PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

Abstract

PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.DOI: http://dx.doi.org/10.7554/eLife.10607.001

PHF13: A new player involved in RNA polymerase II transcriptional regulation and co-transcriptional splicing

“…We recently identified PHF13 as a novel H3K4me2/3 chromatin reader and transcriptional co-regulator. 1 We found that PHF13 interacts with and tethers PRC2 (a H3K27 methyltransferase) to H3K4me3/H3K27me3 bivalent promoters and that its depletion led to increased expression at these targets and reduced PRC2 binding. In addition to bivalent targets, PHF13 was also found at a greater number of active promoters (H3K4me3-only) genome wide and its depletion led to reduced expression from these targets.…”

“…20,21 Furthermore, PHF13 forms a common complex with H3K4me2/3, PRC2 and RNAPII S5P in mouse ESCs as was demonstrated by their co-elution and co-precipitation in column chromatography. 1 Consistently, PHF13 co-localized at a subset of PRC2 bound genes and its depletion led to increased expression from these bivalent targets, arguing that it acts as a transcriptional co-regulator at a subset of polycomb regulated genes. 1 Furthermore, PHF13 depletion led to the reduction of both PRC2 and RNAPII S5P at H3K4me3/H3K27me3 demarcated chromatin, arguing for a specific role of PHF13 in the recruitment or stabilization of these complexes.…”

“…1 Consistently, PHF13 co-localized at a subset of PRC2 bound genes and its depletion led to increased expression from these bivalent targets, arguing that it acts as a transcriptional co-regulator at a subset of polycomb regulated genes. 1 Furthermore, PHF13 depletion led to the reduction of both PRC2 and RNAPII S5P at H3K4me3/H3K27me3 demarcated chromatin, arguing for a specific role of PHF13 in the recruitment or stabilization of these complexes. 1 Taken together, these findings strongly suggest a mutual relationship between PHF13, PRC2 and RNA-PIIS5P in the transcriptional co-regulation of specific targets.…”

“…1 Furthermore, PHF13 depletion led to the reduction of both PRC2 and RNAPII S5P at H3K4me3/H3K27me3 demarcated chromatin, arguing for a specific role of PHF13 in the recruitment or stabilization of these complexes. 1 Taken together, these findings strongly suggest a mutual relationship between PHF13, PRC2 and RNA-PIIS5P in the transcriptional co-regulation of specific targets.…”

“…To this end, we have recently identified the chromatin reader and effector protein PHF13, as a novel RNAPII S5 interacting protein. 1 Modifications of all CTD amino acids have been described (namely; phosphorylation, glycosylation, methylation, acetylation and isomerization) and their timely appearance is required for coordination of the transcription cell cycle. 3 The CTD of RNAPII can be phosphorylated at Y 1 , S 2 , T 4 , S 5 and S 7 and the phosphorylation of each of these residues is affiliated with distinct functions in the transcription cycle.…”