Paul Grini

• Zhang, Yupeng; Fan, Guangxun; Toivainen, Tuomas; Tengs, Torstein; Yakovlev, Igor & Krokene, Paal [Show all 9 contributors for this article] (2023). Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes. Horticulture Research. ISSN 2662-6810. 10(9), p. 1–15. doi: 10.1093/hr/uhad156. Full text in Research Archive Show summary

  Plants must adapt with increasing speed to global warming to maintain their fitness. One rapid adaptation mechanism is epigenetic memory, which may provide organisms sufficient time to adapt to climate change. We studied how the perennial Fragaria vesca adapted to warmer temperatures (28°C vs. 18°C) over three asexual generations. Differences in flowering time, stolon number, and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment. Induced methylome changes differed between the four ecotypes from Norway, Iceland, Italy, and Spain, but shared methylome responses were also identified. Most differentially methylated regions (DMRs) occurred in the CHG context, and most CHG and CHH DMRs were hypermethylated at the warmer temperature. In eight CHG DMR peaks, a highly similar methylation pattern could be observed between ecotypes. On average, 13% of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression. We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. Furthermore, we observed a negative correlation with gene expression when repetitive elements were found near (±2 kb) or inside genes. In conclusion, lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns. Both shared methylation patterns and transcriptome differences between F. vesca accessions were observed, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.

• Bjerkan, Katrine Nergård; Alling, Renate; Myking, Ida Velle; Brysting, Anne Krag & Grini, Paul (2023). Genetic and environmental manipulation of Arabidopsis hybridization barriers uncovers antagonistic functions in endosperm cellularization. Frontiers in Plant Science. ISSN 1664-462X. 14, p. 1–16. doi: 10.3389/fpls.2023.1229060. Full text in Research Archive
• Bramsiepe, Jonathan; Krabberød, Anders Kristian; Bjerkan, Katrine Nergård; Alling, Renate; Nielsen, Ida & Hornslien, Karina Stensland [Show all 9 contributors for this article] (2023). Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. The Plant Journal. ISSN 0960-7412. 116(3), p. 942–961. doi: 10.1111/tpj.16401. Full text in Research Archive
• Zhang, Yupeng; Toivainen, Tuomas; Mackenzie, Kathryn; Yakovlev, Igor; Krokene, Paal & Hytönen, Timo [Show all 8 contributors for this article] (2023). Methylome, transcriptome, and phenotype changes induced by temperature conditions experienced during sexual reproduction in Fragaria vesca. Physiologia Plantarum : An International Journal for Plant Biology. ISSN 0031-9317. 175(4). doi: 10.1111/ppl.13963. Full text in Research Archive Show summary

  Temperature conditions experienced during embryogenesis and seed development may induce epigenetic changes that increase phenotypic variation in plants. Here we investigate if embryogenesis and seed development at two different temperatures (28 vs. 18°C) result in lasting phenotypic effects and DNA methylation changes in woodland strawberry (Fragaria vesca). Using five European ecotypes from Spain (ES12), Iceland (ICE2), Italy (IT4), and Norway (NOR2 and NOR29), we found statistically significant differences between plants from seeds produced at 18 or 28°C in three of four phenotypic features investigated under common garden conditions. This indicates the establishment of a temperature-induced epigenetic memory-like response during embryogenesis and seed development. The memory effect was significant in two ecotypes: in NOR2 flowering time, number of growth points and petiole length were affected, and in ES12 number of growth points was affected. This indicates that genetic differences between ecotypes in their epigenetic machinery, or other allelic differences, impact this type of plasticity. We observed statistically significant differences between ecotypes in DNA methylation marks in repetitive elements, pseudogenes, and genic elements. Leaf transcriptomes were also affected by embryonic temperature in an ecotype-specific manner. Although we observed significant and lasting phenotypic change in at least some ecotypes, there was considerable variation in DNA methylation between individual plants within each temperature treatment. This within-treatment variability in DNA methylation marks in F. vesca progeny may partly be a result of allelic redistribution from recombination during meiosis and subsequent epigenetic reprogramming during embryogenesis.

• Zhang, Yupeng; Viejo, Marcos; Yakovlev, Igor; Tengs, Torstein; Krokene, Paal & Hytönen, Timo [Show all 8 contributors for this article] (2023). Major transcriptomic differences are induced by warmer temperature conditions experienced during asexual and sexual reproduction in Fragaria vesca ecotypes. Frontiers in Plant Science. ISSN 1664-462X. 14, p. 1–16. doi: 10.3389/fpls.2023.1213311. Full text in Research Archive Show summary

