Selected publications authored or contributed to by the Mackenzie laboratory
Last updated June 2023
Robersy Sanchez, Sally A. Mackenzie (2023)
On the thermodynamics of DNA methylation process. Scientific Reports
Isaac Dopp, Kylie Kalac, Sally A. Mackenzie (2023)
Hydrogen peroxide sensor HyPer7 illuminates tissue-specific plastid redox dynamics. Plant Physiology
Ha Eun Jeh, Robersy Sanchez, Jesús Beltrán, Xiaodong Yang, Hardik Kundariya, Yashitola Wamboldt, Isaac Dopp, Alenka Hafner, Sally A. Mackenzie (2023)
Sensory plastid-associated PsbP DOMAIN-CONTAINING PROTEIN 3 triggers plant growth- and defense-related epigenetic responses. the Plant Journal
Alenka Hafner, Sally A. Mackenzie (2023)
Re-analysis of publicly available methylomes using signal detection yields new information. Scientific Reports
Sally A. Mackenzie, Philip M. Mullineaux (2022)
Plant environmental sensing relies on specialized plastids. Journal of Experimental Botany
Hardik Kundariya, Robersy Sanchez, Xiaodong Yang, Alenka Hafner, Sally A. Mackenzie (2022)
Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system. Genome Biology
Dikungwa Ketumile, Xiaodong Yang, Robersy Sanchez, Hardik Kundariya, John Rajewski, Ismail M. Dweikat, Sally A. Mackenzie (2022)
Implementation of Epigenetic Variation in Sorghum Selection and Implications for Crop Resilience Breeding. Frontiers in Plant Science
Isaac Dopp, Xiaodong Yang, Sally A. Mackenzie. (2021)
A new take on organelle‐mediated stress sensing in plants. New Phytologist
Kundariya H, Yang X, Morton K, Sanchez R, Axtell MJ, Hutton SF, Fromm M, Mackenzie SA (2020)
Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants. Nature Communications volume 11, Article number: 5343
Zhao N, Li Z, Zhang L, Yang X, Mackenzie SA, Hu Z, Zhang MF, Yang J. (2020)
MSH1 mediates fertility reversion of CMS in Brassica juncea in response to environment. Plant, Cell & Environment
Xiaodong Yang, Robersy Sanchez, Hardik Kundariya, Tom Maher, Isaac Dopp, Rosemary Schwegel, Kamaldeep Virdi, Michael J. Axtell and Sally A. Mackenzie (2020)
Segregation of an MSH1 RNAi transgene produces heritable non-genetic memory in association with methylome reprogramming. Nature Communications volume 11, Article number: 2214
Xiaodong Yang and Sally A. Mackenzie (2020)
Approaches to Whole-Genome Methylome Analysis in Plants. Plant Epigenetics and Epigenomics pp 15-31
Robersy Sanchez and Sally A. Mackenzie (2020)
Integrative Network Analysis of Differentially Methylated and Expressed Genes for Biomarker Identification in Leukemia. Scientific Reports
Sally A. Mackenzie and Hardik Kundariya (2019)
Organellar protein multi-functionality and phenotypic plasticity in plants. Phil. Trans. R. Soc. B.
Robersy Sanchez, Xiaodong Yang, Thomas Maher and Sally A. Mackenzie (2019)
Discrimination of DNA Methylation Signal from Background Variation for Clinical Diagnostics. International journal of molecular science.
Xiaodong Yang and Sally A. Mackenzie (2019)
Many Facets of Dynamic Plasticity in Plants. Cold spring harbor perspectives in biology.
Beltrán, J., Wamboldt, Y., Sanchez, R., LaBrant, E.W., Kundariya, H., Virdi, K.S., Elowsky, C., and Mackenzie, S.A. (2018).
Specialized Plastids Trigger Tissue-Specific Signaling for Systemic Stress Response in Plants. Plant Physiol.
Raju, S.K.K., Shao, M.R., Sanchez, R., Xu, Y.Z., Sandhu, A., Graef, G., and Mackenzie, S. (2018).
An epigenetic breeding system in soybean for increased yield and stability. Plant Biotechnol. J.
Shao, M.R., Kumar Kenchanmane Raju, S., Laurie, J.D., Sanchez, R., and Mackenzie, S.A. (2017).
Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss. BMC Plant Biol.
Sanchez, R. and Mackenzie, S.A. (2016a).
Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation. Int. J. Mol. Sci. 17.
10.1371/journal.pone.0150427
Sanchez, R. and Mackenzie, S.A. (2016b).
Information Thermodynamics of Cytosine DNA Methylation. PLoS One 11: e0150427.
Zhao, N., Xu, X., Wamboldt, Y., Mackenzie, S.A., Yang, X., Hu, Z., Yang, J., and Zhang, M. (2016).
