katribje

• Hornslien, Karina Stensland; Myking, Ida Velle; Bjerkan, Katrine Nergård; Krabberød, Anders Kristian; Miller, Jason Rafe & Grini, Paul (2026). Parent-of-origin specific allelic expression in outbreeding Arabidopsis arenosa identifies antagonistic parental enrichment in protein degradation pathways. New Phytologist. ISSN 0028-646X. doi: 10.1111/nph.71551. 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 Show summary

  SUMMARY Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome‐wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS‐box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm‐based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS‐box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de‐novo assembled and annotated chromosome‐level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS‐box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS‐box type I loci in endosperm‐based hybridization barriers. We observed substantial differences in type‐I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea , suggesting a genetic cause for the endosperm‐based hybridization barrier between A. arenosa and A. lyrata ssp. petraea .

• 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. 14, p. 1–16. doi: 10.3389/fpls.2023.1229060. Full text in Research Archive Show summary

  Speciation involves reproductive isolation, which can occur by hybridization barriers acting in the endosperm of the developing seed. The nuclear endosperm is a nutrient sink, accumulating sugars from surrounding tissues, and undergoes coordinated cellularization, switching to serve as a nutrient source for the developing embryo. Tight regulation of cellularization is therefore vital for seed and embryonic development. Here we show that hybrid seeds from crosses between Arabidopsis thaliana as maternal contributor and A. arenosa or A. lyrata as pollen donors result in an endosperm based post-zygotic hybridization barrier that gives rise to a reduced seed germination rate. Hybrid seeds display opposite endosperm cellularization phenotypes, with late cellularization in crosses with A. arenosa and early cellularization in crosses with A. lyrata . Stage specific endosperm reporters display temporally ectopic expression in developing hybrid endosperm, in accordance with the early and late cellularization phenotypes, confirming a disturbance of the source-sink endosperm phase change. We demonstrate that the hybrid barrier is under the influence of abiotic factors, and show that a temperature gradient leads to diametrically opposed cellularization phenotype responses in hybrid endosperm with A. arenosa or A. lyrata as pollen donors. Furthermore, different A. thaliana accession genotypes also enhance or diminish seed viability in the two hybrid cross-types, emphasizing that both genetic and environmental cues control the hybridization barrier. We have identified an A. thaliana MADS-BOX type I family single locus that is required for diametrically opposed cellularization phenotype responses in hybrid endosperm. Loss of AGAMOUS-LIKE 35 significantly affects the germination rate of hybrid seeds in opposite directions when transmitted through the A. thaliana endosperm, and is suggested to be a locus that promotes cellularization as part of an endosperm based mechanism involved in post-zygotic hybrid barriers. The role of temperature in hybrid speciation and the identification of distinct loci in control of hybrid failure have great potential to aid the introduction of advantageous traits in breeding research and to support models to predict hybrid admixture in a changing global climate.

• Ekelenburg, Yuri Stephan van; Hornslien, Karina Stensland; Hautegem, Tom Van; Fendrych, Matyáš; Isterdael, Gert Van & 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.

• Bjerkan, Katrine; Hornslien, Karina Stensland; Johannessen, Ida Marie; Krabberød, Anders Kristian; Ekelenburg, Yuri Stephan van & 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 Show summary

  Genomic imprinting regulates parent‐specific transcript dosage during seed development and is mainly confined to the endosperm. Elucidation of the function of many imprinted genes has been hampered by the lack of corresponding mutant phenotypes, and the role of imprinting is mainly associated with genome dosage regulation or allocation of resources. Disruption of imprinted genes has also been suggested to mediate endosperm‐based post‐zygotic hybrid barriers depending on genetic variation and gene dosage. Here, we have analyzed the conservation of a clade from the MADS‐box type I class transcription factors in the closely related species Arabidopsis arenosa, A. lyrata, and A. thaliana, and show that AGL36‐like genes are imprinted and maternally expressed in seeds of Arabidopsis species and in hybrid seeds between outbreeding species. In hybridizations between outbreeding and inbreeding species the paternally silenced allele of the AGL36‐like gene is reactivated in the hybrid, demonstrating that also maternally expressed imprinted genes are perturbed during hybridization and that such effects on imprinted genes are specific to the species combination. Furthermore, we also demonstrate a quantitative effect of genetic diversity and temperature on the strength of the post‐zygotic hybridization barrier. Markedly, a small decrease in temperature during seed development increases the survival of hybrid F1 seeds, suggesting that abiotic and genetic parameters play important roles in post‐zygotic species barriers, pointing at evolutionary scenarios favoring such effects.

• 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 (PNAS). ISSN 0027-8424. 114(6), p. E1027–E1035. doi: 10.1073/pnas.1615123114. Full text in Research Archive
• 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. Full text in Research Archive Show summary

  Background MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism. Results To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively. Conclusions Our analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them.

• 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. 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. Full text in Research Archive
• 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 Show summary

  Seed development in angiosperms is dependent on the interplay among different transcriptional programs operating in the embryo, the endosperm, and the maternally-derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed. Here we have exploited cdka;1 fertilization as a novel tool for the identification of seed regulators and factors involved in parent-of-origin–specific regulation during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds and identified approximately 600 genes that are downregulated in the absence of a paternal genome. Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented. Here, AGL36 was chosen for an in-depth study and shown to be imprinted. We demonstrate that AGL36 parent-of-origin–dependent expression is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds.

• 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. Full text in Research Archive

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• Alling, Renate; Brysting, Anne Krag; Grini, Paul; Bjerkan, Katrine & Myking, Ida Velle (2022). Environmental and genetic factors affecting endosperm based post-zygotic hybridization barriers. Full text in Research Archive 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.

• Bjerkan, Katrine; Butenko, Melinka Alonso & Brysting, Anne Krag (2020). The weed that conquered plant scientists: the model organism Arabidopsis thaliana. NBS-nytt. ISSN 0801-3535. 1, p. 8–11. Full text in Research Archive
• Kenich, Håkon Muland; Bjerkan, Katrine; Bramsiepe, Jonathan; Grini, Paul Eivind & Brysting, Anne Krag (2019). An investigation of potential hybridisation barriers in Cochlearia / Scurvygrasses. Full text in Research Archive
• Bjerkan, Katrine; Hornslien, Karina Stensland; Johannessen, Ida Marie; Ekelenburg, Yuri Stephan van; 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. Full text in Research Archive
• Grini, Paul Eivind; Ekelenburg, Yuri Stephan van; Bjerkan, Katrine & Nowack, Moritz K. (2018). Analysis of Domain Specific Genomic Imprinting in the Arabidopsis Endosperm. Full text in Research Archive
• 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. Full text in Research Archive

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