Whole-genome screening identifies proteins localized to distinct nuclear bodies

Abstract

JCB: Tools The Rockefeller University Press $30.00 J. Cell Biol. Vol. 203 No. 1 149–164 www.jcb.org/cgi/doi/10.1083/jcb.201303145 JCB 149 Correspondence to Junjie Chen: jchen8@mdanderson.org Abbreviations used in this paper: FBL, fibrillarin; GO, Gene Ontology; IP, immuno­ precipitation; IR, ionizing radiation; PML, promyelocytic leukemia; qRT-PCR, quan­ titative RT-PCR; SMN, survival of motor neuron; snRNP, small nuclear RNP. Complete screen data http://jcb-dataviewer.rupress.org/jcb/browse/6852/S152 Introduction The nucleus is enclosed by a double-membrane structure termed the nuclear envelope, which serves as a physical barrier to sepa- rate nuclear contents from the cytoplasm. Numerous nuclear pores exist as large protein complexes across the nuclear enve- lope, which allow the transport of water-soluble molecules. In- terphase chromosomes occupy distinct subnuclear territories. The interchromatin space is also well organized and harbors multiple nuclear bodies that can be visualized as distinct nuclear foci at the microscopic level. To date, nuclear bodies that have been studied extensively are nucleoli, promyelocytic leukemia (PML) bodies, nuclear speckles, Cajal bodies, paraspeckles, and Polycomb bodies (Spector, 2006). Tremendous effort has been made and allowed us to understand the distinct functions of several nuclear bodies: (a) Nucleoli are sites of ribosomal DNA transcription, preribosomal RNA processing, and preribosomal assembly. (b) Nuclear speck- les may serve as storage and/or modification sites for splicing factors and sites for pre-mRNA splicing. In fact, nuclear speck- les are often in close proximity to many active genes, suggest- ing that transcription and RNA splicing are coupled in the cell. (c) Cajal bodies are involved in the assembly and maturation of small nuclear RNPs (snRNPs; Spector, 2006). Recently, telom- erase RNA and telomerase reverse transcription were also shown to localize to Cajal bodies (Zhu et al., 2004; Tomlinson et al., 2