[{"date_published":"2026-05-09T00:00:00Z","article_processing_charge":"Yes (via OA deal)","publisher":"Elsevier","ddc":["570"],"year":"2026","article_number":"102483","external_id":{"arxiv":["2601.19681"]},"_id":"21983","author":[{"full_name":"Mascolo, Elia","id":"776a6ed0-a053-11f0-8635-80b95e0e0d53","last_name":"Mascolo","orcid":"0000-0003-2977-7844","first_name":"Elia"},{"last_name":"Körei","full_name":"Körei, Reka E","id":"50FDE43E-AA30-11E9-A72B-8A12E6697425","first_name":"Reka E"},{"last_name":"Herrera-Álvarez","full_name":"Herrera-Álvarez, Santiago","first_name":"Santiago"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"},{"full_name":"Crocker, Justin","last_name":"Crocker","first_name":"Justin"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"intvolume":"        99","volume":99,"month":"05","corr_author":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"CaGu"},{"_id":"GaTk"}],"doi":"10.1016/j.gde.2026.102483","day":"09","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.gde.2026.102483"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026.","ama":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. 2026;99. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>","apa":"Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>","mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99, 102483, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>.","short":"E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics &#38; Development 99 (2026).","chicago":"Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>.","ista":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics &#38; Development. 99, 102483."},"acknowledgement":"We thank Nick Barton and Noa Ottilie Borst for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.).","scopus_import":"1","article_type":"original","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps","OA_type":"hybrid","oa":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology."}],"publication":"Current Opinion in Genetics & Development","date_created":"2026-06-10T07:37:12Z","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"PlanS_conform":"1","type":"journal_article","date_updated":"2026-06-16T12:37:02Z"},{"scopus_import":"1","acknowledgement":"We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant 101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European Molecular Biology Laboratory (N.O.B., J.C.).","citation":{"apa":"Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102472\">https://doi.org/10.1016/j.gde.2026.102472</a>","ama":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current Opinion in Genetics and Development</i>. 2026;98. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102472\">10.1016/j.gde.2026.102472</a>","ieee":"E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,” <i>Current Opinion in Genetics and Development</i>, vol. 98. Elsevier, 2026.","ista":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 98, 102472.","short":"E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current Opinion in Genetics and Development 98 (2026).","mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” <i>Current Opinion in Genetics and Development</i>, vol. 98, 102472, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102472\">10.1016/j.gde.2026.102472</a>.","chicago":"Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102472\">https://doi.org/10.1016/j.gde.2026.102472</a>."},"status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.gde.2026.102472","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1016/j.gde.2026.102472","day":"15","publication_status":"epub_ahead","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"corr_author":"1","month":"04","date_updated":"2026-06-18T08:34:09Z","type":"journal_article","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"publication":"Current Opinion in Genetics and Development","date_created":"2026-04-26T22:01:46Z","abstract":[{"text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges.","lang":"eng"}],"oa":1,"OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges","OA_place":"publisher","article_type":"review","article_number":"102472","year":"2026","ddc":["570"],"publisher":"Elsevier","project":[{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"article_processing_charge":"Yes (via OA deal)","date_published":"2026-04-15T00:00:00Z","volume":98,"intvolume":"        98","author":[{"orcid":"0000-0003-2977-7844","first_name":"Elia","last_name":"Mascolo","full_name":"Mascolo, Elia","id":"776a6ed0-a053-11f0-8635-80b95e0e0d53"},{"first_name":"Reka E","id":"50FDE43E-AA30-11E9-A72B-8A12E6697425","full_name":"Körei, Reka E","last_name":"Körei"},{"first_name":"Noa O.","last_name":"Borst","full_name":"Borst, Noa O."},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Crocker","full_name":"Crocker, Justin","first_name":"Justin"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"_id":"21759"},{"scopus_import":"1","acknowledgement":"We wish to thank all members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. We apologize to colleagues whose work we could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the discussed topic is supported by ISTA institutional funds, an EMBO LTF (ALTF 994–2023) to F.P., FWF SFB F78 (10.55776/F78) to S.H., and FWF Cluster of Excellence COE16 (10.55776/COE16) to S.H.","status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.gde.2026.102487","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Varela Martínez I, Pipicelli F, Hippenmeyer S. 2026. Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics. Current Opinion in Genetics and Development. 99, 102487.","short":"I. Varela Martínez, F. Pipicelli, S. Hippenmeyer, Current Opinion in Genetics and Development 99 (2026).","chicago":"Varela Martínez, Irene, Fabrizia Pipicelli, and Simon Hippenmeyer. “Tracing Cell Lineages in the Developing Brain: Insights from Mosaic Analysis and Clone-Resolved Transcriptomics.