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Hideaki Takata¹, Hitoshi Nishijima^1,2,*,, Shun-ichiro Ogura³, Takehisa Sakaguchi¹, Paula A. Bubulya⁴, Tohru Mochizuki³ and Kei-ichi Shibahara^1,2,*

¹ Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan
² Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, Mishima 411-8540, Japan
³ Shizuoka Cancer Center Research Institute, Shizuoka 411-877, Japan
⁴ Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA

The interphase nucleus is a highly ordered and compartmentalized organelle. Little is known regarding what elaborate mechanisms might exist to explain these properties of the nucleus. Also unresolved is whether some architectural components might facilitate the formation of functional intranuclear compartments or higher order chromatin structure. As the first step to address these questions, we performed an in-depth proteome analysis of nuclear insoluble fractions of human HeLa-S3 cells prepared by two different approaches: a high-salt/detergent/nuclease-resistant fraction and a lithium 3,5-diiodosalicylate/nuclease-resistant fraction. Proteins of the fractions were analyzed by liquid chromatography electrospray ionization tandem mass spectrometry, identifying 333 and 330 proteins from each fraction respectively. Among the insoluble nuclear proteins, we identified 37 hitherto unknown or functionally uncharacterized proteins. The RNA recognition motif, WD40 repeats, HEAT repeats and the SAP domain were often found in these identified proteins. The subcellular distribution of selected proteins, including DEK protein and SON protein, demonstrated their novel associations with nuclear insoluble materials, corroborating our MS-based analysis. This study establishes a comprehensive catalog of the nuclear insoluble proteins in human cells. Further functional analysis of the proteins identified in our study will significantly improve our understanding of the dynamic organization of the interphase nucleus.

Both authors contributed equally to this work.

^* hnishiji{at}lab.nig.ac.jp or kshibaha{at}lab.nig.ac.jp