Transcriptional memory drives accelerated re-activation of secondary metabolite production in Aspergillus nidulans [ChIP-seq]
Organisms are repeatedly exposed to fluctuating environmental and nutritional conditions. Transcriptional memory has been shown to be a mechanism to cope with these fluctuations because it increases the speed and the magnitude of the cellular response to a certain re-occurring condition and therefore optimizes adaptation and fitness in a given environment. We found that genes coding for sterigmatocystin (ST) production in Aspergillus nidulans are activated stronger when cells are repeatedly exposed to nutrient starvation, compared to cells that experience this condition for the first time. We studied possible underlying mechanisms and found that persistence of the transcription factor AflR as well as a chromatin-based mechanism through histone H3 lysine 4 dimethylation (H3K4me2) are mediating the memory process. Our data indicate that AflR can undergo activation-inactivation cycles. On the other hand, an unknown mechanism mediated by a so far non-identified signal that originates from culture supernatants that were already starved once, specifically enhances the activation of starvation-dependent BGCs, including ST cluster activation.  Finally, our ChIP-Seq data show that the ST cluster harbors i) three loci of constitutive and two of inducible H3K4me2 near the aflR locus, the latter two building up H3K4me3 after sufficient time, ii) bindings sites of histone demethylase KdmB near these H3K4me2 marks. Overall, using the ST cluster as model we provide insights on transcriptional memory and BGC activation dynamics in A. nidulans. Overall design: A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) and then shifted on Salt medium (no C or N source) for 4 hours --> AMM_20h_Salt_4h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) --> AMM_24h A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) , shifted on Salt medium (no C or N source) for 4 hours , shifted on AMM for 2 h --> AMM_20h_Salt_4h_AMM_2h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) , shifted on AMM for 2 h --> AMM_24h_AMM_2h A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) , shifted on Salt medium (no C or N source) for 4 hours , shifted on AMM for 2 h, shifted on Salt medium (no C or N source) for 1 hour  --> AMM_20h_Salt_4h_AMM_2h_Salt_1h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) , shifted on AMM for 2 h, shifted on Salt medium (no C or N source) for 1 hour --> AMM_24h_AMM_2h_Salt_1h A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) , shifted on Salt medium (no C or N source) for 4 hours , shifted on AMM for 2 h, shifted on used medium (C or N source used up by A. nidulans growth for 48h) for 1 hour  --> AMM_20h_Salt_4h_AMM_2h_Old_1h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) , shifted on AMM for 2 h, shifted on used medium (C or N source used up by A. nidulans growth for 48h) for 1 hour --> AMM_24h_AMM_2h_Old_1h A nd B denote biological replicates, 1 and 2 technical replicates