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Stressful high temperatures on plants can limit whole-plant function and decrease crop productivity. However, little is known regarding heat stress effects on microtubule cytoskeleton and chromatin in roots from intact plants. Here we studied high temperature effects on cell division, microtubule and chromatin organization patterns in rye root tips from intact plants subjected to 40ºC for 4 h and after different recovery periods (0RT, 7RT, 24 RT). We showed that heat stress induced changes in nuclear morphology as detected by the unusual presence of interphase cells with irregularly shaped nuclei, probably associated with changes in chromosome segregation at anaphase, leading to micronuclei formation as well as changes in the mitotic index. These alterations were associated to differential effects in microtubules organization in both heat-stressed interphase and mitotic cells at 0RT and 7RT. Although no changes in the distribution of H3 phosphorylation of Ser 10 residues on chromatin were found in cells from heat-stressed plants, marked alterations in chromatin DNA methylation patterns were detected. These effects included higher agglutination of 5-methylcytosine domains in both interphase and metaphase cells compared to controls. Taken together these results seem to suggest that alterations in microtubule conformation upon heat stress influences nuclear chromatin organization and cell cycle progression. However, when seedlings recovered from stress (24RT), root tip cells presented microtubule configurations and chromatin organization patterns similar to controls. We conclude that in spite of heat stress markedly altered cell cycle progression and distribution of epigenetic marks, these responses are transient to cope with such stress conditions in the roots., Caryologia. International Journal of Cytology, Cytosystematics and Cytogenetics, Just Accepted