[{"keyword":["Developmental Biology","Genetics"],"language":[{"iso":"eng"}],"publication":"Genes & Development","oa_version":"Published Version","month":"11","main_file_link":[{"url":"https://doi.org/10.1101/gad.287417.116","open_access":"1"}],"status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","type":"journal_article","date_published":"2016-11-02T00:00:00Z","publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"oa":1,"quality_controlled":"1","page":"2253-2258","publisher":"Cold Spring Harbor Laboratory","article_type":"original","scopus_import":"1","_id":"11070","pmid":1,"issue":"20","author":[{"first_name":"Arkaitz","last_name":"Ibarra","full_name":"Ibarra, Arkaitz"},{"first_name":"Chris","last_name":"Benner","full_name":"Benner, Chris"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"last_name":"Cool","first_name":"Jonah","full_name":"Cool, Jonah"},{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"date_created":"2022-04-07T07:48:08Z","article_processing_charge":"No","publication_status":"published","intvolume":"        30","title":"Nucleoporin-mediated regulation of cell identity genes","volume":30,"extern":"1","year":"2016","citation":{"chicago":"Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2016. <a href=\"https://doi.org/10.1101/gad.287417.116\">https://doi.org/10.1101/gad.287417.116</a>.","ieee":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated regulation of cell identity genes,” <i>Genes &#38; Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.","ama":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation of cell identity genes. <i>Genes &#38; Development</i>. 2016;30(20):2253-2258. doi:<a href=\"https://doi.org/10.1101/gad.287417.116\">10.1101/gad.287417.116</a>","apa":"Ibarra, A., Benner, C., Tyagi, S., Cool, J., &#38; Hetzer, M. (2016). Nucleoporin-mediated regulation of cell identity genes. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.287417.116\">https://doi.org/10.1101/gad.287417.116</a>","ista":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated regulation of cell identity genes. Genes &#38; Development. 30(20), 2253–2258.","short":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes &#38; Development 30 (2016) 2253–2258.","mla":"Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” <i>Genes &#38; Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory, 2016, pp. 2253–58, doi:<a href=\"https://doi.org/10.1101/gad.287417.116\">10.1101/gad.287417.116</a>."},"date_updated":"2022-07-18T08:33:49Z","external_id":{"pmid":["27807035"]},"day":"02","doi":"10.1101/gad.287417.116","abstract":[{"lang":"eng","text":"The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate."}]},{"keyword":["Developmental Biology","Genetics"],"language":[{"iso":"eng"}],"month":"05","oa_version":"Published Version","publication":"Genes & Development","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","main_file_link":[{"url":"https://doi.org/10.1101/gad.280941.116","open_access":"1"}],"oa":1,"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"type":"journal_article","date_published":"2016-05-19T00:00:00Z","article_type":"original","publisher":"Cold Spring Harbor Laboratory","quality_controlled":"1","page":"1155-1171","intvolume":"        30","title":"Evolution of a transcriptional regulator from a transmembrane nucleoporin","article_processing_charge":"No","date_created":"2022-04-07T07:48:20Z","publication_status":"published","issue":"10","author":[{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"full_name":"Benner, Chris","last_name":"Benner","first_name":"Chris"},{"last_name":"Narvaiza","first_name":"Iñigo","full_name":"Narvaiza, Iñigo"},{"first_name":"Maria C.N.","last_name":"Marchetto","full_name":"Marchetto, Maria C.N."},{"full_name":"Young, Janet M.","last_name":"Young","first_name":"Janet M."},{"full_name":"Malik, Harmit S.","first_name":"Harmit S.","last_name":"Malik"},{"full_name":"Gage, Fred H.","last_name":"Gage","first_name":"Fred H."},{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"scopus_import":"1","_id":"11071","pmid":1,"extern":"1","volume":30,"abstract":[{"text":"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.","lang":"eng"}],"day":"19","doi":"10.1101/gad.280941.116","external_id":{"pmid":["27198230"]},"citation":{"apa":"Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M., Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from a transmembrane nucleoporin. