{"entity": "researcher", "timestamp": "2026-07-17T07:56:18.156Z", "family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "affiliations": ["Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc"}}, "publications": [{"entity": "publication", "iuid": "0f085fc75bcd4488adc4980f0630677e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f085fc75bcd4488adc4980f0630677e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f085fc75bcd4488adc4980f0630677e"}}, "title": "Hop stunt viroid infection induces heterochromatin reorganization.", "authors": [{"family": "Marquez-Molins", "given": "Joan", "initials": "J", "orcid": "0000-0002-6487-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/f889dd71d2eb4801aa8293663ec7b52f.json"}}, {"family": "Cheng", "given": "Jinping", "initials": "J", "orcid": "0000-0003-0749-7649", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ac4edf8f9f241ff8fe4fe3b7c6f8dd4.json"}}, {"family": "Corell-Sierra", "given": "Julia", "initials": "J", "orcid": "0000-0003-0751-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff29c1ec8a9a43378a783be1156ad4f7.json"}}, {"family": "Juarez-Gonzalez", "given": "Vasti Thamara", "initials": "VT", "orcid": "0000-0002-2631-8928", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a20b82bd644482bdf3484d338aac95.json"}}, {"family": "Villalba-Bermell", "given": "Pascual", "initials": "P", "orcid": "0000-0001-6057-6755", "researcher": {"href": "https://publications.scilifelab.se/researcher/b286ffcf835f4582a676fe506dc4ed8d.json"}}, {"family": "Annacondia", "given": "Maria Luz", "initials": "ML", "orcid": "0000-0001-7998-8362", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4d89a422254e47a38fe438fe99bdaf.json"}}, {"family": "Gomez", "given": "Gustavo", "initials": "G", "orcid": "0000-0003-3715-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/157cf3e864e5415886f9cb9d7f9544c1.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "243", "issue": "6", "pages": "2351-2367", "issn-l": "0028-646X"}, "abstract": "Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.", "doi": "10.1111/nph.19986", "pmid": "39030826", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-25T10:27:40.991Z", "modified": "2025-02-28T14:20:31.508Z"}, {"entity": "publication", "iuid": "90262d7622894dd583b0207a75b665a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90262d7622894dd583b0207a75b665a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90262d7622894dd583b0207a75b665a6"}}, "title": "Accumulation dynamics of ARGONAUTE proteins during meiosis in Arabidopsis.", "authors": [{"family": "Oliver", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-5231-7910", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fdb426c5e2e48e985eb8939a1c40d6e.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Plant Reprod", "issn": "2194-7961", "volume": "35", "issue": "2", "pages": "153-160", "issn-l": "2194-7953"}, "abstract": "Meiosis is a specialized cell division that is key for reproduction and genetic diversity in sexually reproducing plants. Recently, different RNA silencing pathways have been proposed to carry a specific activity during meiosis, but the pathways involved during this process remain unclear. Here, we explored the subcellular localization of different ARGONAUTE (AGO) proteins, the main effectors of RNA silencing, during male meiosis in Arabidopsis thaliana using immunolocalizations with commercially available antibodies. We detected the presence of AGO proteins associated with posttranscriptional gene silencing (AGO1, 2, and 5) in the cytoplasm and the nucleus, while AGOs associated with transcriptional gene silencing (AGO4 and 9) localized exclusively in the nucleus. These results indicate that the localization of different AGOs correlates with their predicted roles at the transcriptional and posttranscriptional levels and provide an overview of their timing and potential role during meiosis.", "doi": "10.1007/s00497-021-00434-z", "pmid": "34812935", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00497-021-00434-z"}, {"db": "pmc", "key": "PMC9110482"}], "notes": [], "created": "2022-11-09T15:46:54.059Z", "modified": "2024-01-16T13:48:36.366Z"}, {"entity": "publication", "iuid": "70304e2e74c14f8c98b28d736df71cf4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70304e2e74c14f8c98b28d736df71cf4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70304e2e74c14f8c98b28d736df71cf4"}}, "title": "The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.", "authors": [{"family": "Oliver", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-5231-7910", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fdb426c5e2e48e985eb8939a1c40d6e.json"}}, {"family": "Annacondia", "given": "Maria Luz", "initials": "ML", "orcid": "0000-0001-7998-8362", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4d89a422254e47a38fe438fe99bdaf.json"}}, {"family": "Wang", "given": "Zhenxing", "initials": "Z", "orcid": "0000-0001-5102-7121", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b6c9f88c65d4fbc94da6d7598102335.json"}}, {"family": "Jullien", "given": "Pauline E", "initials": "PE", "orcid": "0000-0003-1212-3246", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a97f95d2f1046b3a7027dedf5a31082.json"}}, {"family": "Slotkin", "given": "R Keith", "initials": "RK", "orcid": "0000-0001-9582-3533", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac639e0390ef4140a566e5cbbf65084a.