My laboratory is interested in the relationship between chromatin structure and gene function in animals and in plants. There is a growing recognition of the importance of chromatin structure and of the products of the Pc-G/Trx-G complex as part of a global cellular memory system. Despite the realization that these mechanisms are involved in processes regulating cell-fate and developmental programs, we still know little about the Pc-G/Trx-G functions and chromatin-regulated events in plants.
With the advent of new technologies and groundbreaking new studies, there is a renewed interest in exploring the possibilities for common mechanisms regulating development in animals and in plants.
We are studying a family of Trithorax related genes in the model plant Arabidopsis. We are studying its role in regulating flower development and the molecular/biochemical mechanism of its activity. The unexpected observation that some members of the family (ATX1) are not obligatory nuclear proteins and the determined ability of ATX1 to bind the phospholipid ligand, phosphoinositide-5 phosphate, opened a novel venue of our research: a current goal is to characterize this signaling mechanism connecting cellular signaling with epigenetic gene regulation. We are particularly interested in the evolution of these mechanisms at the molecular level and include a broad array of phylogenetic, bioinformatics, molecular and cellular biology approaches.
- Fromm M and Avramova Z. How ATX1/COMPASS and H3K4me3 activate transcription of dependent genes in Arabidopsis. Current Opinion in Plant Biol (2014), 21: 75-82.
- Virluvet L, Ding Y, Fujii H, Avramova Z, and Fromm M. ABA Signaling is Necessary but not Sufficient for RD29B Transcriptional Memory during Successive Dehydration Stresses in Arabidopsis thaliana. The Plant J. (2014) 79: 150-161.
- Ding Y, Virluvet L, Liu N, Riethoven J-J, Russo S, Avramova Z, and Fromm M. Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana. BMC Plant Biology (2014) 14: 141; doi:10.1186/1471-2229-14-141.
- Liu N, Ding Y, Fromm M and Avramova Z. Different gene-specific mechanisms determine the ‘revised-response’ memory transcription patterns of a subset of A. thaliana dehydration stress responding genes. Nucleic Acid Research (2014) 42: 5556-5566/
- Liu N, Fromm M, and Avramova Z. H3K27me3 and H3K4me3 chromatin environment at superinduced dehydration stress memory genets of Arabidopsis thaliana. Mol. Plant (2014) 7: 502-513.
- Ding Y, Liu N, VirlouvetL, Riethoven J-J, Fromm M, and Avramova Z. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biology (2013), 13:229 http://www.biomedcentral.com/1471-2229/13/229
- Ding Y, Fromm M, and Avramova Z. Multiple exposures to drought induce altered transcriptional responses; trainable Arabidopsis genes and paused polymerase II. Nature Communications (2012) Mar 13; 3:740. doi: 10.1038/ncomms1732
- Ding Y, Ndamukong I, Xu Z, Lapko H, Fromm M, Avramova Z. ATX1-Generated H3K4me3 is Required for Efficient Elongation of Transcription, not Initiation, at ATX1-Regulated Genes. (2012) PLoS Genet. 8(12):e1003111. doi: 10.1371/journal.pgen.1003111. Epub 2012 Dec 20
- Alvarez-VenegasR, AvramovaZ. Evolution of the PWWP-Domain Encoding genes in the Plant and Animal Lineages. BMC Evol Biol. (2012) 12:101-118
- Ding Y, Ndamukong I, Zhao Y, Jones D, Riethoven JJ, Divecha N, Avramova Z. Divergent Functions of the Arabidopsis Myotubularin (MTM) Homologs AtMTM1 and AtMTM2; evolution of the plant MTM family The Plant J. (2012) 70(5):866-78
- Hayot CM, Forouzesh E, AvramovaZ, Turner JA. Viscoelastic Parameters of Cell Walls of Single Living Plant Cells Determined by Dynamic Nanoindentation. J Exp. Bot. (2012) 637:2525-40.
- Ndamukong I, Lapko H, Cerny R, and Avramova Z. A cytoplasm-specific activity encoded by the Trithorax-like ATX1 locus (2011) Nucleic Acid Res. 39: 1-11
- Ding Y, Avramova Z, and Fromm M. Two Distinct Roles of Arabidopsis Homolog of Trithorax, ATX1, at Promoters and within 5’-Transcribed Regions of ATX1 Regulated Genes (2011) The Plant Cell 23:350-363.
- Ding Y, Avramova Z, and Fromm M. The Plant Trithorax-like Factor ATX1 functions in Dehydration Stress Responses in Arabidopsis through ABA-dependent and ABA-independent pathways (2011) The Plant J. 66: 735-744
- van DijkK, Ding Y, MalkaramS, RiethovenJ-JM, Li R, Yang J, Laczko P, ChenH, Xia Y, LadungaI, Avramova Z, and Fromm M. Dynamic Changes of Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana. BMC Plant Biol. 2010 Nov 5;10(1):238.
- Ndamukong I, Jones D, Lapko H, Divecha N. and Avramova Z. (2010) Phosphatidylinositol 5-phosphate links dehydration stress to the activity of ARABIDOPSIS TRITHORAX-LIKE factor ATX1. PLoS One Oct 13;5(10):e13396.
- AvramovaZ. Epigenetic regulatory mechanisms in plants. In: Trygve Tollefsbol, editors, Handbook of Epigenetics. Oxford: Academic Press, 2010, pp. 251-278.
- Ding Y, Lapko H, Ndamukong I, Xia Y, Al-Abdallat A, Sadder M, Lalithambika S, Fromm M., Riethoven JJ., Lu G, and Avramova Z. (2009) Involvement of ATX1 and Myotubularin 1 in the Arabidopsis response to draught stress. Plant Sign. and Behav. 4: 1049-1058.
- Ndamukong I, Chetram A, Saleh A. and Avramova Z. (2009) The Arabidopsis Homolog of Trithorax, ATX1, Regulates Expression of a Multitude of Wall-Modifying Genes; repression of the XTH33 gene by ATX1 as a test case. The Plant J. 58:541-553.
- AvramovaZ. Evolution and pleiotropy of TRITHORAX function in Arabidopsis (2009) J. Dev. Biol. 53:371-381
- Saleh A, Alvarez-VenegasR, and AvramovaZ. (2008) Dynamic and stable histone H3 methylation patterns at the Arabidopsis FLC and AP1 loci. GENE 423, 43-47
- Veerappan C, Avramova, Z, and MoriyamaE. (2008) Evolution of SET-domain families in the unicellular and multicellular Ascomycota fungi. BMC Evolutionary Biology 8, 190-210.
- Saleh A, Alvarez-VenegasR, Yilmaz M, Oahn-Le, Al-AbdallatA, Monther S, XiaY, LadungaI, and AvramovaZ. (2008) The highly similar ARABIDOPSIS HOMOLOGS OF TRITHORAX ATX1 and ATX2 encode divergent biochemical functions The Plant Cell, 20, 568-579
- Pien S, Fleury D, MylneJS, Crevillen P, Inzé D, AvramovaZ, Dean C, and Grossniklaus U. (2008) Unraveling trithorax Function in Plants: ATX1 Dynamically Regulates the Activation of FLC via Histone 3 Lysine 4 Tri-methylation The Plant Cell 20, 580-588
- Saleh A, Alvarez-Venegas R, and Avramova Z. (2008) An efficient chromatin immunoprecipitation protocol (ChIP) for studying histone modifications in Arabidopsis plants. Nature Protocols 3,1018-1025