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CHANGES IN DNA ACCESSIBILITY OCCUR IN PUTATIVE ENHANCER REGIONS OF A SUBSET OF T CELL MEMORY RESPONSIVE GENES

ABSTRACT: Naive T cells exist in a resting state until activated by the antigen they are specific for. Upon activation, T cells produce cytokines and other proteins necessary to fight infections and proliferate to produce more T cells specific for that antigen. Some of these descendants will be long-lived memory T cells, which will return to a resting state but are primed for a more rapid and robust immune response upon re-exposure to the same antigen. The molecular mechanisms responsible for this enhanced response are still unclear. Using a Jurkat cell culture model of transcriptional memory we have investigated the possibility that previously stimulated cells have differences in DNA accessibility compared to non-stimulated cells. We used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in conjunction with high throughput sequencing to identify changes in DNA accessibility in response to stimulation, resting and re-stimulation. We found that although many of the changes in accessibility that were induced upon stimulation, were reversed upon stimulus withdrawal and resting of the cells, a large proportion remain accessible and a subset of these are near genes that have enhanced induction upon re-stimulation. Interestingly the accessibility associated with these ‘memory-responsive’ genes was not always at the transcription start site but sometimes occurred in putative enhancers of these genes. The role of Protein Kinase C in mediating these changes in accessibility was also examined using the inhibitor rottlerin.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63766 | GEO | 2017/03/22

SECONDARY ACCESSION(S): PRJNA269042

REPOSITORIES: GEO

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Project description:Memory T cells respond to stimulation with more rapid expression of effector cell functions than their naM-CM-/ve counterparts, yet the gene expression signature underlying this enhanced recall response is not known. Therefore, we performed comprehensive, whole-genome expression profiling of murine memory CD8 T cells before and shortly after ex vivo stimulation. We compared this differential expression profile to its counterpart from stimulated naive cells. Given that memory cells arise from naive cells, the quiescent state of both cell populations prior to stimulation, and the early time point analyzed (four hours post-stimulation), it was possible that the stimulation-induced changes in gene expression were identical between the two populations. While there was a high degree of overlap, we found that the majority of up-regulated genes were more highly induced following stimulation of memory cells. This more robust increase in transcript levels was observed for a functionally diverse set of genes, including cytokines, chemokines, amino acid metabolic enzymes and transporters, transcription factors and regulators of RNA processing. We also identified the unique, stimulation-induced signatures of naive and memory CD8 T cells and found that the former was enriched for factors involved in regulating chromatin modifications. Specifically, we found that Hdac 5,7 and 8 transcript levels were rapidly down-regulated following stimulation of naive cells, which correlated with an increase in their total level of acetylated histone H3 (AcH3). This was in contrast to stimulated memory cells, which had higher levels of total AcH3 ex vivo that did not change following short-term stimulation. Furthermore, the unique stimulation-induced expression profile of memory cells was enriched for factors involved in regulating transport of molecules between the nucleus and cytoplasm, including multiple members of the nuclear pore complex. Together, these results support a model whereby the chromatin modifications that occur during the differentiation of naM-CM-/ve cells into memory cells are preserved in resting memory populations, facilitating their more robust re-activation of a functionally diverse set of genes that contribute to rapid recall of effector functions. NaM-CM-/ve (CD44lo) and memory phenotype (CD44hi) CD8 T cells from 7-wk old female B6 mice were FACS-purified and cultured in vitro for four hours in the presence or absence of PMA and ionomycin. Total RNA was purified from un-stimulated (resting) naM-CM-/ve, resting memory, stimulated naive, and stimulated memory cells and hybridized to individual single-color arrays. This purification and stimulation protocol was performed four independent times.

Project description:Memory T cells respond to stimulation with more rapid expression of effector cell functions than their naïve counterparts, yet the gene expression signature underlying this enhanced recall response is not known. Therefore, we performed comprehensive, whole-genome expression profiling of murine memory CD8 T cells before and shortly after ex vivo stimulation. We compared this differential expression profile to its counterpart from stimulated naive cells. Given that memory cells arise from naive cells, the quiescent state of both cell populations prior to stimulation, and the early time point analyzed (four hours post-stimulation), it was possible that the stimulation-induced changes in gene expression were identical between the two populations. While there was a high degree of overlap, we found that the majority of up-regulated genes were more highly induced following stimulation of memory cells. This more robust increase in transcript levels was observed for a functionally diverse set of genes, including cytokines, chemokines, amino acid metabolic enzymes and transporters, transcription factors and regulators of RNA processing. We also identified the unique, stimulation-induced signatures of naive and memory CD8 T cells and found that the former was enriched for factors involved in regulating chromatin modifications. Specifically, we found that Hdac 5,7 and 8 transcript levels were rapidly down-regulated following stimulation of naive cells, which correlated with an increase in their total level of acetylated histone H3 (AcH3). This was in contrast to stimulated memory cells, which had higher levels of total AcH3 ex vivo that did not change following short-term stimulation. Furthermore, the unique stimulation-induced expression profile of memory cells was enriched for factors involved in regulating transport of molecules between the nucleus and cytoplasm, including multiple members of the nuclear pore complex. Together, these results support a model whereby the chromatin modifications that occur during the differentiation of naïve cells into memory cells are preserved in resting memory populations, facilitating their more robust re-activation of a functionally diverse set of genes that contribute to rapid recall of effector functions.

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CHANGES IN DNA ACCESSIBILITY OCCUR IN PUTATIVE ENHANCER REGIONS OF A SUBSET OF T CELL MEMORY RESPONSIVE GENES

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