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102487\">https://doi.org/10.1016/j.gde.2026.102487</a>.","mla":"Varela Martínez, Irene, et al. “Tracing Cell Lineages in the Developing Brain: Insights from Mosaic Analysis and Clone-Resolved Transcriptomics.” <i>Current Opinion in Genetics and Development</i>, vol. 99, 102487, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102487\">10.1016/j.gde.2026.102487</a>.","ama":"Varela Martínez I, Pipicelli F, Hippenmeyer S. Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics. <i>Current Opinion in Genetics and Development</i>. 2026;99. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102487\">10.1016/j.gde.2026.102487</a>","apa":"Varela Martínez, I., Pipicelli, F., &#38; Hippenmeyer, S. (2026). Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102487\">https://doi.org/10.1016/j.gde.2026.102487</a>","ieee":"I. Varela Martínez, F. Pipicelli, and S. Hippenmeyer, “Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics,” <i>Current Opinion in Genetics and Development</i>, vol. 99. Elsevier, 2026."},"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","corr_author":"1","month":"05","publication_status":"epub_ahead","department":[{"_id":"SiHi"}],"day":"29","doi":"10.1016/j.gde.2026.102487","PlanS_conform":"1","type":"journal_article","date_updated":"2026-06-08T07:42:16Z","abstract":[{"lang":"eng","text":"The cerebral cortex comprises diverse neuron and glial cell types generated by radial glial progenitors (RGPs) during development. Although RGPs broadly differentiate according to temporally and spatially regulated molecular logics, the lineage hierarchies linking individual progenitors to defined cell (sub)types are not well understood. Clone-resolved transcriptomics, combining molecular barcoding and single-cell RNA sequencing, allow high-resolution lineage tracing at the single-clone/cell level across different species and models. In this mini-review, we synthesize recent advances in this field, uncovering unexpected lineage relationships in the developing brain, with a particular focus on the cerebral cortex. We further highlight new insights into species-specific differences in the developmental programs generating cell-type diversity, linking changes in clonal architecture to lineage diversification during cortical evolution."}],"publication":"Current Opinion in Genetics and Development","date_created":"2026-06-07T22:01:35Z","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"has_accepted_license":"1","oa":1,"article_type":"original","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics","OA_type":"hybrid","year":"2026","article_number":"102487","project":[{"name":"Role of cell lineage in generating cell-type diversity in developing neocortex’","grant_number":"ALTF 994-2023","_id":"7c084566-9f16-11ee-852c-c88a1dbbf1cf"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"publisher":"Elsevier","ddc":["570"],"article_processing_charge":"Yes (via OA deal)","pmid":1,"date_published":"2026-05-29T00:00:00Z","volume":99,"intvolume":"        99","author":[{"id":"a69b5985-8829-11f0-8fc2-d0af58f64471","full_name":"Varela Martínez, Irene","last_name":"Varela Martínez","first_name":"Irene"},{"first_name":"Fabrizia","last_name":"Pipicelli","id":"649134fd-d012-11ed-8f82-db1e5050f9ba","full_name":"Pipicelli, Fabrizia"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"external_id":{"pmid":["42214837"]},"_id":"21948"},{"article_processing_charge":"Yes (via OA deal)","date_published":"2023-08-01T00:00:00Z","pmid":1,"year":"2023","article_number":"102087","publisher":"Elsevier","ddc":["570"],"isi":1,"author":[{"first_name":"Elizabeth","last_name":"Hollwey","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"last_name":"Howard","full_name":"Howard, Martin","first_name":"Martin"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"_id":"13965","issue":"8","external_id":{"pmid":["37441873"],"isi":["001047020200001"]},"volume":81,"intvolume":"        81","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","month":"08","corr_author":"1","department":[{"_id":"DaZi"}],"day":"01","doi":"10.1016/j.gde.2023.102087","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"a294cd9506b80ed6ef218ef44ed32765","file_id":"13980","date_created":"2023-08-07T08:32:26Z","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","date_updated":"2023-08-07T08:32:26Z","file_size":2568632,"creator":"dernst"}],"citation":{"ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 81(8), 102087.","chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.gde.2023.102087\">https://doi.org/10.1016/j.gde.2023.102087</a>.","mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion in Genetics and Development</i>, vol. 81, no. 8, 102087, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.gde.2023.102087\">10.1016/j.gde.2023.102087</a>.","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023).","apa":"Hollwey, E., Briffa, A., Howard, M., &#38; Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2023.102087\">https://doi.org/10.1016/j.gde.2023.102087</a>","ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion in Genetics and Development</i>. 2023;81(8). doi:<a href=\"https://doi.org/10.1016/j.gde.2023.102087\">10.1016/j.gde.2023.102087</a>","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” <i>Current Opinion in Genetics and Development</i>, vol. 81, no. 8. Elsevier, 2023."