  A major challenge for plants in a rapidly changing climate is to adapt to rising temperatures. Some plants adapt to temperature conditions by generating an epigenetic memory that can be transmitted both meiotically and mitotically. Such epigenetic memories may increase phenotypic variation to global warming and provide time for adaptation to occur through classical genetic selection. The goal of this study was to understand how warmer temperature conditions experienced during sexual and asexual reproduction affect the transcriptomes of different strawberry (Fragaria vesca) ecotypes. We let four European F. vesca ecotypes reproduce at two contrasting temperatures (18 and 28°C), either asexually through stolon formation for several generations, or sexually by seeds (achenes). We then analyzed the transcriptome of unfolding leaves, with emphasis on differential expression of genes belonging to the epigenetic machinery. For asexually reproduced plants we found a general transcriptomic response to temperature conditions but for sexually reproduced plants we found less significant responses. We predicted several splicing isoforms for important genes (e.g. a SOC1, LHY, and SVP homolog), and found significantly more differentially presented splicing event variants following asexual vs. sexual reproduction. This difference could be due to the stochastic character of recombination during meiosis or to differential creation or erasure of epigenetic marks during embryogenesis and seed development. Strikingly, very few differentially expressed genes were shared between ecotypes, perhaps because ecotypes differ greatly both genetically and epigenetically. Genes related to the epigenetic machinery were predominantly upregulated at 28°C during asexual reproduction but downregulated after sexual reproduction, indicating that temperature-induced change affects the epigenetic machinery differently during the two types of reproduction.

• van Ekelenburg, Yuri Stephan; Hornslien, Karina Stensland; Hautegem, Tom Van; Fendrych, Matyáš; Van Isterdael, Gert & Bjerkan, Katrine Nergård [Show all 9 contributors for this article] (2022). Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm. Plant Physiology. ISSN 0032-0889. 191(2), p. 986–1001. doi: 10.1093/plphys/kiac520. Full text in Research Archive Show summary

  Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.

• Davik, Jahn; Wilson, Robert Charles; Njah, Relindis Ghai; Grini, Paul Eivind; Randall, Stephen K. & Alsheikh, Muath K [Show all 7 contributors for this article] (2021). Genetic mapping and identification of a QTL determining tolerance to freezing stress in Fragaria vesca L. PLOS ONE. ISSN 1932-6203. 16(5). doi: 10.1371/journal.pone.0248089. Full text in Research Archive Show summary

  Extreme cold and frost cause significant stress to plants which can potentially be lethal. Low temperature freezing stress can cause significant and irreversible damage to plant cells and can induce physiological and metabolic changes that impact on growth and development. Low temperatures cause physiological responses including winter dormancy and autumn cold hardening in strawberry (Fragaria) species, and some diploid F. vesca accessions have been shown to have adapted to low-temperature stresses. To study the genetics of freezing tolerance, a F. vesca mapping population of 143 seedlings segregating for differential responses to freezing stress was raised. The progeny was mapped using ‘Genotyping-by-Sequencing’ and a linkage map of 2,918 markers at 851 loci was resolved. The mapping population was phenotyped for freezing tolerance response under controlled and replicated laboratory conditions and subsequent quantitative trait loci analysis using interval mapping revealed a single significant quantitative trait locus on Fvb2 in the physical interval 10.6 Mb and 15.73 Mb on the F. vesca v4.0 genome sequence. This physical interval contained 896 predicted genes, several of which had putative roles associated with tolerance to abiotic stresses including freezing. Differential expression analysis of the 896 QTL-associated gene predictions in the leaves and crowns from ‘Alta’ and ‘NCGR1363’ parental genotypes revealed genotype-specific changes in transcript accumulation in response to low temperature treatment as well as expression differences between genotypes prior to treatment for many of the genes. The putative roles, and significant interparental differential expression levels of several of the genes reported here identified them as good candidates for the control of the effects of freezing tolerance at the QTL identified in this investigation and the possible role of these candidate genes in response to freezing stress is discussed.

• Hubin, Aliaksandr; Storvik, Geir Olve; Grini, Paul Eivind & Butenko, Melinka Alonso (2020). A Bayesian binomial regression model with latent gaussian processes for modelling DNA methylation. Austrian Journal of Statistics. ISSN 1026-597X. 49(4), p. 46–56. doi: 10.17713/ajs.v49i4.1124. Full text in Research Archive Show summary

  Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can influence the probability of success in a particular region. Moreover, there is a strong spatial (alongside the genome) dependence of these probabilities. We incorporate dependence on the covariates and the spatial dependence of the methylation probability for observations from a pool of cells by means of a binomial regression model with a latent Gaussian field and a logit link function. We apply a Bayesian approach including prior specifications on model configurations. We run a mode jumping Markov chain Monte Carlo algorithm (MJMCMC) across different choices of covariates in order to obtain the joint posterior distribution of parameters and models. This also allows finding the best set of covariates to model methylation probability within the genomic region of interest and individual marginal inclusion probabilities of the covariates.

