Research Interests - Plant Developmental Genetics
What are the underlying genetic mechanisms that determine plant form, and how are these controlled? What are the key genes that influence agriculturally important traits such as flowering? What parallels exist between plant and human development, and can studies in plants shed light on issues such as cancer and stem cell biology?
Exploiting chromatin landmarks to characterize complex plant genomes. Progress is the science of genomics is no longer limited by the technologies that obtain genomic DNA sequence, but rather by the ability to interpret this information and uncover biologically relevant features of the genome. In addition, DNA sequence is only one component of the information content of the genome. Additional information - called epigenetic information - is encoded partly by the proteinaceous matrix called chromatin in which the DNA is packaged. Specific modifications to the histone proteins, which make up the bulk of chromatin, are closely associated with the characteristics of the genes to which they are affixed. The objective of this project is to evaluate novel approaches to facilitate sequence analysis of gene-rich regions in plants with complex genomes, identify chromatin landmarks useful for genome annotation, and identify polymorphic sequences most useful for genetic map construction, utilizing a wild apple species as a reference. The project is expected to help uncover how epigenetic information is linked to gene activity, add accuracy to annotation efforts, and uncover cryptic and previously unanticipated features of the genome. (MORE INFO)
Transcriptional memory and epigenetic mechanisms. As an organism develops, cells may proliferate to maintain a pool of stem cells, or differentiate to form specialized tissues. We are studying the mechanisms by which states of gene activity are propagated within and across mitotic boundaries, specifically in relation to chromatin-associated proteins and modifications of DNA and histones at specific genetic sites. In Arabidopsis, we identified a class of protein required for maintaining transcriptional activity of a subset of developmental regulatory genes by counteracting the repressive activity of the so-called Polycomb-group proteins. As part of this project, we recently published the first genome-wide map of transcriptional-activating chromatin modifications in a plant genome (Oh et al 2008). This project also involves gene mapping and cloning, identification of unknown, related proteins through purification and mass spectrometry.
Flowering. Plants have evolved an enormous diversity of strategies to flower at the time of year best suited to their reproduction. Most have intricate mechanisms to perceive daylength and temperature, which are superimposed onto an endogenous flowering program. We are using genetic and molecular techniques to elucidate the networks of gene expression involved in triggering flowering in plants, using Arabidopsis as a model. We are focusing on vernalization (acceleration of flowering by cold) which, in Arabidopsis, results in the downregulation of the FLC/MAF family of MADS-box flowering-inhibitor genes. This project involves genetic screens, mapping, gene cloning, and analyses of genetic interactions. For more information on the genetic mechanisms of flowering, see our review (van Nocker and Ek-Ramos 2004).
Juvenility. Higher plants, like people, transition through a juvenile phase before attaining adulthood. Juvenility is possibly the single most important factor limiting rapid development of new and superior cultivars of woody plants including tree fruits and nuts, and the general nature of phase change is also among the most intriguing and longstanding questions in plant biology. Through exhaustive genome-wide ChIP-seq and RNA-seq experiments, we have linked phase-dependent transcriptional switches with locus-specific chromatin transitions. This knowledge may be employed for the engineering of rapid-cycling genotypes for more efficient breeding.
