Dot1 regulates nucleosome dynamics by its inherent histone chaperone activity in yeast

Abstract

Dot1 (disruptor of telomeric silencing-1, DOT1L in humans) is the only known enzyme responsible for histone H3 lysine 79 methylation (H3K79me) and is evolutionarily conserved in most eukaryotes. Yeast Dot1p lacks a SET domain and does not methylate free histones and thus may have different actions with respect to other histone methyltransferases. Here we show that Dot1p displays histone chaperone activity and regulates nucleosome dynamics via histone exchange in yeast. We show that a methylation-independent function of Dot1p is required for the cryptic transcription within transcribed regions seen following disruption of the Set2–Rpd3S pathway. Dot1p can assemble core histones to nucleosomes and facilitate ATP-dependent chromatin-remodeling activity through its nucleosome-binding domain, in vitro. Global analysis indicates that Dot1p appears to be particularly important for histone exchange and chromatin accessibility on the transcribed regions of long-length genes. Our findings collectively suggest that Dot1p-mediated histone chaperone activity controls nucleosome dynamics in transcribed regions.

Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase

“…These results suggest that the DOT1L binding to the nucleosome might destabilize the nucleosome structure. Consistent with these observations, a recent study showed that DOT1L-bound nucleosome is more readily remodeled by the CHD1 ATP-dependent chromatin remodeler than the nucleosome alone (Lee et al 2018).…”

“…Furthermore, these results add another layer of complexity to the cross-talk, where H2B ubiquitination regulates the DOT1L-mediated nucleosome destabilization in addition to histone H3 Lys79 methylation. As previous works showed that H2B ubiquitination plays important roles in transcription elongation and nucleosome dynamics, DOT1L-mediated DNA unwrapping might facilitate this process (Wu et al 2014;Krajewski et al 2018;Lee et al 2018). At this moment, it is not clear how DOT1L binding induces the detachment of DNA with the concomitant disorder of the parts of histones.…”

“…In addition to their catalytic activities, histone methyltransferases have been shown to have noncatalytic activities (Kim et al 2015). A recent study showed that yeast Dot1 has nucleosome chaperone activity and enhances the ATP-dependent chromatin remodeling by CHD1, which is independent of Dot1 methyltransferase activity (Lee et al 2018). This work suggested that Dot1/DOT1L might destabilize the nucleosome structure and help the remodeler to alter the nucleosome structure.…”

Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L‐dose dependency in HDAC1‐deficient thymic lymphoma

“…Histone acetylation is increased in the absence of the deacetylase HDAC1, and histone acetylation has been previously linked to DOT1L recruitment through the YEATS domain transcription elongation proteins AF9 and ENL (Li et al , ; Kuntimaddi et al , ; Erb et al , ; Wan et al , ). Very recently, preferential Dot1 binding to acetylated H4K16 has been shown, and the histone acetyltransferase Sas2 was found to be a positive regulator of H3K79 methylation in yeast, probably via acetylation of H4K16 (Lee et al , ). Our identification of Rpd3/HDAC1 as a regulator of DOT1L underscores the intimate relationship between histone acetylation and H2Bub and H3K79me and provides evidence for a specific HDAC involved in the crosstalk: HDAC1.…”

Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism

“…Current evidence from studies in yeast and with DOT1L in vitro suggest that H2Bub1 promotes the activity of Dot1 not by increased recruitment, but instead by physically corralling the enzyme into a productive binding orientation, promoting all methylation steps from unmethylated H3K79 to H3K79me1, -me2 and -me3 ( 19 , 27 ). As a consequence, co-transcriptional H2Bub1 deposition leads to a high methylation state (H3K79me3) in transcribed regions, whereas in intergenic regions or silent chromatin, where H2Bub1 is low, only lower methylation states (H3K79me1 and -me2) are deposited ( 20 , 28 , 29 ). Recently, several additional mechanisms of regulation of Dot1 have been described, some of which also impinge on the H2Bub-H3K79me crosstalk ( 20 ).…”