About

Sally Mackenzie is a professor associated with Penn State College of Agricultural Sciences. The page does not provide specific details about her research focus, background, or key contributions.

Research topics

• Computer Science
• Biology
• Genetics
• Political Science
• Engineering ethics
• Geography
• Data science
• Botany
• Chemistry
• Engineering

Selected publications

• Plastid perturbations trigger epigenetic programs during environmental sensing in plants

  PLANT PHYSIOLOGY · 2026-03-17 · 1 citations

  articleSenior author

  Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process remains unclear. Sensing and adjusting to environmental changes are more pronounced in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are enriched in stress response proteins. We investigated the effects of perturbation of four sensory plastid-localized proteins, MutS HOMOLOG 1 (MSH1), PsbP DOMAIN-CONTAINING PROTEIN 3 (PPD3), CAB UNDEREXPRESSED 1 (CUE1), and 3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE 1 (SAL1), on the Arabidopsis (Arabidopsis thaliana) epigenome, detecting gene expression and DNA methylation changes within gene networks associated with environmental sensing. These effects significantly overlapped with a set of CHG hypermethylated genes identified within the chromatin remodeler mutant histone deacetylase 6 (hda6) at 12-hr daylength. At 16-hr daylength, hda6 lost this CHG hypermethylation in gene bodies, and the sensory plastid mutants showed milder adjustments in phenotype and methylation- and gene expression- associated gene networks. We detected daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also found that the hda6 mutation conferred daylength memory and, with msh1, enhanced tolerance to heat and biotic stresses. These results support a model of epigenetically programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in direct response to daylength and environmental cues.

  PublisherDOI

• Intragenic methylation repatterning is associated with alternative splicing and unique epigenetic phenotypes

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-19

  articleOpen accessSenior authorCorresponding

  Abstract The role of intragenic cytosine methylation in shaping phenotypes has been contentious. Recent studies show association between stress and alternative splicing of transcripts, but without functional genome-wide or single-position analysis. We utilized the msh1 experimental system in Arabidopsis as a model of reproducible epigenetic states with stress-responsive phenotypes, including commitment to heritable memory for at least seven generations. We mapped the methylome to single-cytosine resolution with signal-detection, verified by machine learning. Differentially methylated genes were overlapped with msh1 -derived transcript isoforms to show that different patterns of exonic methylation led to different levels of isoform expression. Alternatively spliced and differentially methylated genes were enriched in key regulators of growth and development and spliceosome components. Genes targeted for differential methylation also contained a known CTT motif. These results demonstrate a direct relationship in plants between environmentally responsive differential methylation and alternative splicing behavior leading to phenotype changes.

  PublisherDOI

• The daily rhythms of temperature preference are conserved in nocturnal and blind fish

  Journal of Thermal Biology · 2025-11-20

  articleOpen access

  Light and temperature are key environmental cues that synchronize circadian clocks, and in nature, these cycles are tightly linked. As ectotherms, fish cope with these daily cycles by adjusting their body temperature through behavioural strategies, as moving to warmer/colder areas depending on their internal state. While this pattern has been described in diurnal fish, it remains poorly explored whether nocturnal fish species show similar or opposite daily patterns, or whether blind cave-dwelling fish exhibit daily variations in thermal preference. To this end, we investigated potential circadian rhythms of thermal preference in two nocturnal species of commercial interest (Tinca tinca and Ameiurus melas) and two blind cavefish (blind Astyanax mexicanus and Phreatichthys andruzzii), both models for studying adaptive and regressive evolutionary traits. Using multi-chambered tanks with a horizontal thermal gradient, fish were allowed to choose preferred temperature over 27 days under different Light/Dark conditions (LD, DL), and constant darkness (DD). All species showed significant daily rhythms of thermal preference, moving to warmer temperatures during the day and cooler ones at night. After shifting from LD to DL, fish quickly resumed diurnal rhythms. Under DD, nocturnal species maintained significant behavioural rhythms of temperature selection, while both cavefish species became arrhythmic. These results reveal a conserved daily rhythm of thermal selection, regardless of the fish's daily activity pattern, pointing to a primarily circadian control. Our results may be applied to improve welfare of fish reared in captivity by providing different time-temperature niches that mimic natural daily light/temperature cycles.