},"oa":1,"has_accepted_license":"1","article_type":"original","title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-08-07T08:32:26Z","type":"journal_article","date_updated":"2024-10-09T21:06:16Z","abstract":[{"text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.","lang":"eng"}],"date_created":"2023-08-06T22:01:10Z","publication":"Current Opinion in Genetics and Development","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]}},{"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","related_material":{"record":[{"id":"8620","relation":"dissertation_contains","status":"public"}]},"corr_author":"1","month":"12","department":[{"_id":"GaNo"}],"publication_status":"published","doi":"10.1016/j.gde.2020.06.004","ec_funded":1,"day":"01","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_updated":"2020-07-22T06:47:45Z","file_size":1381545,"creator":"dernst","date_created":"2020-07-22T06:47:45Z","file_id":"8146","file_name":"2020_CurrentOpGenetics_Basilico.pdf","content_type":"application/pdf","relation":"main_file","success":1,"access_level":"open_access"}],"citation":{"ama":"Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. <i>Current Opinion in Genetics and Development</i>. 2020;65(12):126-137. doi:<a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">10.1016/j.gde.2020.06.004</a>","apa":"Basilico, B., Morandell, J., &#38; Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">https://doi.org/10.1016/j.gde.2020.06.004</a>","ieee":"B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” <i>Current Opinion in Genetics and Development</i>, vol. 65, no. 12. Elsevier, pp. 126–137, 2020.","ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","chicago":"Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">https://doi.org/10.1016/j.gde.2020.06.004</a>.","short":"B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137.","mla":"Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” <i>Current Opinion in Genetics and Development</i>, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:<a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">10.1016/j.gde.2020.06.004</a>."},"has_accepted_license":"1","oa":1,"article_type":"original","title":"Molecular mechanisms for targeted ASD treatments","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-07-22T06:47:45Z","type":"journal_article","date_updated":"2026-06-24T22:31:01Z","abstract":[{"text":"The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.","lang":"eng"}],"publication":"Current Opinion in Genetics and Development","date_created":"2020-07-19T22:00:58Z","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"article_processing_charge":"Yes (via OA deal)","page":"126-137","date_published":"2020-12-01T00:00:00Z","pmid":1,"year":"2020","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","grant_number":"F7807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}],"publisher":"Elsevier","ddc":["570"],"author":[{"orcid":"0000-0003-1843-3173","first_name":"Bernadette","last_name":"Basilico","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","last_name":"Morandell"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"_id":"8131","issue":"12","external_id":{"isi":["000598918900019"],"pmid":["32659636"]},"volume":65,"intvolume":"        65"},{"scopus_import":"1","citation":{"apa":"Ötvös, K., &#38; Benková, E. (2017). Spatiotemporal mechanisms of root branching. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">https://doi.org/10.1016/j.gde.2017.03.010</a>","ama":"Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. <i>Current Opinion in Genetics &#38; Development</i>. 2017;45:82-89. doi:<a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">10.1016/j.gde.2017.03.010</a>","ieee":"K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 45. Elsevier, pp. 82–89, 2017.","ista":"Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics &#38; Development. 45, 82–89.","mla":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 45, Elsevier, 2017, pp. 82–89, doi:<a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">10.1016/j.gde.2017.03.010</a>.","chicago":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">https://doi.org/10.1016/j.gde.2017.03.010</a>.","short":"K. Ötvös, E. Benková, Current Opinion in Genetics &#38; Development 45 (2017) 82–89."},"file":[{"file_size":364133,"creator":"dernst","date_updated":"2019-04-17T08:00:36Z","file_name":"Otvos_Benkova_CurOpDevBiol_2017.pdf","file_id":"6336","date_created":"2019-04-17T08:00:36Z","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","oa_version":"Submitted Version","language":[{"iso":"eng"}],"quality_controlled":"1","day":"01","doi":"10.1016/j.gde.2017.03.010","department":[{"_id":"EvBe"}],"publication_status":"published","month":"08","date_updated":"2026-04-16T09:56:36Z","type":"journal_article","file_date_updated":"2019-04-17T08:00:36Z","publication_identifier":{"issn":["0959-437X"]},"publication":"Current Opinion in Genetics & Development","date_created":"2018-12-11T11:49:38Z","abstract":[{"text":"The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment.","lang":"eng"}],"oa":1,"has_accepted_license":"1","title":"Spatiotemporal mechanisms of root branching","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pubrep_id":"1017","year":"2017","ddc":["575"],"publisher":"Elsevier","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"page":"82 - 89","article_processing_charge":"No","pmid":1,"date_published":"2017-08-01T00:00:00Z","volume":45,"publist_id":"6394","intvolume":"        45","isi":1,"author":[{"full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","orcid":"0000-0002-5503-4983","first_name":"Krisztina"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"external_id":{"isi":["000404880400013"],"pmid":["28391060"]},"_id":"1004"},{"status":"public","citation":{"ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. 2012;22(2):132-138. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>","apa":"Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>.","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138."