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.280941.116\">https://doi.org/10.1101/gad.280941.116</a>","ama":"Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator from a transmembrane nucleoporin. <i>Genes &#38; Development</i>. 2016;30(10):1155-1171. doi:<a href=\"https://doi.org/10.1101/gad.280941.116\">10.1101/gad.280941.116</a>","chicago":"Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto, Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2016. <a href=\"https://doi.org/10.1101/gad.280941.116\">https://doi.org/10.1101/gad.280941.116</a>.","ieee":"T. M. Franks <i>et al.</i>, “Evolution of a transcriptional regulator from a transmembrane nucleoporin,” <i>Genes &#38; Development</i>, vol. 30, no. 10. Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.","mla":"Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” <i>Genes &#38; Development</i>, vol. 30, no. 10, Cold Spring Harbor Laboratory, 2016, pp. 1155–71, doi:<a href=\"https://doi.org/10.1101/gad.280941.116\">10.1101/gad.280941.116</a>.","short":"T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik, F.H. Gage, M. Hetzer, Genes &#38; Development 30 (2016) 1155–1171.","ista":"Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes &#38; Development. 30(10), 1155–1171."},"year":"2016","date_updated":"2022-07-18T08:33:50Z"},{"extern":"1","volume":29,"abstract":[{"lang":"eng","text":"Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation."}],"day":"01","doi":"10.1101/gad.256495.114","external_id":{"pmid":["25691464"]},"year":"2015","citation":{"mla":"Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control of Genome Functions.” <i>Genes &#38; Development</i>, vol. 29, no. 4, Cold Spring Harbor Laboratory, 2015, pp. 337–49, doi:<a href=\"https://doi.org/10.1101/gad.256495.114\">10.1101/gad.256495.114</a>.","short":"A. Ibarra, M. Hetzer, Genes &#38; Development 29 (2015) 337–349.","ista":"Ibarra A, Hetzer M. 2015. Nuclear pore proteins and the control of genome functions. Genes &#38; Development. 29(4), 337–349.","ama":"Ibarra A, Hetzer M. Nuclear pore proteins and the control of genome functions. <i>Genes &#38; Development</i>. 2015;29(4):337-349. doi:<a href=\"https://doi.org/10.1101/gad.256495.114\">10.1101/gad.256495.114</a>","apa":"Ibarra, A., &#38; Hetzer, M. (2015). Nuclear pore proteins and the control of genome functions. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.256495.114\">https://doi.org/10.1101/gad.256495.114</a>","chicago":"Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control of Genome Functions.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2015. <a href=\"https://doi.org/10.1101/gad.256495.114\">https://doi.org/10.1101/gad.256495.114</a>.","ieee":"A. Ibarra and M. Hetzer, “Nuclear pore proteins and the control of genome functions,” <i>Genes &#38; Development</i>, vol. 29, no. 4. Cold Spring Harbor Laboratory, pp. 337–349, 2015."},"date_updated":"2022-07-18T08:43:20Z","article_type":"original","publisher":"Cold Spring Harbor Laboratory","quality_controlled":"1","page":"337-349","intvolume":"        29","title":"Nuclear pore proteins and the control of genome functions","date_created":"2022-04-07T07:49:21Z","article_processing_charge":"No","publication_status":"published","issue":"4","author":[{"last_name":"Ibarra","first_name":"Arkaitz","full_name":"Ibarra, Arkaitz"},{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"scopus_import":"1","pmid":1,"_id":"11076","status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.256495.114"}],"oa":1,"publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"type":"journal_article","date_published":"2015-02-01T00:00:00Z","keyword":["Developmental Biology","Genetics"],"language":[{"iso":"eng"}],"month":"02","oa_version":"Published Version","publication":"Genes & Development"},{"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"oa":1,"date_published":"2015-06-16T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1101/gad.260919.115","open_access":"1"}],"status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"Published Version","month":"06","publication":"Genes & Development","language":[{"iso":"eng"}],"keyword":["Developmental