Identification of preferentially reactivated genes during early G1 phase using nascent mRNA as an index of transcriptional activity

Abstract

During mammalian mitosis, transcription is silenced due to dissociation of transcription factors from DNA and chromosome condensation. At the end of mitosis, transcription is reactivated through chromosome relaxation and reloading of these factors to the DNA. Early G1 genes, which are preferentially reactivated during M/G1 transition, are important for maintenance of cellular function and are known to be strictly regulated. As only few early G1 genes have been identified to date, screening for early G1 genes by genome-wide analysis using nascent mRNA could contribute to the elucidation of the regulatory mechanisms during early G1. Here, we performed a detailed expression analysis for the M/G1 transition of mammalian cells by microarray analysis of nascent mRNA, and identified 298 early G1 genes. Analysis of these genes provides two important insights. Firstly, certain motifs are enriched in the upstream sequences of early G1 genes; from this we could predict candidate cognate transcription factors, including Sp1, which is recruited to the DNA in the early G1 phase. Secondly, we discovered that neighboring genes of early G1 genes were also frequently up-regulated in the G1 phase. Information about these numerous newly identified early G1 genes will likely contribute to an understanding of the regulatory mechanisms of the early G1 genes.

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition

“…Our analyses thus far have relied on the use of cell cycle synchronization methods, as have previous studies of transcription at the mitosis-G1 transition (Blobel et al 2009;Anup Dey et al 2009;Zhao et al 2011;Fukuoka et al 2012;Caravaca et al 2013). While the resolution of cell cycle synchrony provided unambiguous visualization of the pioneering round of transcription upon reversal of mitotic silencing ( Fig.…”

“…Several studies have directly quantified transcriptional activity over time in cells transitioning from mitosis to interphase (Blobel et al 2009;Anup Dey et al 2009;Muramoto et al 2010;Zhao et al 2011;Fukuoka et al 2012;Caravaca et al 2013), using RT-qPCR of primary transcripts of candidate genes (Blobel et al 2009;Anup Dey et al 2009;Fukuoka et al 2012;Caravaca et al 2013), live-cell imaging of transcription of act-5 in Dictyostelium (Muramoto et al 2010) and a multi-copy reporter locus in a human cell line (Zhao et al 2011), and microarray-based measurements of nascent transcripts (Fukuoka et al 2012). Several of these studies suggest or assume that transcriptional output early after mitosis starts off low and rises monotonically with G1 progression at varying kinetics (Blobel et al 2009;Zhao et al 2011;Fukuoka et al 2012;Caravaca et al 2013). However, some genes show non-monotonic changes in transcriptional output with cell cycle progression after mitosis, but no explanations for these observations have been proposed (Anup Dey et al 2009;Muramoto et al 2010;Fukuoka et al 2012;Caravaca et al 2013).…”

“…Several of these studies suggest or assume that transcriptional output early after mitosis starts off low and rises monotonically with G1 progression at varying kinetics (Blobel et al 2009;Zhao et al 2011;Fukuoka et al 2012;Caravaca et al 2013). However, some genes show non-monotonic changes in transcriptional output with cell cycle progression after mitosis, but no explanations for these observations have been proposed (Anup Dey et al 2009;Muramoto et al 2010;Fukuoka et al 2012;Caravaca et al 2013). It remains unclear which transcriptional pattern represents the general rule, as these previous approaches lacked genome-wide extraction of the most prominent patterns.…”

Control of cell cycle transcription during G1 and S phases

“…These waves of transcription coincide with the different transition points during the cell cycle, namely G1-to-S, G2-to-M and M-to-G1. Although all three cell cycle transcript waves are well-characterized in yeast, transcription that occurs during the M-to-G1 phase transition in human cells is less well-defined 13 . Largely on the basis of work carried out in the budding yeast Saccharomyces cerevisiae , it is thought that the subsequent waves of transcription form a continuous regulatory network in which each wave is activated by the previous one and contains activators of the following wave 14 .…”

Mitotic transcription and waves of gene reactivation during mitotic exit

“…4A, table S16–17)(24, 25). Therefore, genes that reconstitute basic cell structure and growth are prioritized immediately following mitosis, expanding on the ribosomal and metabolic genes seen elsewhere (26). The next wave of reactivation is enriched for adhesion genes, consistent with the epithelial nature of HUH7 cells (table S18–19).…”