- van Nocker S and Gardiner SE. 2014. Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops. Horticulture Research 1:14022 (PDF)
- Alkio M, Jonas U, Declercq M, van Nocker S and Knoche M. 2014. Transcriptional dynamics of the developing sweet cherry (Prunus avium L. ) fruit: sequencing, annotation and expression profiling of exocarp-associated genes. Horticulture Research 1:11 (PDF)
- Gottschalk C and van Nocker S. 2013. Diversity in seasonal bloom time and floral development among apple (Malus) species and hybrids. J Amer Soc Hort Sci 138:367-374 (PDF)
- Park S, Oh S and van Nocker S. 2012. Genomic and gene-level distribution of histone H3 dimethyl lysine-27 (H3K27me2) in Arabidopsis. PLoS One 7(12):e52855
- Alkio M, Jonas U, Sprink T, van Nocker S and Knoche M. 2012. Identification of putative candidate genes involved in cuticle formation in sweet cherry fruit. Ann Bot 110, 101-112
- van Nocker S, Berry G, Najdowski J, Michelutti R, Luffman M, Forsline P, Alsmairat N, Beaudry R, Nair MG and Ordidge M. 2012. Genetic diversity of red-fleshed apples (Malus). Euphytica 185: 281-293 (PDF)
- Park S, Ek-Ramos J, Oh S and van Nocker S. 2011. The Arabidopsis PHP gene encodes an accessory subunit of Paf1C required for proper regulation of genes within H3K27me3 chromatin domains. Plant Signaling and Behavior 6:8, 1-3 (PDF)
- Liu Y, Geyer R, van Zanten M, Carles A, Li Y, Hoerold A, van Nocker S and Soppe WJJ. 2011. Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the Polymerase Associated Factor 1 complex in seed dormancy. PLos ONE 6(7):e22241 (PDF)
- Park S, Oh S, Ek-Ramos J and van Nocker S. 2010. PLANT HOMOLOGOUS TO PARAFIBROMIN is a Component of PAF1C and Assists in Regulating Expression of Genes within H3K27me3-Enriched Chromatin. Plant Physiol 153, 821-831 (PDF) (Access through journal)
- Sun L and van Nocker S. 2010. Analysis of promoter activity of members of the PECTATE LYASE-LIKE (PLL) gene family in cell separation in Arabidopsis. BMC Plant Biology, 10:152 (PDF) (Access through journal)
- Mookerjee S and van Nocker S. 2010. Genetics of flowering in apple. In Genomics of fruits and vegetable crops: Apples. Ed. Aldwinckle HS and Malnoy M. Science Publishers, Enfield NH. (Preprint)
- van Nocker S. 2009. Development of the abscission zone. Stewart Postharvest Review 5:1-5 (Reprint) (Access through journal)
- Sun L, Bukovac MJ, Forsline PL and van Nocker S. 2009. Natural variation in fruit abscission-related traits in apple (Malus). Euphytica 165(1): 55-67 (Reprint) (Access through journal)
- Oh S, Park S and van Nocker S. 2008. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet 4(8): e1000077 (Reprint) (Access through journal)
- van Nocker S and Ek-Ramos J. 2007. Control of flowering time. In Regulation of transcription in plants, Grasser KD Ed. Plant Reviews (Blackwell Publishing, Ltd.) (Reprint)
- Mulabagal V, van Nocker S, Dewitt D and Nair M. 2007. Cultivars of apple fruits that are not marketed with potential for anthocyanin production. J Agric Food Chem 55, 8165-8169 (Reprint) (Access through journal)
- Park S, Sugimoto N, Larson MD, Beaudry R and van Nocker S. 2006. Identification of genes with potential roles in apple fruit development and biochemistry through large-scale statistical analysis of expressed sequence tags. Plant Physiol 141, 811-824.
- Oh S, Zhang H, Ludwig P and van Nocker S. 2004. A mechanism related to the yeast transcriptional regulator Paf1C is required for expression of the Arabidopsis FLC/MAF MADS-box gene family. Plant Cell 16, 2940-2953.
- van Nocker S. 2003. CAF-1 and MSI1-related proteins: Linking nucleosome assembly with epigenetics. Trends Plant Sci 8, 471-473.
- van Nocker S and Ludwig P. 2003. The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. BMC Genomics 4, 50.
- Yoo SD, Gao Z, Cantini C, Loescher WH and van Nocker S. 2003. Fruit ripening in sour cherry (P. cerasus L.): Changes in expression of genes encoding expansins and other cell-wall-modifying enzymes. J Amer Soc Hort Sci 128, 16-22.
- Zhang H, Ransom C, Ludwig P and van Nocker S. 2003. Genetic analysis of early-flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for activity of the flowering-time switch FLC. Genetics 164, 347-358.
- Gao Z, Maurousset L, Lemoine R, Yoo SD, van Nocker S and Loescher W. 2003 Cloning, expression, and characterization of sorbitol transporters from developing sour cherry fruit and leaf sink tissues. Plant Physiol 131, 1566-1575.
- Zhang H and van Nocker S. 2002. The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C. Plant J 31, 663-673.
- van Nocker S and Ransom C. 2002. Towards a Molecular Understanding of Vernalization: A Genetic Analysis of Pleiotropic Regulators of the Flowering-Time Switch FLC. Flowering Newsletter (G. Bernier, Ed.). 34, 37-44.
- Liu J, Gilmour SJ, Thomashow MF and van Nocker S. 2002. Cold signalling associated with vernalization in Arabidopsis thaliana does not involve CBF1 or abscisic acid. Physiol Plant 114, 125-134.