Biology","Genetics"],"doi":"10.1101/gad.260919.115","day":"16","abstract":[{"text":"Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that mediate nuclear transport across the nuclear envelope. Recent evidence suggests that several Nups have additional roles in controlling the activation and silencing of developmental genes; however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the derepression of developmental genes and induction of early differentiation. This loss of stem cell identity is not associated with defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds around the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its target loci. Our results demonstrate a chromatin-associated role of Nup153 in maintaining stem cell pluripotency by functioning in mammalian epigenetic gene silencing.","lang":"eng"}],"date_updated":"2022-07-18T08:43:51Z","year":"2015","citation":{"apa":"Jacinto, F. V., Benner, C., &#38; Hetzer, M. (2015). The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.260919.115\">https://doi.org/10.1101/gad.260919.115</a>","ama":"Jacinto FV, Benner C, Hetzer M. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. <i>Genes &#38; Development</i>. 2015;29(12):1224-1238. doi:<a href=\"https://doi.org/10.1101/gad.260919.115\">10.1101/gad.260919.115</a>","chicago":"Jacinto, Filipe V., Chris Benner, and Martin Hetzer. “The Nucleoporin Nup153 Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2015. <a href=\"https://doi.org/10.1101/gad.260919.115\">https://doi.org/10.1101/gad.260919.115</a>.","ieee":"F. V. Jacinto, C. Benner, and M. Hetzer, “The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing,” <i>Genes &#38; Development</i>, vol. 29, no. 12. Cold Spring Harbor Laboratory, pp. 1224–1238, 2015.","short":"F.V. Jacinto, C. Benner, M. Hetzer, Genes &#38; Development 29 (2015) 1224–1238.","mla":"Jacinto, Filipe V., et al. “The Nucleoporin Nup153 Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” <i>Genes &#38; Development</i>, vol. 29, no. 12, Cold Spring Harbor Laboratory, 2015, pp. 1224–38, doi:<a href=\"https://doi.org/10.1101/gad.260919.115\">10.1101/gad.260919.115</a>.","ista":"Jacinto FV, Benner C, Hetzer M. 2015. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes &#38; Development. 29(12), 1224–1238."},"external_id":{"pmid":["26080816"]},"volume":29,"extern":"1","publication_status":"published","date_created":"2022-04-07T07:49:31Z","article_processing_charge":"No","title":"The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing","intvolume":"        29","_id":"11077","pmid":1,"scopus_import":"1","author":[{"full_name":"Jacinto, Filipe V.","first_name":"Filipe V.","last_name":"Jacinto"},{"full_name":"Benner, Chris","last_name":"Benner","first_name":"Chris"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"issue":"12","publisher":"Cold Spring Harbor Laboratory","article_type":"original","page":"1224-1238","quality_controlled":"1"},{"issue":"24","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"}],"scopus_import":"1","_id":"9532","pmid":1,"intvolume":"        29","title":"Evolution and function of genomic imprinting in plants","date_created":"2021-06-08T09:56:24Z","department":[{"_id":"DaZi"}],"article_processing_charge":"No","publication_status":"published","file_date_updated":"2021-06-08T09:55:10Z","quality_controlled":"1","page":"2517–2531","article_type":"review","publisher":"Cold Spring Harbor Laboratory Press","external_id":{"pmid":["26680300"]},"citation":{"chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>."},"year":"2015","date_updated":"2021-12-14T07:58:15Z","abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"day":"15","doi":"10.1101/gad.269902.115","ddc":["570"],"extern":"1","volume":29,"has_accepted_license":"1","publication":"Genes and Development","month":"12","oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2015-12-15T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"oa":1,"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","file":[{"date_created":"2021-06-08T09:55:10Z","checksum":"086a88cfca4677646da26ed960cb02e9","file_size":1116846,"date_updated":"2021-06-08T09:55:10Z","content_type":"application/pdf","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","access_level":"open_access","success":1,"relation":"main_file","file_id":"9533","creator":"asandaue"}]}]