Biology, Center of Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.
Michael F
MF
Jantsch
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
Supriya G
SG
Prasanth
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
Kannanganattu V
KV
Prasanth
Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19202-7
23129630
Mol Biol Cell. 2010 Nov 15;21(22):4020-7
20881053
Nature. 2000 Jul 6;406(6791):78-81
10894545
RNA. 2008 Oct;14(10):2050-60
18719245
Science. 2008 Dec 12;322(5908):1713-7
18948503
Genome Res. 2012 May;22(5):885-98
22406755
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2525-30
19188602
Genes Dev. 2015 Mar 15;29(6):630-45
25792598
Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3221-6
26951683
Mol Cell. 2009 Mar 27;33(6):717-26
19217333
Nucleic Acids Res. 2012 Sep 1;40(17):8637-45
22735697
J Cell Biol. 2001 Oct 15;155(2):181-5
11604416
Cold Spring Harb Perspect Biol. 2010 Dec;2(12):a000711
21068152
Genome Res. 2009 Mar;19(3):347-59
19106332
Dev Cell. 2009 Nov;17(5):639-47
19922869
Biol Reprod. 2006 Sep;75(3):352-9
16641145
Annu Rev Biochem. 2002;71:817-46
12045112
Mol Biol Cell. 2014 Jan;25(1):169-83
24173718
Genes Dev. 2012 Nov 1;26(21):2392-407
23073843
Genes Dev. 2013 Jul 1;27(13):1495-510
23824540
Development. 2014 Dec;141(23):4618-27
25359727
Nat Cell Biol. 2011 Jan;13(1):95-101
21170033
EMBO J. 2012 Oct 17;31(20):4020-34
22960638
Nucleic Acids Res. 2001 May 1;29(9):e45
11328886
Mol Cell. 2014 Feb 6;53(3):393-406
24507715
J Cell Biol. 2011 Apr 4;193(1):31-9
21444682
Nat Cell Biol. 2011 Feb;13(2):167-73
21240286
J Biol Chem. 2004 Feb 6;279(6):4894-902
14615479
Curr Opin Genet Dev. 2012 Apr;22(2):179-87
22281031
Genome Res. 2016 Jun;26(6):852-62
27197207
Curr Biol. 2002 Jan 8;12(1):13-25
11790299
Cell. 2001 Aug 24;106(4):465-75
11525732
Mol Cell. 2010 Sep 24;39(6):925-38
20797886
Mol Cell. 2009 Aug 28;35(4):467-78
19716791
Cell. 2007 Feb 23;128(4):787-800
17320514
Trends Biochem Sci. 2010 Jul;35(7):377-83
20382028
BMC Genomics. 2007 Feb 01;8:39
17270048
RNA. 2014 Dec;20(12):1844-9
25316907
RNA Biol. 2013 Mar;10(3):456-61
23324609
Trends Genet. 2011 Aug;27(8):295-306
21680045
Mol Biol Cell. 2005 Dec;16(12 ):5579-91
16195339
Oncogene. 2015 Aug 20;34(34):4482-90
25417700
Cell. 2005 Oct 21;123(2):249-63
16239143
Cold Spring Harb Perspect Biol. 2011 Feb 01;3(2):null
20926517
EMBO J. 2008 Jun 18;27(12):1694-705
18497743