• Hubin, Aliaksandr; Storvik, Geir Olve; Grini, Paul Eivind & Butenko, Melinka Alonso (2019). Bayesian binomial regression model with a latent Gaussian field for analysis of epigenetic data. In Kharin, Y & Filzmoser, Peter (Ed.), Proceedings of Computer Data Analysis and Modeling: Stochastics and Data Science 2019. Belarusian State University Press. ISSN 978-985-566-811-5. p. 167–171.
• Bjerkan, Katrine; Hornslien, Karina Stensland; Johannessen, Ida Marie; Krabberød, Anders Kristian; van Ekelenburg, Yuri Stephan & Kalantarian, Maryam [Show all 11 contributors for this article] (2019). Genetic variation and temperature affects hybrid barriers during interspecific hybridization. The Plant Journal. ISSN 0960-7412. 101, p. 122–140. doi: 10.1111/tpj.14523. Full text in Research Archive
• Hornslien, Karina Stensland; Miller, Jason Rafe & Grini, Paul Eivind (2019). Regulation of Parent-of-Origin Allelic Expression in the Endosperm. Plant Physiology. ISSN 0032-0889. 180(3), p. 1498–1519. doi: 10.1104/pp.19.00320.
• Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Haraldsen, Arthur Alexander Blørstad; Tarver, James E. & Suga, Hiroshi [Show all 11 contributors for this article] (2018). Unicellular origin of the animal microRNA machinery. Current Biology. ISSN 0960-9822. 28(20), p. 3288–3295.e5. doi: 10.1016/j.cub.2018.08.018. Full text in Research Archive
• Glöckle, Barbara; Urban, W.; Nagahara, Shiori; Andersen, Ellen Dehnes; Higashiyama, Tetsuya & Grini, Paul Eivind [Show all 7 contributors for this article] (2018). Pollen differentiation as well as pollen tube guidance and discharge are independent of the presence of gametes. Development. ISSN 0950-1991. 145(1), p. 1–8. doi: 10.1242/dev.152645. Full text in Research Archive
• Lafon-Placette, Clément; Johannessen, Ida Marie; Hornslien, Karina Stensland; Ali, Mohammad F.; Bjerkan, Katrine & Bramsiepe, Jonathan [Show all 11 contributors for this article] (2017). Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 114(6), p. E1027–E1035. doi: 10.1073/pnas.1615123114.
• Oh, Sung-Aeong; Jeon, Jien; Park, Hyo-Jin; Grini, Paul Eivind; Twell, David & Park, Soon Ki (2016). Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis. The Plant Journal. ISSN 0960-7412. 87(2), p. 188–201. doi: 10.1111/tpj.13192.
• Bjerkan, Katrine & Grini, Paul Eivind (2013). The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development. Plant Signalling & Behavior. ISSN 1559-2316. 8(9). doi: 10.4161/psb.25347.
• Gregis, Veronica; Andrès, Fernandio; Sessa, Alice; Guerra, Rosalinda F; Simonini, Sara & Mateos, Julieta L [Show all 15 contributors for this article] (2013). Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis. Genome Biology. ISSN 1465-6906. 14(6). doi: 10.1186/gb-2013-14-6-r56.
• Meza, Trine Johansen; Moen, Marivi; Vågbø, Cathrine Broberg; Krokan, Hans Einar; Klungland, Arne & Grini, Paul Eivind [Show all 7 contributors for this article] (2012). The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage. Nucleic Acids Research (NAR). ISSN 0305-1048. 40(14), p. 6620–6631. doi: 10.1093/nar/gks327. Full text in Research Archive
• Bjerkan, Katrine; Jung-Romeo, S; Jurgens, G; Genschik, P & Grini, Paul Eivind (2012). Arabidopsis WD REPEAT DOMAIN55 Interacts with DNA DAMAGED BINDING PROTEIN1 and Is Required for Apical Patterning in the Embryo. The Plant Cell. ISSN 1040-4651. 24(3), p. 1013–1033. doi: 10.1105/tpc.111.089425.
• Leihne, VIbeke; Kirpekar, F; Vågbø, Cathrine Broberg; Van den Born, Erwin; Krokan, Hans Einar & Grini, Paul Eivind [Show all 8 contributors for this article] (2011). Roles of Trm9-and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA. Nucleic Acids Research (NAR). ISSN 0305-1048. 39(17), p. 7688–7701. doi: 10.1093/nar/gkr406. Full text in Research Archive
• Thorstensen, Tage; Grini, Paul Eivind & Aalen, Reidunn B. (2011). SET domain proteins in plant development. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. ISSN 1874-9399. 1809(8), p. 407–420. doi: 10.1016/j.bbagrm.2011.05.008.
• Masiero, S; Colombo, L; Grini, Paul Eivind; Schnittger, A & Kater, MM (2011). The Emerging Importance of Type I MADS Box Transcription Factors for Plant Reproduction. The Plant Cell. ISSN 1040-4651. 23(3), p. 865–872. doi: 10.1105/tpc.110.081737.
• Bouyer, D; Roudier, F; Heese, M; Andersen, Ellen Dehnes; Gey, D & Nowack, MK [Show all 11 contributors for this article] (2011). Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition. PLoS Genetics. ISSN 1553-7390. 7(3). doi: 10.1371/journal.pgen.1002014.
• Shirzadi, Reza; Andersen, Ellen Dehnes; Bjerkan, Katrine; Gloeckle, Barbara M; Heese, Maren & Ungru, Alexander [Show all 11 contributors for this article] (2011). Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin-Dependent Regulation of AGAMOUS-LIKE36. PLoS Genetics. ISSN 1553-7390. 7(2). doi: 10.1371/journal.pgen.1001303. Full text in Research Archive
• Nowack, MK; Ungru, Alexander; Bjerkan, Katrine; Grini, Paul Eivind & Schnittger, Arp (2010). Reproductive cross-talk: seed development in flowering plants. Biochemical Society Transactions. ISSN 0300-5127. 38, p. 604–612. doi: 10.1042/BST0380604.
• Stangeland, B; Rosenhave, EM; Winge, Per; Berg, Anita; Berg, A & Amundsen, SS [Show all 11 contributors for this article] (2009). AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana. Physiologia Plantarum : An International Journal for Plant Biology. ISSN 0031-9317. 136(1), p. 110–126. doi: 10.1111/j.1399-3054.2009.01218.x.
• Grini, Paul Eivind; Alm, Vibeke; Thorstensen, Tage; Vizcay-Barrena, Gema; Windju, Susanne & Tommy S., Jørstad [Show all 8 contributors for this article] (2009). The ASH1 HOMOLOG 2 (ASHH2) Histone H3 Methyltransferase Is Required for Ovule and Anther Development in Arabidopsis. PLOS ONE. ISSN 1932-6203. 4(11), p. e7817–e7817.
• Thorstensen, Tage; Grini, Paul E. ; Mercy, Inderjit S.; Alm, Vibeke; Erdal, Sigrid & Aasland, Rein [Show all 7 contributors for this article] (2008). The Arabidopsis SET-domain protein ASHR3 is involved in stamen development and interacts with the bHLH transcription factor ABORTED MICROSPORES (AMS). Plant Molecular Biology. ISSN 0167-4412. 66(1), p. 47–59. doi: 10.1007/s11103-007-9251-y.
• Ungru, A; Nowack, MK; Reymond, M; Shirzadi, Reza; Kumar, M & Biewers, S [Show all 8 contributors for this article] (2008). Natural variation in the degree of autonomous endosperm formation reveals independence and constraints of embryo growth during seed development in Arabidopsis thaliana. Genetics. ISSN 0016-6731. 179, p. 829–841. doi: 10.1534/genetics.107.084889.
• Nowack, MK; Shirzadi, Reza; Dissmeyer, N; Dolf, A; Endl, E & Grini, Paul Eivind [Show all 7 contributors for this article] (2007). Bypassing genomic imprinting allows seed development. Nature. ISSN 0028-0836. 447. doi: 10.1038/nature05770.
• Dissmeyer, N; Nowack, MK; Pusch, S; Stals, H; Inze, D & Grini, Paul Eivind [Show all 7 contributors for this article] (2007). T-loop phosphorylation of Arabidopsis CDKA;1 is required for its function and can be partially substituted by an aspartate residue. The Plant Cell. ISSN 1040-4651. 19. doi: 10.1105/tpc.050401.
• Berger, Frederick; Grini, Paul Eivind & Schnittger, Arp (2006). Endosperm: an integrator of seed growth and development. Current opinion in plant biology. ISSN 1369-5266. 9, p. 664–670.
• Nowack, MK; Grini, Paul Eivind; Jakoby, MJ; Lafos, M; Koncz, C & Schnittger, A (2006). A positive signal from the fertilization of the egg cell sets off endosperm proliferation in angiosperm embryogenesis. Nature Genetics. ISSN 1061-4036. 38.
• Thorstensen, Tage; Fischer, Andreas; Sandvik, Silje; Johnsen, Sylvia; Grini, Paul Eivind & Reuter, Gunter [Show all 7 contributors for this article] (2006). The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9. Nucleic Acids Research (NAR). ISSN 0305-1048. 34(19), p. 5461–5470. doi: 10.1093/nar/gkl687.
• Stangeland, Biljana; Nestestog, Ragnhild; Grini, Paul; Skrbo, Nirma; Berg, Anita & Salehian, Zhian [Show all 8 contributors for this article] (2005). Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes. Journal of Experimental Botany. ISSN 0022-0957. 419(Sep;56), p. 2495–505. Show summary

