Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

Activation of Clustered IFNγ Target Genes Drives Cohesin-Controlled Transcriptional Memory

“…Enhancer activation of genes results not in increased transcription amplitude or longer bursts but, rather, in an increased frequency of bursts (Fukaya et al, 2016). Similarly, a recent study of transcriptional memory in yeast showed priming to result primarily in an increased frequency in transcription engagement, not an increased rate of transcription (Bheda et al, 2020). We suspect that the population-level priming we observed for GBP5 may be related and represents a general phenomenon in transcriptional memory.…”

The past determines the future: sugar source history and transcriptional memory

“…Validating results and comparing published data is further complicated by the fact that GAL memory protocols have varied greatly in the composition of the media (especially the sugar carbon source for repression) as well as the time of exposure to a particular media (i.e. lengths of inductions and repressions), which can significantly affect the role of various factors (Table 1 ) (Bheda et al 2020 ; Brickner et al 2007 ; Cerulus et al 2018 ; Kundu et al 2007 ; Stockwell and Rifkin 2017 ; Tan-Wong et al 2009 ; Zacharioudakis et al 2007 ; Zhou and Zhou 2011 ). Although the effect of some factors appears to be robust between different types of media changes (such as Swi2, Set3, and Cit1) (Bheda et al 2020 ; Cerulus et al 2018 ; Kim et al 2012 ; Kundu et al 2007 ), we and others have found that the effect of some factors is less consistent (such as Set1 and Htz1) (Bheda et al 2020 ; Brickner et al 2007 ; Kundu et al 2007 ; Kundu and Peterson 2010 ; Laine et al 2009 ; Zhou and Zhou 2011 ).…”

“…For example, in Zhou et al the memory experiment began with long-term growth in repressive glucose medium, whereas Kundu et al initially grew the cells in a neutral raffinose medium, which results in two distinct promoter chromatin conformations (Kundu et al 2007 ; Zhou and Zhou 2011 ). In Bheda et al, we chose to grow cells long-term in raffinose and then repress for the same length of time with glucose prior to each induction in order to keep the initial repression level as similar as possible to the repression between inductions (Bheda et al 2020 ). In addition, while some protocols used rich media (YP), we and others have used synthetic media (SC) to minimize background fluorescence.…”

“…Thus, Stockwell et al used a microfluidics device for automated media changes and observed transient bimodality and unimodality in levels of Gal1p from populations of single cells during galactose induction and reinduction, respectively (Stockwell and Rifkin 2017 ). We recently implemented a high-throughput microfluidics setup in combination with a time-lapse imaging-based screening for analyzing hundreds of mutants on a single-cell level by observing fluorescence from tagged Gal1p as the strains were subjected to repeated inductions (Bheda et al 2020 ). With microfluidics it is possible to follow single cells over time, registering gene expression, cell division and cell growth, among other phenotypes.…”

“…This requires not only observing single cells as they undergo repeated inductions but also simultaneously tracing cell lineages through divisions. We have recently reported a study using new methods and analyses to tackle the above challenges and decipher the role of chromatin-associated factors in the maintenance and inheritance of galactose-induced transcriptional memory in S. cerevisiae (Bheda et al 2020 ).

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