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

Fei, Jingyi; Jadaliha, Mahdieh; Harmon, Tyler S.; Li, Isaac T.  S.; Hua, Boyang; Hao, Qinyu; Holehouse, Alex S.; Reyer, Matthew; Sun, Qinyu; Freier, Susan M.; Pappu, Rohit V.; Prasanth, Kannanganattu V.; Ha, Taekjip

doi:10.1242/jcs.206854

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

Journal Article · Mon Nov 13 00:00:00 EST 2017 · Journal of Cell Science

DOI:https://doi.org/10.1242/jcs.206854· OSTI ID:1524073

Fei, Jingyi ^[1]; Jadaliha, Mahdieh ^[2]; Harmon, Tyler S. ^[3]; Li, Isaac T. S. ^[4]; Hua, Boyang ^[5]; Hao, Qinyu ^[6]; Holehouse, Alex S. ^[3]; Reyer, Matthew ^[7]; Sun, Qinyu ^[6]; Freier, Susan M. ^[8]; Pappu, Rohit V. ^[3];

^[2];

^[9]

Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology; Univ. of Chicago, IL (United States). Inst. for Biophysical Dynamics
Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Cell and Developmental Biology
Washington Univ., St. Louis, MO (United States). Dept. of Biomedical Engineering and Center for Biological Systems Engineering
Univ. of British Columbia Okanagan, Kelowna, BC (Canada). Dept. of Chemistry
Univ. of Illinois, Urbana, IL (United States). Center for Biophysics and Quantitative Biology
University of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Cell and Developmental Biology
Univ. of Chicago, IL (United States). Inst. for Biophysical Dynamics
Ionis Pharmaceuticals Inc., Carlsbad, CA (United States)
Univ. of Illinois, Urbana, IL (United States). Center for Biophysics and Quantitative Biology; Univ. of Illinois at Urbana-Champaign, IL (United States). Center for the Physics of Living Cells, Dept. of Physics; Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Inst. for Genomic Biology; Johns Hopkins Univ., Baltimore, MD (United States). Howard Hughes Medical Inst.

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.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE

OSTI ID:: 1524073

Journal Information:: Journal of Cell Science, Vol. 130, Issue 24; ISSN 0021-9533

Country of Publication:: United States

Language:: English

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