  Random insertions of promoterless reporter genes in genomes are a common tool for identifying marker lines with tissue-specific expression patterns. Such lines are assumed to reflect the activity of endogenous promoters and should facilitate the cloning of genes expressed in the corresponding tissues. To identify genes active in seed organs, plant DNA flanking T-DNA insertions (T-DNAs) have been cloned in 16 Arabidopsis thaliana GUS-reporter lines. T-DNAs were found in proximal promoter regions, 5' UTR or intron with GUS in the same (sense) orientation as the tagged gene, but contrary to expectations also in inverted orientation in the 5' end of genes or in intergenic regions. RT-PCR, northern analysis, and data on expression patterns of tagged genes, compared with the expression pattern of the reporter lines, suggest that the expression pattern of a reporter gene will reflect the pattern of a tagged gene when inserted in sense orientation in the 5' UTR or intron. When inserted in the promoter region, the reporter-gene expression patterns may be restricted compared with the endogenous gene. Among the trapped genes, the previously described nitrate transporter gene AtNRT1.1, the cyclophilin gene ROC3, and the histone deacetylase gene AtHD2C were found. Reporter-gene expression when positioned in antisense orientation, for example, in the SLEEPY1 gene, is indicative of antisense expression of the tagged gene. For T-DNAs found in intergenic regions, it is suggested that the reporter gene is transcribed from cryptic promoters or promoters of as yet unannotated genes.