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}], "type": "journal article", "published": "2022-02-03", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "34", "issue": "2", "pages": "784-801", "issn-l": "1040-4651"}, "abstract": "Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.", "doi": "10.1093/plcell/koab280", "pmid": "34755870", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8824631"}, {"db": "pii", "key": "6424912"}], "notes": [], "created": "2022-11-29T09:51:29.116Z", "modified": "2022-11-29T09:51:29.270Z"}, {"entity": "publication", "iuid": "2b6302172b5c4073976116e40f945d60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b6302172b5c4073976116e40f945d60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b6302172b5c4073976116e40f945d60"}}, "title": "Polymerase IV Plays a Crucial Role in Pollen Development in Capsella.", "authors": [{"family": "Wang", "given": "Zhenxing", "initials": "Z", "orcid": "0000-0001-5102-7121", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b6c9f88c65d4fbc94da6d7598102335.json"}}, {"family": "Butel", "given": "Nicolas", "initials": "N", "orcid": "0000-0003-2484-4980", "researcher": {"href": "https://publications.scilifelab.se/researcher/f05a8316c3504f84abcc8cc66e770879.json"}}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "Borges", "given": "Filipe", "initials": "F", "orcid": "0000-0002-7388-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/08f47b282fc04126bb3359ec05ba9d02.json"}}, {"family": "Yi", "given": "Jun", "initials": "J", "orcid": "0000-0001-5539-0016", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3fd9fa6dfce4a76996f52f7a8611b87.json"}}, {"family": "Martienssen", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-1285-9608", "researcher": {"href": "https://publications.scilifelab.se/researcher/d40eed1e991b4eb08d5756886f50da55.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Plant Cell", "issn": "1532-298X", "issn-l": "1040-4651", "volume": "32", "issue": "4", "pages": "950-966"}, "abstract": "In Arabidopsis (Arabidopsis thaliana), DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA transcripts. These transcripts are processed by DICER-LIKE3 into 24-nucleotide small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nucleotide epigenetically activated siRNAs, which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernible pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV, in the Brassicaceae species Capsella (Capsella rubella), caused postmeiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nucleotide and 24-nucleotide siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella compared with Arabidopsis, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.", "doi": "10.1105/tpc.19.00938", "pmid": "31988265", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "tpc.19.00938"}, {"db": "pmc", "key": "PMC7145478"}], "notes": [], "created": "2020-12-08T23:35:28.348Z", "modified": "2021-11-10T12:52:33.683Z"}, {"entity": "publication", "iuid": "bcb394512c2e411aa9ce831cde4aa7d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bcb394512c2e411aa9ce831cde4aa7d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bcb394512c2e411aa9ce831cde4aa7d9"}}, "title": "Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon.", "authors": [{"family": "Sanz-Carbonell", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1969-5557", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132a132afcd44ba909dbbb86df6b23a.json"}}, {"family": "Marques", "given": "Maria Carmen", "initials": "MC", "orcid": "0000-0001-8392-453X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5022479d8564ebb8f59739d5073deb7.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}, {"family": "Gomez", "given": "Gustavo", "initials": "G", "orcid": "0000-0003-3715-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/157cf3e864e5415886f9cb9d7f9544c1.json"}}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "RNA Biol", "issn": "1555-8584", "volume": "17", "issue": "2", "pages": "292-308", "issn-l": "1547-6286"}, "abstract": "miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.", "doi": "10.1080/15476286.2019.1697487", "pmid": "31766933", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6973316"}], "notes": [], "created": "2020-12-08T23:34:40.772Z", "modified": "2021-11-10T12:54:27.181Z"}]}