MutS HOMOLOG1 silencing mediates ORF220 substoichiometric shifting and causes male sterility in Brassica juncea. J. Exp. Bot. 67: 435–444.
Jinghua Yang, Dongyuan Liu, Xiaowu Wang, Changmian Ji, Feng Cheng, Baoning Liu, Zhongyuan Hu, Sheng Chen, Deepak Pental, Youhui Ju, Pu Yao, Xuming Li, Kun Xie, Jianhui Zhang, Jianlin Wang, Fan Liu, Weiwei Ma, Jannat Shopan, Hongkun Zheng, Sally A Mackenzie & Mingfang Zhang
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection Nature Genetics volume 48, pages 1225–1232 (2016) doi:10.1038/ng.3657
Zhao N, Xu X, Wamboldt Y, Mackenzie SA, Yang X, Hu Z, Yang J, Zhang M.
MutS HOMOLOG1 silencing mediates ORF220 substoichiometric shifting and causes male sterility in Brassica juncea. J Exp Bot. 2016 Jan;67(1):435-44.
Virdi KS, Wamboldt Y, Kundariya H, Laurie JD, Keren I, Kumar KR, Block A, Basset G, Luebker S, Elowsky C, Day PM, Roose JL, Bricker TM, Elthon T, Mackenzie SA.
MSH1 Is a Plant Organellar DNA Binding and Thylakoid Protein under Precise Spatial Regulation to Alter Development. Mol Plant. 2015 Nov 14;S1674-2052(15)00428-1.
Yang X, Kundariya H, Xu YZ, Sandhu A, Yu J, Hutton SF, Zhang M, Mackenzie SA.
MutS HOMOLOG1-Derived Epigenetic Breeding Potential in Tomato. Plant Physiol. 2015 May;168(1):222-32.
Virdi KS, Laurie JD, Xu YZ, Yu J, Shao MR, Sanchez R, Kundariya H, Wang D, Riethoven JJ, Wamboldt Y, Arrieta-Montiel MP, Shedge V, Mackenzie SA.
Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth. Nat Commun. 2015 Feb 27;6:6386.
de la Rosa Santamaria R, Shao MR, Wang G, Nino-Liu DO, Kundariya H, Wamboldt Y, Dweikat I, Mackenzie SA.
MSH1-induced non-genetic variation provides a source of phenotypic diversity in Sorghum bicolor. PLoS One. 2014 Oct 27;9(10):e108407.
Block A, Widhalm JR, Fatihi A, Cahoon RE, Wamboldt Y, Elowsky C, Mackenzie SA, Cahoon EB, Chapple C, Dudareva N, Basset GJ.
The Origin and Biosynthesis of the Benzenoid Moiety of Ubiquinone (Coenzyme Q) in Arabidopsis. Plant Cell. 2014 May 16;26(5):1938-1948.
Block A, Fristedt R, Rogers S, Kumar J, Barnes B, Barnes J, Elowsky CG, Wamboldt Y, Mackenzie SA, Redding K, Merchant SS, Basset GJ.
Functional modeling identifies paralogous solanesyl-diphosphate synthases that assemble the side chain of plastoquinone-9 in plastids. J Biol Chem. 2013 Sep 20;288(38):27594-606.
Forouzesh E, Goel A, Mackenzie SA, Turner JA.
In vivo extraction of Arabidopsis cell turgor pressure using nanoindentation in conjunction with finite element modeling. Plant J. 2013 Feb;73(3):509-20.
Sun P, Arrieta-Montiel MP, Mackenzie SA.
Utility of in vitro culture to the study of plant mitochondrial genome configuration and its dynamic features. Theor Appl Genet. 2012 Aug;125(3):449-54.
Xu YZ, De la Rosa Santamaria R, Virdi KS, Arrieta-Montiel MP, Razvi F, Li S, Ren G, Yu B, Alexander D, Guo L, Feng X, Dweikat IM, Clemente TE, Mackenzie SA.
The chloroplast triggers developmental reprogramming when MUTS HOMOLOG1 is suppressed in plants. Plant Physiol. 2012 Jun;159(2):710-20.
Ducluzeau AL, Wamboldt Y, Elowsky CG, Mackenzie SA, Schuurink RC, Basset GJ.
Gene network reconstruction identifies the authentic trans-prenyl diphosphate synthase that makes the solanesyl moiety of ubiquinone-9 in Arabidopsis. Plant J. 2012 Jan;69(2):366-75.
Davila JI, Arrieta-Montiel MP, Wamboldt Y, Cao J, Hagmann J, Shedge V, Xu YZ, Weigel D, Mackenzie SA.
Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis. BMC Biol. 2011 Sep 27;9:64.
Xu YZ, Arrieta-Montiel MP, Virdi KS, de Paula WB, Widhalm JR, Basset GJ, Davila JI, Elthon TE, Elowsky CG, Sato SJ, Clemente TE, Mackenzie SA.