• Stangeland, Biljana; Nestestog, Ragnhild; Grini, Paul Eivind; Skrbo-Larssen, Nirma; Berg, Anita & Salehian, Zhian [Show all 8 contributors for this article] (2005). Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes. Journal of Experimental Botany. ISSN 0022-0957. 56(419), p. 2495–2505. doi: 10.1093/jxb/eri242.
• Haslekås, Camilla; Grini, Paul Eivind; Nordgard, Silje H.; Thorstensen, Tage; Viken, Marte K. & Nygaard, Vigdis [Show all 7 contributors for this article] (2003). ABI3 mediates expression of the peroxiredoxin antioxidant AtPER1 gene and induction by oxidative stress. Plant Molecular Biology. ISSN 0167-4412. 53, p. 313–326.
• Haslekås, Camilla; Viken, Marte K.; Grini, Paul Eivind; Nygaard, Vigdis; Nordgard, Silje H. & Meza, Trine Johansen [Show all 7 contributors for this article] (2003). Seed 1-Cys peroxiredoxin antioxidants are not involved in dormancy, but contribute to inhibition of germination during stress. Plant Physiology. ISSN 0032-0889. 133, p. 1148–1157.
• Butenko, Melinka Alonso; Patterson, Sara E.; Grini, Paul Eivind; Stenvik, Grethe-Elisabeth; Amundsen, Svanstrøm Silja & Mandal, Abul [Show all 7 contributors for this article] (2003). INFLORESCENCE DEFICIENT IN ABSCISSION Controls Floral Organ Abscission in Arabidopsis and Identifies a Novel Family of Putative Ligands in Plants. The Plant Cell. ISSN 1040-4651. 15, p. 2296–2307.
• Kirik, V.; Grini, Paul Eivind; Mathur, J.; Klinkhammer, I.; Adler, K. & Bechtold, N. [Show all 9 contributors for this article] (2002). The Arabidopsis TUBULIN-FOLDING COFACTOR A gene is involved in the control of the alpha/beta-tubulin monomer balance. The Plant Cell. ISSN 1040-4651. p. 2265–2276. Show summary

  The control of the stoichiometric balance of alpha- and beta-tubulin is important during microtubule biogenesis. This process involves several tubulin-folding cofactors (TFCs), of which only TFC A is not essential in mammalian in vitro systems or in vivo in yeast. Here, we show that the TFC A gene is important in vivo in plants. The Arabidopsis gene KIESEL (KIS) shows sequence similarity to the TFC A gene. Expression of the mouse TFC A gene under the control of the 35S promoter rescues the kis mutation, indicating that KIS is the Arabidopsis ortholog of TFC A. kis plants exhibit a range of defects similar to the phenotypes associated with impaired microtubule function: plants are reduced in size and show meiotic defects, cell division is impaired, and trichomes are bulged and less branched. Microtubule density was indistinguishable from that of the wild type, but microtubule organization was affected in trichomes and hypocotyl cells of dark-grown kis plants. The kis phenotype was rescued by overexpression of an alpha-tubulin, indicating that KIS is involved in the control of the correct balance of alpha- and beta-tubulin monomers.

• Kirik, V.; Mathur, J.; Grini, Paul Eivind; Klinkhammer, I.; Adler, K. & Bechtold, N. [Show all 9 contributors for this article] (2002). Functional analysis of the tubulin-folding cofactor C in Arabidopsis thaliana. Current Biology. ISSN 0960-9822. 12(17), p. 1519–1523. Show summary

  The biogenesis of microtubules comprises several steps, including the correct folding of alpha- and beta-tubulin and heterodimer formation. In vitro studies and the genetic analysis in yeast revealed that, after translation, alpha- and beta-tubulin are processed by several chaperonins and microtubule-folding cofactors (TFCs) to produce assembly-competent alpha-/beta-tubulin heterodimers. One of the TFCs, TFC-C, does not exist in yeast, and a potential function of TFC-C is thus based only on the biochemical analysis. In this study and in a very recently published study by Steinborn and coworkers, the analysis of the Arabidopsis porcino (por) mutant has shown that TFC-C is important for microtubule function in vivo. The predicted POR protein shares weak amino acid similarity with the human TFC-C (hTFC-C). Our finding that hTFC-C under the control of the ubiquitously expressed 35S promoter can rescue the por mutant phenotype shows that the POR gene encodes the Arabidopsis ortholog of hTFC-C. The analysis of plants carrying a GFP:POR fusion construct showed that POR protein is localized in the cytoplasm and is not associated with microtubules. While, in por mutants, microtubule density was indistinguishable from wild-type, their organization was affected.

• Grini, Paul Eivind; Jürgens, Gerd & Hülskamp, Martin (2002). Embryo and Endosperm Development Is Disrupted in the Female Gametophytic capulet Mutants of Arabidopsis. Genetics. ISSN 0016-6731. 162(4), p. 1911–1925. Show summary

  The female gametophyte of higher plants gives rise, by double fertilization, to the diploid embryo and triploid endosperm, which develop in concert to produce the mature seed. What roles gametophytic maternal factors play in this process is not clear. The female-gametophytic effects on embryo and endosperm development in the Arabidopsis mea, fis, and fie mutants appear to be due to gametic imprinting that can be suppressed by METHYL TRANSFERASE1 antisense (MET1 a/s) transgene expression or by mutation of the DECREASE IN DNA METHYLATION1 (DDM1) gene. Here we describe two novel gametophytic maternal-effect mutants, capulet1 (cap1) and capulet2 (cap2). In the cap1 mutant, both embryo and endosperm development are arrested at early stages. In the cap2 mutant, endosperm development is blocked at very early stages, whereas embryos can develop to the early heart stage. The cap mutant phenotypes were not rescued by wild-type pollen nor by pollen from tetraploid plants. Furthermore, removal of silencing barriers from the paternal genome by MET1 a/s transgene expression or by the ddm1 mutation also failed to restore seed development in the cap mutants. Neither cap1 nor cap2 displayed autonomous seed development, in contrast to mea, fis, and fie mutants. In addition, cap2 was epistatic to fis1 in both autonomous endosperm and sexual development. Finally, both cap1 and cap2 mutant endosperms, like wild-type endosperms, expressed the paternally inactive endosperm-specific FIS2 promoter GUS fusion transgene only when the transgene was introduced via the embryo sac, indicating that imprinting was not affected. Our results suggest that the CAP genes represent novel maternal functions supplied by the female gametophyte that are required for embryo and endosperm development.

