Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin
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Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Evolution of a transcriptional regulator from a transmembrane nucleoporin Tobias M. Franks,1 Chris Benner,1 Iñigo Narvaiza,2 Maria C.N. Marchetto,2 Janet M. Young,3 Harmit S. Malik,3,4 Fred H. Gage,2,5 and Martin W. Hetzer1 1Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA; 2Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA; 3Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 4Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 5Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California 92093, USA Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components. [Keywords: evolution; hominoid; Pom121; Nup98; transcription; nuclear pore complex (NPC)] Supplemental material is available for this article. Received March 15, 2016; revised version accepted April 26, 2016. The nuclear pore complex (NPC) is an intricate assembly membrane-curving module, the “proto-coatomer” (Devos of ∼30 different nucleoporins (Nups) that promotes regu- et al. 2004, 2006; Brohawn et al. 2008; Leksa and Schwartz lated transport of cargo to and from the nucleus (Wente 2010). Other components of the NPC, including the nu- and Rout 2010; Hoelz et al. 2011; Solmaz et al. 2011; Rai- clear basket and cytoplasmic filaments, are, for the most ces and D’Angelo 2012; Hurt and Beck 2015). Although part, also well conserved throughout eukaryotes (Field the nucleotide sequences of Nup genes have undergone et al. 2014). In contrast, the transmembrane (TM) com- significant evolutionary changes, the structure of the ponents of the NPC are often lineage-restricted and NPC has remained remarkably well conserved, with es- have undergone dramatic changes from yeast to humans sentially no change in protein organization occurring after (Neumann et al. 2010; Field et al. 2014). This is best ex- the appearance of the last eukaryotic common ancestor emplified by the recent appearance of Pom121, which (LECA) (Devos et al. 2004, 2006; Alber et al. 2007; Bro- emerged in vertebrates, where it has an essential role in in- hawn et al. 2008; DeGrasse et al. 2009). In particular, terphase NPC assembly (Doucet et al. 2010; Dultz and the NPC scaffold Nups, composed of the Nup107/160 Ellenberg 2010; Funakoshi et al. 2011; Talamas and Het- and Nup93/205 complexes, typically contain α-solenoid zer 2011; Field et al. 2014). and β-propeller domains that share strong structural sim- Although the composition of the NPC is highly con- ilarities to proteins that coat transport vesicles (Devos served, the functional repertoire of many Nups has ex- et al. 2004, 2006; Alber et al. 2007; Brohawn et al. 2008). panded throughout evolutionary history. One possible Based on such similarities, the proto-coatomer hypothesis driver of this functional diversity might be the NPC’s re- proposed that NPCs and clathrin, COPI, and COPII vesicle markable ability to act as a scaffold for protein assemblies coats share a common evolutionary origin in an early involved in diverse cellular processes, including the re- gulation of the cell cycle, DNA damage response, and transcription regulation (Raices and D’Angelo 2012; Corresponding author: [email protected] Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.280941.116. Free- © 2016 Franks et al. This article, published in Genes & Development,is ly available online through the Genes & Development Open Access available under a Creative Commons License (Attribution 4.0 Internation- option. al), as described at http://creativecommons.org/licenses/by/4.0/. GENES & DEVELOPMENT 30:1–17 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/16; www.genesdev.org 1 Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Franks et al. Burns and Wente 2014; Ptak et al. 2014; Ibarra and Hetzer reducing the adaptive capacity of the NPC (Orr 2000). 2015). One potential limitation for the NPC in regulating Gene duplication has been proposed as one mechanism processes such as transcription is the strict localization that can relieve the deleterious effects of such antagonis- of Nups to the NPC at the nuclear envelope (NE), which tic pleiotropy of functions under certain conditions (Guil- limits the number of genes that can be regulated to those laume and Otto 2012). However, the possibility of such that are in close proximity to the nuclear periphery. For subfunctionalization in the NPC has not been previously example, in yeast, gene regulation by the NPC is most explored. likely confined to a small subset of genes that are targeted Here, we identify a variant of the TM Nup gene to active transcriptional regions around NPCs to promote POM121 that produces a soluble (i.e., non-membrane- gene induction or those that are organized in gene loops, bound) form of Pom121 (sPom121) that lacks its TM which stimulate rapid transcriptional reinitiation of genes domain and is no longer incorporated into the NPC. In following a period of suppression (Brickner and Walter hominoids, the sPom121 transcript is expressed from an 2004; Casolari et al. 2004; O’Sullivan et al. 2004; Cabal alternative transcriptional start site that arose from a ge- et al. 2006; Taddei et al. 2006; Tan-Wong et al. 2009; Brick- nomic rearrangement. This novel isoform includes new ner and Brickner 2011). Thus, in order to increase the 5′ untranslated region (UTR) exons and bypasses the ca- number of transcriptional targets that can potentially be nonical TM-coding exon to encode an N-terminally trun- regulated by Nups, it would be necessary to uncouple cated form of Pom121. Functionally, sPom121 and Nup98 the specific functions of Nups in NPC-mediated transport cobind specific gene promoters to regulate transcription from those in gene regulation. Consistent with such a in human cells. Thus, sPom121 represents the first vali- notion, previous research in human cells demonstrated dated example of an NPC component that has eschewed that a subset of peripheral Nups can move on and off hu- its role in nucleo–cytoplasmic transport to specialize in man NPCs, raising the possibility that Nups’ influence an unrelated process; namely, gene regulation. In addition, on gene expression could extend beyond genomic regions we show that sPom121 can promote retention of Nup107/ associated with the NE (Rabut et al. 2004). Supporting 160 complexes in the nucleoplasm during NPC forma- this hypothesis, the dynamic movement of a subset of tion, suggesting that the evolution of sPom121 brought Nups, including Nup50, Nup98, and Nup153, was slowed about dramatic functional expansion of other scaffold in the presence of transcriptional inhibitory drugs, sug- Nups in hominoid cells. gesting a role for Nup98 and potentially other Nups in the regulation of transcription (Griffis et al. 2002, 2004; Buchwalter et al. 2014). A breakthrough in our under- Results standing of the function of mobile Nups came from Alternative transcription initiation produces studies in Drosophila and mammalian cells, which deter- a sPom121 isoform in humans mined that Nup98 and several other peripheral Nups such as Nup50, Nup62, and Nup153 can detach from the NPC, While investigating expressed sequence tags (ESTs) for bind to intranuclear promoters distal to the NE, and affect human Pom121 transcripts, we noticed, consistent with regulation of adjacent genes (Capelson et al. 2010; Kal- previous reports (Funakoshi et al. 2007), that there is an verda and Fornerod 2010; Liang et al. 2013). Although abundance of sequences that contain a noncanonical the mechanism of Nup98-mediated gene regulation in 5′ UTR sequence and lack the TM-coding sequence of the nucleoplasm is yet to be determined in detail, recent Pom121 (Fig. 1A, “sPom121 isoform”). These noncanoni- evidence suggests that Nup98 interacts with CBP/p300 cal transcripts, here called the sPom121 mRNA, are pre- and MBD-R2/NSL chromatin-modifying complexes in hu- dicted to initiate at an alternative transcription start site man and Drosophila cells, respectively, suggesting a pos- ∼40 kb upstream of the TM-encoding canonical first sible mechanism