MutS HOMOLOG1 is a nucleoid protein that alters mitochondrial and plastid properties and plant response to high light. Plant Cell. 2011 Sep;23(9):3428-41.
Shedge V, Davila J, Arrieta-Montiel MP, Mohammed S, Mackenzie SA.
Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance. Plant Physiol. 2010 Apr;152(4):1960-70.
Arrieta-Montiel MP, Shedge V, Davila J, Christensen AC, Mackenzie SA.
Diversity of the Arabidopsis mitochondrial genome occurs via nuclear-controlled recombination activity. Genetics. 2009 Dec;183(4):1261-8.
Feng X, Kaur AP, Mackenzie SA, Dweikat IM.
Substoichiometric shifting in the fertility reversion of cytoplasmic male sterile pearl millet. Theor Appl Genet. 2009 May;118(7):1361-70.
Wamboldt Y, Mohammed S, Elowsky C, Wittgren C, de Paula WB, Mackenzie SA.
Participation of leaky ribosome scanning in protein dual targeting by alternative translation initiation in higher plants. Plant Cell. 2009 Jan;21(1):157-67.
Shedge V, Arrieta-Montiel M, Christensen AC, Mackenzie SA.
Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs. Plant Cell. 2007 Apr;19(4):1251-64.
Sandhu AP, Abdelnoor RV, Mackenzie SA.
Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants. Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1766-70.
Abdelnoor RV, Christensen AC, Mohammed S, Munoz-Castillo B, Moriyama H, Mackenzie SA.
Mitochondrial genome dynamics in plants and animals: convergent gene fusions of a MutS homologue. J Mol Evol. 2006 Aug;63(2):165-73.
Vallejos CE, Astua-Monge G, Jones V, Plyler TR, Sakiyama NS, Mackenzie SA.
Genetic and molecular characterization of the I locus of Phaseolus vulgaris. Genetics. 2006 Feb;172(2):1229-42.
Christensen AC, Lyznik A, Mohammed S, Elowsky CG, Elo A, Yule R, Mackenzie SA.
Dual-domain, dual-targeting organellar protein presequences in Arabidopsis can use non-AUG start codons. Plant Cell. 2005 Oct;17(10):2805-16.
Mackenzie SA.
Plant organellar protein targeting: a traffic plan still under construction. Trends Cell Biol. 2005 Oct;15(10):548-54.
Elo A, Lyznik A, Gonzalez DO, Kachman SD, Mackenzie SA.
Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome. Plant Cell. 2003 Jul;15(7):1619-31.
Abdelnoor RV, Yule R, Elo A, Christensen AC, Meyer-Gauen G, Mackenzie SA.
Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5968-73.
Astua-Monge G, Lyznik A, Jones V, Mackenzie SA, Vallejos CE.
Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases. Theor Appl Genet. 2002 Jan;104(1):48-53.
Janska H, Sarria R, Woloszynska M, Arrieta-Montiel M, Mackenzie SA.
Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility Plant Cell. 1998 Jul;10(7):1163-80.
Sarria R, Lyznik A, Vallejos CE, Mackenzie SA.
A cytoplasmic male sterility-associated mitochondrial peptide in common bean is post-translationally regulated. Plant Cell. 1998 Jul;10(7):1217-28.
He S, Abad AR, Gelvin SB, Mackenzie SA.
A cytoplasmic male sterility-associated mitochondrial protein causes pollen disruption in transgenic tobacco. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11763-8.
Moeykens CA, Mackenzie SA, Shoemaker RC.
Mitochondrial genome diversity in soybean: repeats and rearrangements. Plant Mol Biol. 1995 Oct;29(2):245-54.
Abad AR, Mehrtens BJ, Mackenzie SA.
Specific expression in reproductive tissues and fate of a mitochondrial sterility-associated protein in cytoplasmic male-sterile bean. Plant Cell. 1995 Mar;7(3):271-85.
Janska H, Mackenzie SA.
Unusual mitochondrial genome organization in cytoplasmic male sterile common bean and the nature of cytoplasmic reversion to fertility. Genetics. 1993 Nov;135(3):869-79.
Mackenzie SA.
Identification of a sterility-inducing cytoplasm in a fertile accession line of Phaseolus vulgaris L. Genetics. 1991 Feb;127(2):411-6.
Mackenzie SA, Chase CD.
Fertility Restoration Is Associated with Loss of a Portion of the Mitochondrial Genome in Cytoplasmic Male-Sterile Common Bean. Plant Cell. 1990 Sep;2(9):905-912.
Mackenzie SA, Pring DR, Bassett MJ, Chase CD.
Mitochondrial DNA rearrangement associated with fertility restoration and cytoplasmic reversion to fertility in cytoplasmic male sterile Phaseolus vulgaris L. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2714-7.