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• Fossdal, Carl Gunnar; Yakovlev, Igor; Viejo, Marcos; Grini, Paul; Krokene, Paal & Zhang, Yupeng [Show all 7 contributors for this article] (2023). Epigenetic memory induced by elevated temperature conditions in the Gymnosperm Norway spruce and the Angiosperm Woodland strawberry.
• Zhang, Yupeng; Fan, Guangxun; Toivenen, Tuomas; Tengs, Torstein; Yakovlev, Igor & Andrés, Javier [Show all 10 contributors for this article] (2022). Methylome and transcriptome changes induced by temperature conditions during asexual reproduction in Fragaria vesca .
• Alling, Renate; Brysting, Anne Krag; Grini, Paul; Bjerkan, Katrine & Myking, Ida Velle (2022). Environmental and genetic factors affecting endosperm based post-zygotic hybridization barriers. Show summary

  Proper development of the triploid endosperm is vital for seed viability. During the early stages of development, the endosperm works as a nutrient sink, accumulating sugars from the surrounding tissues. During this developmental phase, endosperm division is devoid of cytokinesis, resulting in a syncytium. After sufficient accumulation of nutrients, the endosperm nuclei undergo cellularization, switching to serve as a nutrient source for the embryo. Tight regulation of cellularization is therefore vital for embryo development. Crosses between Arabidopsis thaliana as maternal contributor and A. arenosa as pollen donor cause late cellularization and reduced germination rate in hybrid seeds. Here we show the opposite cellularization phenotype in hybrid seeds when using A. lyrata as pollen donor also resulting in low germination rate. Stage specific endosperm reporters display ectopic expression in developing hybrid endosperm confirming disturbance of the source-sink endosperm phase change. We also observe accession genotype as well as single loci effects on the severity of the barrier. Interestingly, we found that temperature can alleviate this hybridization barrier in opposite directions depending on whether the hybrid seed exhibit early or late endosperm cellularization. We postulate that temperature dependency might be a general mechanism affecting endosperm-based hybridization barriers.

• Hubin, Aliaksandr; Storvik, Geir Olve; Grini, Paul Eivind & Butenko, Melinka Alonso (2019). Bayesian binomial regression model with a latent Gaussian field for analysis of epigenetic data.
• Kenich, Håkon Muland; Bjerkan, Katrine; Bramsiepe, Jonathan; Grini, Paul Eivind & Brysting, Anne Krag (2019). An investigation of potential hybridisation barriers in Cochlearia / Scurvygrasses.
• Bjerkan, Katrine; Hornslien, Karina Stensland; Johannessen, Ida Marie; van Ekelenburg, Yuri Stephan; Bramsiepe, Jonathan & Brysting, Anne Krag [Show all 7 contributors for this article] (2019). Temperature and genetic variation alter strength of the post-zygotic endosperm based barrier between A. thaliana and A.arenosa.
• Grini, Paul Eivind; Miller, Jason Rafe & Hornslien, Karina Stensland (2019). Imprinting revisited: Genetic and phenotypic routes to postzygotic hybrid barriers and bridges.
• Zhang, Yupeng; Fan, Guangxun; Toivainen, Tuomas; Yakovlev, Igor; Hytönen, Timo & Krokene, Paal [Show all 8 contributors for this article] (2018). BEYOND THE GENOME: EPIGENETICS OF CLIMATIC ADAPTATION IN PLANTS. Full text in Research Archive Show summary

  Climate change is one of the greatest challenges for the biosphere. As sessile organisms, plants must adapt quickly to keep pace with the rapidly changing climatic conditions. Epigenetic memory is one mechanism which would provide sufficient plasticity under rapid climate change and enable long-lived organisms to survive long enough to adapt by classical genetic selection. In Norway spruce, the timing of bud burst and bud set are regulated by an epigenetic memory established by the temperature sum endured during embryogenesis. The resulting epitypes display a life-long shift in seasonal timing of the bud phenology, a trait previously presumed to be under strict classical selection and highly heritable. However, Norway spruce is a difficult plant to study because it has a very long generation time and an extensive genome size. We therefore seek to find a suitable perennial model plant to study the phenomenon of epigenetic climatic memory. Woodland strawberry (Fragaria vesca) may be an ideal model to research the role of epigenetic memory on plant phenology. Fragaria vesca is a perennial plant with a small well-characterized genome, a short sexual reproduction cycle and can also propagate asexually trough clonal daughter plants formed by stolons. We will explore whether the temperature sum experienced during sexual and asexual reproduction impact on the phenology of Fragaria vesca and use this as a model to decipher the molecular mechanism underlying epigenetic memory in plants.