},"scopus_import":"1","month":"04","publication_status":"published","department":[{"_id":"DaZi"}],"doi":"10.1016/j.gde.2012.01.007","oa_version":"None","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory."}],"publication":"Current Opinion in Genetics and Development","date_created":"2021-06-08T08:58:52Z","publication_identifier":{"issn":["0959-437X"]},"type":"journal_article","date_updated":"2021-12-14T08:32:38Z","article_type":"review","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","publisher":"Elsevier","year":"2012","date_published":"2012-04-01T00:00:00Z","pmid":1,"article_processing_charge":"No","page":"132-138","intvolume":"        22","volume":22,"external_id":{"pmid":["22336527"]},"_id":"9528","issue":"2","extern":"1","author":[{"last_name":"Huff","full_name":"Huff, Jason T.","first_name":"Jason T."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649"}]},{"volume":18,"publist_id":"1918","intvolume":"        18","author":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"},{"full_name":"Solnica Krezel, Lilianna","last_name":"Solnica Krezel","first_name":"Lilianna"}],"extern":"1","_id":"4198","external_id":{"pmid":["18721878"]},"issue":"4","year":"2008","publisher":"Elsevier","page":"311 - 316","article_processing_charge":"No","pmid":1,"date_published":"2008-01-01T00:00:00Z","date_updated":"2026-05-28T14:03:47Z","type":"journal_article","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"publication":"Current Opinion in Genetics & Development","date_created":"2018-12-11T12:07:32Z","abstract":[{"text":"Animal body plan arises during gastrulation and organogenesis by the coordination of inductive events and cell movements. Several signaling pathways, such as BMP, FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate specification during vertebrate embryogenesis. Growing evidence indicates that BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so through mechanisms distinct from those that specify cell fates. Moreover, pathways controlling cell movements can also indirectly influence cell fate specification by regulating dimensions and relative positions of interacting tissues. The current challenge is to delineate the molecular mechanisms via which the major signaling pathways regulate cell fate specification and movements, and how these two processes are coordinated to ensure normal development.","lang":"eng"}],"OA_type":"closed access","title":"Back and forth between cell fate specification and movement during vertebrate gastrulation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"review","citation":{"chicago":"Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">https://doi.org/10.1016/j.gde.2008.07.011</a>.","short":"C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics &#38; Development 18 (2008) 311–316.","mla":"Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 18, no. 4, Elsevier, 2008, pp. 311–16, doi:<a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">10.1016/j.gde.2008.07.011</a>.","ista":"Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics &#38; Development. 18(4), 311–316.","ieee":"C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate specification and movement during vertebrate gastrulation,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.","ama":"Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification and movement during vertebrate gastrulation. <i>Current Opinion in Genetics &#38; Development</i>. 2008;18(4):311-316. doi:<a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">10.1016/j.gde.2008.07.011</a>","apa":"Heisenberg, C.-P. J., &#38; Solnica Krezel, L. (2008). Back and forth between cell fate specification and movement during vertebrate gastrulation. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">https://doi.org/10.1016/j.gde.2008.07.011</a>"},"status":"public","oa_version":"None","language":[{"iso":"eng"}],"doi":"10.1016/j.gde.2008.07.011","day":"01","publication_status":"published","month":"01"},{"publisher":"Elsevier","year":"2005","pmid":1,"date_published":"2005-10-01T00:00:00Z","page":"557-562","article_processing_charge":"No","intvolume":"        15","volume":15,"extern":"1","_id":"9529","issue":"5","external_id":{"pmid":["16085410"]},"author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"citation":{"apa":"Zilberman, D., &#38; Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: Selective silence. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">https://doi.org/10.1016/j.gde.2005.07.002</a>","ama":"Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence. <i>Current Opinion in Genetics and Development</i>. 2005;15(5):557-562. doi:<a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">10.1016/j.gde.2005.07.002</a>","ieee":"D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.","ista":"Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.","short":"D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">https://doi.org/10.1016/j.gde.2005.07.002</a>.","mla":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5, Elsevier, 2005, pp. 557–62, doi:<a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">10.1016/j.gde.2005.07.002</a>."},"status":"public","scopus_import":"1","department":[{"_id":"DaZi"}],"publication_status":"published","doi":"10.1016/j.gde.2005.07.002","month":"10","language":[{"iso":"eng"}],"oa_version":"None","quality_controlled":"1","date_created":"2021-06-08T09:05:56Z","publication":"Current Opinion in Genetics and Development","publication_identifier":{"issn":["0959-437X"]},"abstract":[{"lang":"eng","text":"Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes."}],"type":"journal_article","date_updated":"2021-12-14T09:13:13Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Epigenetic inheritance in Arabidopsis: Selective silence","article_type":"review"}]