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FitzGerald, P. C.

Publications and source records attributed to FitzGerald, P. C..

2 recordsLinked to original sources

The ETS Transcription Factor ERF controls the exit from the naive pluripotent state

The naive epiblast undergoes a transition to a pluripotent primed state during embryo implantation. Despite the relevance of the FGF pathway during this period, little is known about the downstream effectors regulating this signaling. Here, we examined the molecular mechanisms coordinating the naive to primed transition by using inducible ESC to genetically eliminate all RAS proteins. We show that differentiated RASKO ESC remain trapped in an intermediate state of pluripotency with naive-associated features. Elimination of the transcription factor ERF overcomes the developmental blockage of RAS-deficient cells by naive enhancer decommissioning. Mechanistically, ERF regulates NANOG expression and ensures naive pluripotency by strengthening naive transcription factor binding at ESC enhancers. Moreover, ERF negatively regulates the expression of the de novo methyltransferase DNMT3B, which participates in the extinction of the naive transcriptional program. Collectively, we demonstrated an essential role for ERF controlling the exit from naive pluripotency during the progression to primed pluripotency. TeaserERF is the MAPK-dependent switch controlling the transition between naive and primed pluripotency during embryonic development.

developmental biology

Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria

Promoter-proximal pausing regulates expression of many eukaryotic genes and serves as checkpoints for assembly of elongation/splicing machinery. Little is known how broadly the pausing is employed in transcriptional regulation in bacteria. We applied NET-seq combined with RNase I footprinting for genome-wide analysis of {sigma}70-dependent transcription pauses in Escherichia coli. Many E. coli genes appear to contain clusters of strong backtracked pauses at 10-20-bp distance from the transcription start site caused by retention of {sigma}70 subunit in RNA polymerase. The pauses in 10-15-bp register of the promoter are dictated by binding of {sigma}70 to canonical -10 element, 6-7 nt spacer and "YR+1Y" motif centered at transcription start site all characteristic for strong E. coli promoters. The promoters for the pauses in 16-20-bp register contain an additional -10-like sequence positioned on the same face of the DNA duplex as the original -10 element suggesting that {sigma}70 hopping was responsible for these pauses. Our in vitro analysis reveals that RNA polymerase backtracking and DNA scrunching are involved in these pauses that are relieved by Gre transcript cleavage factors. The genes coding for transcription factors are enriched in these pauses suggesting that {sigma}70 and Gre proteins regulate transcription in response to changing environmental cues.

microbiology