• Grini, Paul Eivind; van Ekelenburg, Yuri Stephan & Guiterrez-Marcos, Jose (2018). CAPULET2 controls endosperm development in a parent-of-origin dependent manner.
• Grini, Paul Eivind; van Ekelenburg, Yuri Stephan; Bjerkan, Katrine & Nowack, Moritz K. (2018). Analysis of Domain Specific Genomic Imprinting in the Arabidopsis Endosperm.
• Grini, Paul Eivind; Hornslien, Karina Stensland & Miller, Jason Rafe (2018). Imprinting Revisited: Regulation of Parent-of-Origin Allelic Expression in Arabidopsis thaliana endosperm.
• Grini, Paul Eivind (2018). Imprinting Revisited: Regulation of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Endosperm.
• Johannessen, Ida Marie; Hornslien, Karina Stensland; Krabberød, Anders Kristian; Bramsiepe, Jonathan; Brysting, Anne Krag & Grini, Paul Eivind (2018). The Genetic Basis of Post-Zygotic Hybridization Barriers Between Arabidopsis lyrata and A. arenosa.
• Brysting, Anne Krag & Grini, Paul Eivind (2017). The molecular basis of postzygotic hybridization barriers in plants.
• Johannessen, Ida Marie; Hornslien, Karina Stensland; Krabberød, Anders Kristian; Bramsiepe, Jonathan; Brysting, Anne Krag & Grini, Paul Eivind (2017). The genetic basis of post-zygotic hybridization barriers between Arabidopsis lyrata and A. arenosa.
• Johannessen, Ida Marie; Lafon-Placette, Clément; Hornslien, Karina Stensland; Bramsiepe, Jonathan; Bjerkan, Katrine & Brysting, Anne Krag [Show all 8 contributors for this article] (2017). The effect of gene and genome dosage on hybridization barriers in Arabidopsis lyrata and Arabidospsis arenosa.
• Hubin, Aliaksandr; Storvik, Geir Olve & Grini, Paul Eivind (2017). Variable selection in binomial regression with latent Gaussian field models for analysis of epigenetic data.
• Haraldsen, Arthur Alexander Blørstad; Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Grini, Paul Eivind & Shalchian-Tabrizi, Kamran (2016). Pre-metazoan origin of animal microRNAs.
• Eskeland, Ragnhild & Grini, Paul Eivind (2015). Epigenetikk – hadde Lamarck rett? In Hessen, Dag Olav; Lie, Thore & Stenseth, Nils Christian (Ed.), Mendels arv - Genetikkens æra. Gyldendal Norsk Forlag A/S. ISSN 978-82-05-45818-5. p. 182–215.
• Roell, Marc-Sven; Noordzij, Hanna Theodora; Skar Mjønes, Caroline; Boye, Ole; Levchenko, Vladimir & Kimara, Chiharu [Show all 12 contributors for this article] (2015). Methane Incorporated - iGEM Lecture.
• Roell, Marc-Sven; Noordzij, Hanna Theodora; Skar Mjønes, Caroline; Boye, Ole; Levchenko, Vladimir & Kimara, Chiharu [Show all 12 contributors for this article] (2015). Methane Incorporated.
• Meza, Trine Johansen; Moen, Marivi N.; Vågbø, Cathrine B.; Ulleland, Marius; Krokan, Hans Einar & Arne, Klungland [Show all 8 contributors for this article] (2010). The DNA dioxygenase AtALKBH2 protects Arabidopsis thaliana against methylation damage.
• Aalen, Reidunn B.; Grini, Paul Eivind; Thorstensen, Tage; Alm, Vibeke; Vizcay-Barrena, Gema & Windju, Susanne S. [Show all 7 contributors for this article] (2009). The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis. Show summary

  SET-domain proteins add methyl groups to lysine (K) residues of histone tails, which may function as marks activating or repressing transcription. The ASH1 HOMOLOG 2 (ASHH2) protein of Arabidopsis thaliana groups with Drosophila ASH1, a positive maintainer of gene expression, and yeast Set2, a histone H3K36 methyltransferase, and has been implicated as a histone H3K4 or H3K36 methyltransferase. ashh2 mutants display pleiotropic developmental defects, including early flowering. Here we focus on the role of ASHH2 in plant reproduction, of homeotic changes in floral organ identity and specific effects on the development of the reproductive organs. On the female side, close to 80% of the mature ovules lack embryo sac. On the male side, anthers frequently develop without pollen sacs and where present show specific defects in the tapetum layer. As a result, the number of functional pollen per anther was reduced by up to ~90%. Transcriptional profiling identified more than 600 down-regulated genes in ashh2 mutant inflorescences, including genes involved in determination of floral organ identity, embryo sac development and anther/pollen development. Currently, there is a discrepancy in the literature on the primary substrate of ASHH2 methylation. We observed a reduction of H3K36 trimethylation (me3) but not H3K4me3 or H3K36me2 in chromatin from selected down-regulated genes. Thus, our analysis strongly suggests that ASHH2 works via H3K36 trimethylation in the regulation of genes essential in reproductive development.

