Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Abstract

In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and -1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these ''fragile'' nucleosomes play an important role in regulating RPG transcriptional output.

Molecular mechanisms of ribosomal protein gene coregulation

“…Several transcription factors are associated with RPG regulation (Jorgensen et al 2004;Marion et al 2004;Martin et al 2004;Schawalder et al 2004;Wade et al 2004;Rudra et al 2005;Hall et al 2006;Zhao et al 2006;Joo et al 2011;Knight et al 2014). Of these, Rap1 (repressor activator protein 1) is the clearest sequence-specific DNA-binding protein (Shore 1994), binding ∼90% of RPG promoters (Warner 1999;Lieb et al 2001).…”

“…Of these, Rap1 (repressor activator protein 1) is the clearest sequence-specific DNA-binding protein (Shore 1994), binding ∼90% of RPG promoters (Warner 1999;Lieb et al 2001). Rap1-binding sites at RPGs predominantly occur in pairs, 5-15 base pairs (bp) apart, and with preference for one orientation (Kurtz and Shore 1991;Bosio et al 2011;Knight et al 2014).…”

“…Fhl1 binding also depends on Hmo1 but only where Hmo1 is normally bound (Hall et al 2006;Kasahara et al 2011); there may also be Hmo1-independent Fhl1 recruitment mechanisms (Zeevi et al 2011;Knight et al 2014), which needs to be reconciled. Fhl1 interacts with Ifh1 to activate RPG transcription, which is stimulated by the TOR and PKA signaling pathways, Sirtuins, and Sfp1 (Jorgensen et al 2004;Marion et al 2004;Martin et al 2004;Schawalder et al 2004;Wade et al 2004;Rudra et al 2005;Hall et al 2006;Zhao et al 2006;Berger et al 2007;Xiao et al 2011;Downey et al 2013).…”

Transcriptional control of yeast ribosome biogenesis: A multifaceted role for general regulatory factors

“…These additional regulators generally require promoter-bound GRF for recruitment and, with the exception of Fhl1, are modulated in their promoter association and activity by the two major nutrient-sensing kinase pathways, target of rapamycin complex 1 (TORC1) and protein kinase A (PKA), but also by casein kinase 2. 1,[6][7][8][9][10][11] According to a well-established paradigm, Rap1 is necessary for Fhl1 recruitment. Under rich growth conditions, Fhl1 in turn recruits the transcriptional activator Ifh1 to drive gene expression.…”

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

“…Is it their unusually long (for yeast) introns or their near-consensus GUAUG 5 ′ SS? Is it their stereotypical transcription factors or promoter architecture (Knight et al 2014), or distinctive complement of interacting RNA-binding proteins (Hogan et al 2008)? Could it be connected to reciprocal regulation of ribosomal protein and ribosomal RNA production (Lempiäinen and Shore 2009)?…”