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Henriksson, Johan
Publications (5 of 5) Show all publications
Hench, J., Henriksson, J., Abou-Zied, A. M., Lüppert, M., Dethlefsen, J., Mukherjee, K., . . . Bürglin, T. R. (2015). The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis. PLoS ONE, 10(5), Article ID e0126947.
Open this publication in new window or tab >>The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis
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2015 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 5, article id e0126947Article in journal (Refereed) Published
Abstract [en]

Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-27668 (URN)10.1371/journal.pone.0126947 (DOI)000355319400026 ()26024448 (PubMedID)2-s2.0-84932606751 (Scopus ID)
Funder
Swedish Research Council, 621-2010-5634Swedish Foundation for Strategic Research Wenner-Gren Foundations
Available from: 2015-06-08 Created: 2015-06-08 Last updated: 2018-11-13Bibliographically approved
Henriksson, J., Hench, J., Tong, Y. G., Johansson, A., Johansson, D. & Bürglin, T. R. (2013). Endrov: an integrated platform for image analysis. Nature Methods, 10(6), 454-456
Open this publication in new window or tab >>Endrov: an integrated platform for image analysis
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2013 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 10, no 6, p. 454-456Article in journal (Refereed) Published
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-19422 (URN)10.1038/nmeth.2478 (DOI)000319668700005 ()2-s2.0-84880784676 (Scopus ID)
Available from: 2013-07-11 Created: 2013-07-11 Last updated: 2017-12-06Bibliographically approved
Xue-Franzen, Y., Johnsson, A., Brodin, D., Henriksson, J., Bürglin, T. R. & Wright, A. P. H. (2010). Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles. BMC Genomics, 11, Article ID 200.
Open this publication in new window or tab >>Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles
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2010 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, article id 200Article in journal (Refereed) Published
Abstract [en]

Background: Gcn5 is a transcriptional coactivator with histone cetyltransferase activity that is conserved with regard to structure as ell as its histone substrates throughout the eukaryotes. Gene egulatory networks within cells are thought to be evolutionarily iverged. The use of evolutionarily divergent yeast species, such as S. erevisiae and S. pombe, which can be studied under similar nvironmental conditions, provides an opportunity to examine the nterface between conserved regulatory components and their cellular pplications in different organisms. esults: We show that Gcn5 is important for a common set of stress esponses in evolutionarily diverged yeast species and that the activity f the conserved histone acetyltransferase domain is required. We define group of KCl stress response genes in S. cerevisiae that are pecifically dependent on Gcn5. Gcn5 is localised to many Gcn5-dependent enes including Gcn5 repressed targets such as FLO8. Gcn5 regulates ivergent sets of KCl responsive genes in S. cerevisiae and S. pombe. enome-wide localization studies showed a tendency for redistribution of cn5 during KCl stress adaptation in S. cerevisiae from short genes to he transcribed regions of long genes. An analogous redistribution was ot observed in S. pombe. onclusions: Gcn5 is required for the regulation of divergent sets of Cl stress-response genes in S. cerevisiae and S. pombe even though it s required a common group of stress responses, including the response o KCl. Genes that are physically associated with Gcn5 require its ctivity for their repression or activation during stress adaptation, roviding support for a role of Gcn5 as a corepressor as well as a oactivator. The tendency of Gcn5 to re-localise to the transcribed egions of long genes during KCl stress adaptation suggests that Gcn5 lays a specific role in the expression of long genes under adaptive onditions, perhaps by regulating transcriptional elongation as has been een for Gcn5 in S. pombe. Interestingly an analogous redistribution of cn5 is not seen in S. pombe. The study thus provides important new nsights in relation to why coregulators like Gcn5 are required for the orrect expression of some genes but not others.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:sh:diva-13712 (URN)10.1186/1471-2164-11-200 (DOI)000277270600002 ()20338033 (PubMedID)2-s2.0-77952260641 (Scopus ID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Functional aspects of the Gcn5 histone acetyltransferase in stress responses of evolutionarily diverged yest species

Available from: 2011-12-06 Created: 2011-12-06 Last updated: 2017-12-08Bibliographically approved
Bratic, I., Hench, J., Henriksson, J., Antebi, A., Bürglin, T. R. & Trifunovic, A. (2009). Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development. Nucleic Acids Research, 37(6), 1817-1828
Open this publication in new window or tab >>Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development
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2009 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 37, no 6, p. 1817-1828Article in journal (Refereed) Published
Abstract [en]

A number of studies showed that the development and the lifespan of Caenorhabditis elegans is dependent on mitochondrial function. In this study, we addressed the role of mitochondrial DNA levels and mtDNA maintenance in development of C. elegans by analyzing deletion mutants for mitochondrial polymerase gamma (polg-1(ok1548)). Surprisingly, even though previous studies in other model organisms showed necessity of polymerase gamma for embryonic development, homozygous polg-1(ok1548) mutants had normal development and reached adulthood without any morphological defects. However, polg-1 deficient animals have a seriously compromised gonadal function as a result of severe mitochondrial depletion, leading to sterility and shortened lifespan. Our results indicate that the gonad is the primary site of mtDNA replication, whilst the mtDNA of adult somatic tissues mainly stems from the developing embryo. Furthermore, we show that the mtDNA copy number shows great plasticity as it can be almost tripled as a response to the environmental stimuli. Finally, we show that the mtDNA copy number is an essential limiting factor for the worm development and therefore, a number of mechanisms set to maintain mtDNA levels exist, ensuring a normal development of C. elegans even in the absence of the mitochondrial replicase.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-13907 (URN)10.1093/nar/gkp018 (DOI)000265097400017 ()19181702 (PubMedID)2-s2.0-64549151315 (Scopus ID)
Available from: 2011-12-14 Created: 2011-12-14 Last updated: 2017-07-18Bibliographically approved
Hench, J., Henriksson, J., Lüppert, M. & Bürglin, T. R. (2009). Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps. Developmental Biology, 333(1), 1-13
Open this publication in new window or tab >>Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps
2009 (English)In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 333, no 1, p. 1-13Article in journal (Refereed) Published
Abstract [en]

The nematode Caenorhabditis elegans has been used as a model for developmental biology for decades. Still, the few publicly available spatio-temporal (4D) data sets have conflicting information regarding variability of cell positions and are not well-suited for a standard 4D embryonic model, due to compression. We have recorded six uncompressed embryos, and determined their lineage and 4D coordinates, including nuclear radii, until the end of gastrulation. We find a remarkable degree of stability in the cell positions, as well as little rotational movement, which allowed us to combine the data into a single reference model of C. elegans embryogenesis. Using Voronoi decomposition we generated the list of all predicted cell contacts during early embryogenesis and calculated these contacts up to the similar to 150 cell stage, and find that about 1500 contacts last 2.5 min or longer. The cell contact map allows for comparison of multiple 4D data sets, e. g., mutants or related species, at the cellular level. A comparison of our uncompressed 4D model with a compressed embryo shows that up to 40% of the cell contacts can be different. To visualize the 4D model interactively we developed a software utility. Our model provides an anatomical resource and can serve as foundation to display 4D expression data, a basis for developmental systems biology.

National Category
Developmental Biology
Identifiers
urn:nbn:se:sh:diva-13885 (URN)10.1016/j.ydbio.2009.06.014 (DOI)000272260100001 ()19527702 (PubMedID)2-s2.0-68349155699 (Scopus ID)
Available from: 2011-12-14 Created: 2011-12-14 Last updated: 2017-12-08Bibliographically approved
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