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J Cell Sci. 2017 Dec 15;130(24):4180-4192. doi: 10.1242/jcs.206854. Epub 2017 Nov 13.

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution.

Author information

1
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA jingyifei@uchicago.edu kumarp@illinois.edu.
2
Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
3
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
4
Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
5
Department of Chemistry, University of British Columbia Okanagan, Kelowna, British Columbia, Canada, V1V 1V7.
6
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
7
Ionis Pharmaceuticals Inc., Carlsbad, CA 92010, USA.
8
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA jingyifei@uchicago.edu kumarp@illinois.edu.
9
Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
10
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
11
Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA.

Abstract

Nuclear speckles are self-assembled organelles composed of RNAs and proteins. They are proposed to act as structural domains that control distinct steps in gene expression, including transcription, splicing and mRNA export. Earlier studies identified differential localization of a few components within the speckles. It was speculated that the spatial organization of speckle components might contribute directly to the order of operations that coordinate distinct processes. Here, by performing multi-color structured illumination microscopy, we characterized the multilayer organization of speckles at a higher resolution. We found that SON and SC35 (also known as SRSF2) localize to the central region of the speckle, whereas MALAT1 and small nuclear (sn)RNAs are enriched at the speckle periphery. Coarse-grained simulations indicate that the non-random organization arises due to the interplay between favorable sequence-encoded intermolecular interactions of speckle-resident proteins and RNAs. Finally, we observe positive correlation between the total amount of RNA present within a speckle and the speckle size. These results imply that speckle size may be regulated to accommodate RNA accumulation and processing. Accumulation of RNA from various actively transcribed speckle-associated genes could contribute to the observed speckle size variations within a single cell.

KEYWORDS:

Long noncoding RNA; Nuclear domain; Splicing factor; Sub-nuclear compartmentalization

PMID:
29133588
PMCID:
PMC5769577
DOI:
10.1242/jcs.206854
[Indexed for MEDLINE]
Free PMC Article

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