• Aalen, Reidunn B.; Grini, Paul Eivind; Thorstensen, Tage & Alm, Vibeke (2009). The ASHH2 histone 3 lysine methyltransferase is required for ovule and anther development in Arabidopsis thaliana. Show summary

  SET-domain proteins are methyltransferases that add methyl groups to lysine (K) residues of histone tails, which function as marks activating or repressing transcription. SET-domain proteins can be divided into evolutionarily conserved classes in animals and plants. Mutation of the ASH1 HOMOLOG 2 (ASHH2) gene of the model plant Arabidopsis has severe pleiotropic effects on growth, development and fertility, in that it results in homoetic changes of floral organ identity, affects male and female gametogenesis, and especially the development of the reproductive organs. On the female side, close to 80 percent of the mature ovules lack embryo sac. On the male side, anthers in part develop without pollen sacs (locules) and in developed locules the tapetum layer, which provides material to the pollen wall, is distorted. Together this results in a more that 75 percent reduction in mature functional pollen grains. Transcriptional profiling was used to identify changes in gene expression in ashh2 mutant inflorescences. Genes involved in determination of floral organ identity, embryo sac development and anther/pollen development were found down-regulated. On such genes ChIP detected reduction of H3K36me3 but not H3K4me3 or H3K36me2. Our study indicates that ASHH2 is a major global H3K36 trimethyltransferase in Arabidopsis.

• Aalen, Reidunn B.; Grini, Paul Eivind; Thorstensen, Tage; Alm, Vibeke; Vizcay-Barrena, Gema & Windju, Susanne S. [Show all 7 contributors for this article] (2009). The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis. Show summary

  The more than 30 SET-domain proteins of Arabidopsis can be classified in evolutionarily conserved subgroups that methylate different lysine residues on histone tails (1).The ASH1 HOMOLOG 2 (ASHH2) protein is similar to the Drosophila transcriptional activator ASH1, and the histone H3K36 methyltransferase Set2 from yeast. ashh2 mutants display pleiotropic developmental defects, including early flowering (2,3). We have focused on the role of ASHH2 in plant reproduction, of homeotic changes in floral organ identity and specific effects on the development of the reproductive organs. On the female side, close to 80% of the mature ovules lack embryo sac. On the male side, anthers frequently develop without pollen sacs and where present show specific defects in the tapetum layer, reducing the number of functional pollen per anther by up to ~90%. Transcriptional profiling identified more than 600 down-regulated genes in ashh2 mutant inflorescences, including genes involved in determination of floral organ identity, embryo sac development and anther/pollen development. We observed a reduction of H3K36 trimethylation (me3) but not H3K4me3 or H3K36me2 in chromatin of such genes. Thus, our analysis strongly suggests that ASHH2 works via H3K36 trimethylation in the regulation of genes essential in reproductive development.

• Aalen, Reidunn B.; Thorstensen, Tage; Alm, Vibeke & Grini, Paul Eivind (2007). Chromatin modification in Arabidopsis: SET-domain proteins with localization in euchromatin or the nucleolus and identification of a novel histone methyltransferase specificity.
• Thorstensen, Tage; Grini, Paul Eivind; Alm, Vibeke; Butenko, Melinka Alonso; Rosenhave, E. Maryann & Aalen, Reidunn (2004). Identification of new gene families and their function using bioinformatics tools and reverse genetics.
• Butenko, Melinka Alonso; Patterson, Sara E.; Grini, Paul Eivind; Stenvik, Grethe-Elisabeth; Amundsen, Svanstrøm Silja & Mandal, Abul [Show all 7 contributors for this article] (2003). IDA controls floral organ abscission in Arabidopsis, and identifies a novel family of putative ligands in plants.
• Thorstensen, Tage; Grini, Paul Eivind; Mercy, Inderjit Singh & Aalen, Reidunn (2003). A SET-domain encoding gene possibly involved in embryo development in Arabidopsis thaliana.
• Grini, Paul Eivind; Skrbo, Nirma; Stangeland, Biljana & Aalen, Reidunn (2003). Genetic and molecular analysis of gametophytic maternal effect mutants in Arabidopsis.
• Butenko, Melinka Alonso; Patterson, Sara E.; Stenvik, Grethe-Elisabeth; Grini, Paul Eivind; Thorstensen, Tage & Mandal, Abul [Show all 7 contributors for this article] (2003). The IDA gene, controlling floral organ abscission in Arabidopsis, identifies a novel family of putative ligands in plants.
• Haslekås, Camilla; Viken, Marte K.; Nordgard, Silje H.; Grini, Paul Eivind; Thorstensen, Tage & Nygaard, Vigdis [Show all 8 contributors for this article] (2003). Study of thte potential function and regulation of the peroxiredoxin AtPER1.
• Grini, Paul Eivind; Skrbo, Nirma; Stangeland, Biljana; Hülskamp, Martin; Jürgens, Gerd & Aalen, Reidunn (2003). Genetic and molecular analysis of gametophytic maternal effect mutants in Arabidopsis.
• Skrbo, Nirma; Grini, Paul Eivind & Aalen, Reidunn (2003). Towards molecular cloning of the capulet2 gametophyte maternal-effect mutant in Arabidopsis thaliana.
• Skrbo, Nirma; Grini, Paul Eivind; Jürgens, Gerd; Hülskamp, Martin & Aalen, Reidunn (2003). Towards molecular cloning of the capulet2 gametophytic maternal-efect mutant in Arabidopsis thaliana.

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