  PublisherDOI

• Short‐Term High Light Stress Analysis Through Differential Methylation Identifies Root Architecture and Cell Size Responses

  Plant Cell & Environment · 2024-12-25 · 5 citations

  articleOpen accessSenior authorCorresponding

  DNA methylation repatterning is an epigenomic component of plant stress response, but the extent that methylome data can elucidate changes in plant growth following stress onset is not known. We applied high-resolution DNA methylation analysis to decode plant responses to short- and long-term high light stress and, integrating with gene expression data, attempted to predict components of plant growth response. We identified 105 differentially methylated genes (DMGs) following 1 h of high light treatment and 193 DMGs following 1 week of intermittent high light treatment. Two distinct methylome-predicted plant growth responses to high light treatment could be confirmed by linking methylome changes in auxin response pathways to observed changes in root architecture and methylome changes in cell cycle pathway components to endoreduplication and palisade cell enlargement. We observed methylome changes in a cyclic GMP-dependent protein kinase in association with high light stress signalling. The ability to associate intragenic methylation repatterning with predictable plant phenotypic outcomes after a limited period of high light treatment allows for data-based early prediction of plant growth responses. The approach also permits the dissection of gene networks underpinning plant growth adjustments during environmental change to uncover dynamic phenotype determinants.

  PublisherOA PDFDOI

• Hydrogen peroxide sensor HyPer7 illuminates tissue-specific plastid redox dynamics

  PLANT PHYSIOLOGY · 2023-05-24 · 20 citations

  articleOpen accessSenior authorCorresponding

  The visualization of photosynthesis-derived reactive oxygen species has been experimentally limited to pH-sensitive probes, unspecific redox dyes, and whole-plant phenotyping. Recent emergence of probes that circumvent these limitations permits advanced experimental approaches to investigate in situ plastid redox properties. Despite growing evidence of heterogeneity in photosynthetic plastids, investigations have not addressed the potential for spatial variation in redox and/or reactive oxygen dynamics. To study the dynamics of H2O2 in distinct plastid types, we targeted the pH-insensitive, highly specific probe HyPer7 to the plastid stroma in Arabidopsis (Arabidopsis thaliana). Using HyPer7 and glutathione redox potential (EGSH) probe for redox-active green fluorescent protein 2 genetically fused to the redox enzyme human glutaredoxin-1 with live cell imaging and optical dissection of cell types, we report heterogeneities in H2O2 accumulation and redox buffering within distinct epidermal plastids in response to excess light and hormone application. Our observations suggest that plastid types can be differentiated by their physiological redox features. These data underscore the variation in photosynthetic plastid redox dynamics and demonstrate the need for cell-type-specific observations in future plastid phenotyping.

  PublisherOA PDFDOI

• Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef‐building corals

  Molecular Ecology · 2023-12-28 · 19 citations

  articleOpen access

  Acclimatization through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms' performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant-like properties. They are light dependent with a sessile and modular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes within the colony. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally advance our understanding of how reef-building corals repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.

  PublisherOA PDFDOI

• Sensory plastid‐associated <i>PsbP DOMAIN‐CONTAINING PROTEIN 3</i> triggers plant growth‐ and defense‐related epigenetic responses

  The Plant Journal · 2023-04-10 · 8 citations

  articleOpen accessSenior authorCorresponding

  Sensory plastids are important in plant responses to environmental changes. Previous studies show that MutS HOMOLOG 1 (MSH1) perturbation in sensory plastids induces heritable epigenetic phenotype adjustment. Previously, the PsbP homolog DOMAIN-CONTAINING PROTEIN 3 (PPD3), a protein of unknown function, was postulated to be an interactor with MSH1. This study investigates the relationship of PPD3 with MSH1 and with plant environmental sensing. The ppd3 mutant displays a whole-plant phenotype variably altered in growth rate, flowering time, reactive oxygen species (ROS) modulation and response to salt, with effects on meristem growth. Present in both chloroplasts and sensory plastids, PPD3 colocalized with MSH1 in root tips but not in leaf tissues. The suppression or overexpression of PPD3 affected the plant growth rate and stress tolerance, and led to a heritable, heterogenous 'memory' state with both dwarfed and vigorous growth phenotypes. Gene expression and DNA methylome data sets from PPD3-OX and derived memory states showed enrichment in growth versus defense networks and meristem effects. Our results support a model of sensory plastid influence on nuclear epigenetic behavior and ppd3 as a second trigger, functioning within meristem plastids to recalibrate growth plasticity.

