[ { "id": "authors:khdd7-31b07", "collection": "authors", "collection_id": "khdd7-31b07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170522-112731942", "type": "article", "title": "Histone-Binding of DPF2 Mediates Its Repressive Role in Myeloid Differentiation", "author": [ { "family_name": "Huber", "given_name": "Ferdinand M.", "orcid": "0000-0001-8647-6971", "clpid": "Huber-Ferdinand-M" }, { "family_name": "Greenblatt", "given_name": "Sarah M.", "clpid": "Greenblatt-Sarah-M" }, { "family_name": "Davenport", "given_name": "Andrew M.", "clpid": "Davenport-Andrew-M" }, { "family_name": "Martinez", "given_name": "Concepcion", "clpid": "Martinez-Concepcion" }, { "family_name": "Xu", "given_name": "Ye", "clpid": "Xu-Ye" }, { "family_name": "Vu", "given_name": "Ly P.", "clpid": "Vu-Ly-P" }, { "family_name": "Nimer", "given_name": "Stephen D.", "clpid": "Nimer-Stephen-D" }, { "family_name": "Hoelz", "given_name": "Andr\u00e9", "orcid": "0000-0003-1726-0127", "clpid": "Hoelz-A" } ], "abstract": "Double plant homeodomain finger 2 (DPF2) is a highly evolutionarily conserved member of the d4 protein family that is ubiquitously expressed in human tissues and was recently shown to inhibit the myeloid differentiation of hematopoietic stem/progenitor and acute myelogenous leukemia cells. Here, we present the crystal structure of the tandem plant homeodomain finger domain of human DPF2 at 1.6-\u00c5 resolution. We show that DPF2 interacts with the acetylated tails of both histones 3 and 4 via bipartite binding pockets on the DPF2 surface. Blocking these interactions through targeted mutagenesis of DPF2 abolishes its recruitment to target chromatin regions as well as its ability to prevent myeloid differentiation in vivo. Our findings suggest that the histone binding of DPF2 plays an important regulatory role in the transcriptional program that drives myeloid differentiation.", "doi": "10.1073/pnas.1700328114", "pmcid": "PMC5468650", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2017-06-06", "series_number": "23", "volume": "114", "issue": "23", "pages": "6016-6021" }, { "id": "authors:0ddes-yya74", "collection": "authors", "collection_id": "0ddes-yya74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-150533638", "type": "article", "title": "Architecture of the symmetric core of the nuclear pore", "author": [ { "family_name": "Lin", "given_name": "Daniel H.", "clpid": "Lin-Daniel-H" }, { "family_name": "Stuwe", "given_name": "Tobias", "clpid": "Stuwe-Tobias" }, { "family_name": "Schilbach", "given_name": "Sandra", "orcid": "0000-0001-9071-8515", "clpid": "Schilbach-Sandra" }, { "family_name": "Rundlet", "given_name": "Emily J.", "clpid": "Rundlet-Emily-J" }, { "family_name": "Perriches", "given_name": "Thibaud", "clpid": "Perriches-Thibaud" }, { "family_name": "Mobbs", "given_name": "George", "orcid": "0000-0003-2405-3345", "clpid": "Mobbs-George-W" }, { "family_name": "Fan", "given_name": "Yanbin", "clpid": "Fan-Yanbin" }, { "family_name": "Thierbach", "given_name": "Karsten", "clpid": "Thierbach-Karsten" }, { "family_name": "Huber", "given_name": "Ferdinand M.", "orcid": "0000-0001-8647-6971", "clpid": "Huber-Ferdinand-M" }, { "family_name": "Collins", "given_name": "Leslie N.", "clpid": "Collins-Leslie-N" }, { "family_name": "Davenport", "given_name": "Andrew M.", "clpid": "Davenport-Andrew-M" }, { "family_name": "Jeon", "given_name": "Young E.", "clpid": "Jeon-Young-E" }, { "family_name": "Hoelz", "given_name": "Andr\u00e9", "orcid": "0000-0003-1726-0127", "clpid": "Hoelz-A" } ], "abstract": "INTRODUCTION: The nuclear pore complex (NPC) is the primary gateway for the transport of macromolecules between the nucleus and cytoplasm, serving as both a critical mediator and regulator of gene expression. NPCs are very large (~120 MDa) macromolecular machines embedded in the nuclear envelope, each containing ~1000 protein subunits, termed nucleoporins. Despite substantial progress in visualizing the overall shape of the NPC by means of cryoelectron tomography (cryo-ET) and in determining atomic-resolution crystal structures of nucleoporins, the molecular architecture of the assembled NPC has thus far remained poorly understood, hindering the design of mechanistic studies that could investigate its many roles in cell biology. \n\nRATIONALE: Existing cryo-ET reconstructions of the NPC are too low in resolution to allow for de novo structure determination of the NPC or unbiased docking of nucleoporin fragment crystal structures. We sought to bridge this resolution gap by first defining the interaction network of the NPC, focusing on the evolutionarily conserved symmetric core. We developed protocols to reconstitute NPC protomers from purified recombinant proteins, which enabled the generation of a high-resolution biochemical interaction map of the NPC symmetric core. We next determined high-resolution crystal structures of key nucleoporin interactions, providing spatial restraints for their relative orientation. By superposing crystal structures that overlapped in sequence, we generated accurate full-length structures of the large scaffold nucleoporins. Lastly, we used sequential unbiased searches, supported by the biochemical data, to place the nucleoporin crystal structures into a previously determined cryo-ET reconstruction of the intact human NPC, thus generating a composite structure of the entire NPC symmetric core. \n\nRESULTS: Our analysis revealed that the inner and outer rings of the NPC use disparate mechanisms of interaction. Whereas the structured coat nucleoporins of the outer ring form extensive surface contacts, the scaffold proteins of the inner ring are bridged by flexible sequences in linker nucleoporins. Our composite structure revealed a defined spoke architecture in which each of the eight spokes spans the nuclear envelope, with limited cross-spoke interactions. Most nucleoporins are present in 32 copies, with the exceptions of Nup170 and Nup188, which are present in 48 and 16 copies, respectively. Lastly, we observed the arrangement of the channel nucleoporins, which orient their N termini into two 16-membered rings, thus ensuring that their N-terminal FG repeats project evenly into the central transport channel. \n\nCONCLUSION: Our composite structure of the NPC symmetric core can be used as a platform for the rational design of experiments to investigate NPC structure and function. Each nucleoporin occupies multiple distinct biochemical environments, explaining how such a large macromolecular complex can be assembled from a relatively small number of genes. Our integrated, bottom-up approach provides a paradigm for the biochemical and structural characterization of similarly large biological mega-assemblies.", "doi": "10.1126/science.aaf1015", "pmcid": "PMC5207208", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2016-04-15", "series_number": "6283", "volume": "352", "issue": "6283", "pages": "Art. No. aaf1015" } ]