@article{d5e463291dac4cc095555155fd2cd8fc,
title = "Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution",
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 asSRSF2) 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 sequenceencoded 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 sizemay 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",
author = "Jingyi Fei and Mahdieh Jadaliha and Harmon, {Tyler S.} and Li, {Isaac T.S.} and Boyang Hua and Qinyu Hao and Holehouse, {Alex S.} and Matthew Reyer and Qinyu Sun and Freier, {Susan M.} and Pappu, {Rohit V.} and Prasanth, {Kannanganattu V.} and Taekjip Ha",
note = "Funding Information: J.F. acknowledges support from the National Science Foundation (NSF) (PHY-1430124) and the Searle Scholars Program. I.T.S.L. acknowledges supports from the National Science Foundation (PHY-1430124) and Natural Sciences and Engineering Research Council of Canada (NERSC) (RGPIN201704407). T.H. is a Howard Hughes Medical Institute investigator. K.V.P. acknowledges support from the National Institutes of Health (1RO1GM088252), American Cancer Society and a National Science Foundation EAGER grant. R.V.P. acknowledges support from the National Science Foundation (MCB1614766) and National Institutes of Health (R01NS056114). T.S.H. was a graduate student scholar in the Center for Biological Systems Engineering at the University of Washington and A.S.H. was supported in part by the Bonnie and Kent Lattig scholarship. M.J. is supported by the Cancer Scholars for Translational and Applied Research (C*STAR) graduate educational program from the University of Illinois and Carle Foundation Hospital. Deposited in PMC for release after 12 months. Funding Information: We thank the core facilities and service at Carl R. Woese Institute for Genomic Biology at University of Illinois Urbana-Champaign for SIM microscopy and imaging reconstruction software, Drs P. Bubulya (Wright State University, USA), Fu X-D (University of San Diego, USA), W. van Venrooij (Radbound University Nijmegen, Netherlands) for the gift of reagents, and Dr. V. Tripathi for technical assistance.J.F. acknowledges support from the National Science Foundation (NSF) (PHY-1430124) and the Searle Scholars Program. I.T.S.L. acknowledges supports from the National Science Foundation (PHY-1430124) and Natural Sciences and Engineering Research Council of Canada (NERSC) (RGPIN201704407). T.H. is a Howard Hughes Medical Institute investigator. K.V.P. acknowledges support from the National Institutes of Health (1RO1GM088252), American Cancer Society and a National Science Foundation EAGER grant. R.V.P. acknowledges support from the National Science Foundation (MCB1614766) and National Institutes of Health (R01NS056114). T.S.H. was a graduate student scholar in the Center for Biological Systems Engineering at the University of Washington and A.S.H. was supported in part by the Bonnie and Kent Lattig scholarship. M.J. is supported by the Cancer Scholars for Translational and Applied Research (C*STAR) graduate educational program from the University of Illinois and Carle Foundation Hospital. Deposited in PMC for release after 12 months. Publisher Copyright: {\textcopyright} 2017. Published by The Company of Biologists Ltd.",
year = "2017",
month = dec,
day = "1",
doi = "10.1242/jcs.206854",
language = "English (US)",
volume = "130",
pages = "4180--4192",
journal = "The Quarterly journal of microscopical science",
issn = "0021-9533",
publisher = "Company of Biologists Ltd",
number = "24",
}