  PublisherOA PDFDOI

• On the thermodynamics of DNA methylation process

  Scientific Reports · 2023-06-01 · 5 citations

  articleOpen accessSenior authorCorresponding

  DNA methylation is an epigenetic mechanism that plays important roles in various biological processes including transcriptional and post-transcriptional regulation, genomic imprinting, aging, and stress response to environmental changes and disease. Consistent with thermodynamic principles acting within living systems and the application of maximum entropy principle, we propose a theoretical framework to understand and decode the DNA methylation process. A central tenet of this argument is that the probability density function of DNA methylation information-divergence summarizes the statistical biophysics underlying spontaneous methylation background and implicitly bears on the channel capacity of molecular machines conforming to Shannon's capacity theorem. On this theoretical basis, contributions from the molecular machine (enzyme) logical operations to Gibb entropy (S) and Helmholtz free energy (F) are intrinsic. Application to the estimations of S on datasets from Arabidopsis thaliana suggests that, as a thermodynamic state variable, individual methylome entropy is completely determined by the current state of the system, which in biological terms translates to a correspondence between estimated entropy values and observable phenotypic state. In patients with different types of cancer, results suggest that a significant information loss occurs in the transition from differentiated (healthy) tissues to cancer cells. This type of analysis may have important implications for early-stage diagnostics. The analysis of entropy fluctuations on experimental datasets revealed existence of restrictions on the magnitude of genome-wide methylation changes originating by organismal response to environmental changes. Only dysfunctional stages observed in the Arabidopsis mutant met1 and in cancer cells do not conform to these rules.

  PublisherOA PDFDOI

• Re-analysis of publicly available methylomes using signal detection yields new information

  Scientific Reports · 2023-02-27 · 5 citations

  articleOpen accessSenior author

  Cytosine methylation is an epigenetic mark that participates in regulation of gene expression and chromatin stability in plants. Advancements in whole genome sequencing technologies have enabled investigation of methylome dynamics under different conditions. However, the computational methods for analyzing bisulfite sequence data have not been unified. Contention remains in the correlation of differentially methylated positions with the investigated treatment and exclusion of noise, inherent to these stochastic datasets. The prevalent approaches apply Fisher's exact test, logistic, or beta regression, followed by an arbitrary cut-off for differences in methylation levels. A different strategy, the MethylIT pipeline, utilizes signal detection to determine cut-off based on a fitted generalized gamma probability distribution of methylation divergence. Re-analysis of publicly available BS-seq data from two epigenetic studies in Arabidopsis and applying MethylIT revealed additional, previously unreported results. Methylome repatterning in response to phosphate starvation was confirmed to be tissue-specific and included phosphate assimilation genes in addition to sulfate metabolism genes not implicated in the original study. During seed germination plants undergo major methylome reprogramming and use of MethylIT allowed us to identify stage-specific gene networks. We surmise from these comparative studies that robust methylome experiments must account for data stochasticity to achieve meaningful functional analyses.

  PublisherOA PDFDOI

• Phenotypic plasticity in coral skeletal features: Molecular signatures from DNA methylation and transcriptional interaction networks

  2023-05-16

  preprintOpen access

  Acclimation through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms’ performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant properties. They are light-dependent with a sessile and modular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes at the local level. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled with significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally alter our understanding of how cnidarian invertebrates repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.

  PublisherOA PDFDOI

Recent grants

• EAGER: Documenting Epigenetic Influence on Plant Quantitative Phenotypic Variation

  NSF · $300k · 2018–2021

• Modeling stress-induced, de novo epiallele architecture in the model Arabidopsis as a tractable entrypoint

  NIH · $320k · 2019–2023

• Nuclear Mechanisms that Influence Mitochondrial Genome Stability

  NSF · $450k · 2008–2011

• NIH Grant R21GM054154

  NIH · $182k · 1998

• TRMS: An Integrative Study of Plant Mitochondrial Biology

  NSF · $1.4M · 2008–2011

Frequent coauthors

• Robersy Sánchez

  Pennsylvania State University

  35 shared

• Xiaodong Yang

  Yangzhou University

  33 shared

• Maria P. Arrieta-Montiel

  University of Nebraska–Lincoln

  22 shared

• Hardik Kundariya

  Pennsylvania State University

  21 shared

• Yashitola Wamboldt

  University of Nebraska–Lincoln

  16 shared

• Kamaldeep S. Virdi

  University of Minnesota

  16 shared

• Ismail Dweikat

  University of Nebraska–Lincoln

  15 shared

• Anna Lyznik

  University of Nebraska–Lincoln

  11 shared

Education

• Ph.D., Botany

  University of California, Berkeley

  1985

• M.S., Botany

  University of California, Berkeley

  1981

• B.S., Botany

  University of California, Davis

  1978