Structural Paradigms in the Recognition of the Nucleosome Core Particle by Histone Lysine Methyltransferases

Janna, Ashley; Davarinejad, Hossein; Joshi, Monika; Couture, Jean-François

doi:10.3389/fcell.2020.00600

Cited by 8 publications

(7 citation statements)

References 95 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…During transcription elongation, H2B is ubiquitinated at lysine 123 in budding yeast (lysine 120 in humans) by the E2 ubiquitin conjugase Rad6 (UBE2A in humans) and E3 ligase Bre1 (RNF20/40 heterodimer in humans) in a process that also depends on Paf1C [ 106 , 200 , 220 ]. H2Bub stimulates the activity of the H3K4 methyltransferase Set1 and H3K79 methyltransferase Dot1, which is termed trans histone cross-talk [ 47 , 84 , 182 , 188 , 192 ]. H2Bub also stimulates Set2 H3K36 trimethylation activity [ 16 , 191 ].…”

Section: Regulation Of Set2/setd2 Activity and Substrate Recognitionmentioning

confidence: 99%

SETD2: from chromatin modifier to multipronged regulator of the genome and beyond

Molenaar

Leeuwen

2022

Cell. Mol. Life Sci.

View full text Add to dashboard Cite

Histone modifying enzymes play critical roles in many key cellular processes and are appealing proteins for targeting by small molecules in disease. However, while the functions of histone modifying enzymes are often linked to epigenetic regulation of the genome, an emerging theme is that these enzymes often also act by non-catalytic and/or non-epigenetic mechanisms. SETD2 (Set2 in yeast) is best known for associating with the transcription machinery and methylating histone H3 on lysine 36 (H3K36) during transcription. This well-characterized molecular function of SETD2 plays a role in fine-tuning transcription, maintaining chromatin integrity, and mRNA processing. Here we give an overview of the various molecular functions and mechanisms of regulation of H3K36 methylation by Set2/SETD2. These fundamental insights are important to understand SETD2’s role in disease, most notably in cancer in which SETD2 is frequently inactivated. SETD2 also methylates non-histone substrates such as α-tubulin which may promote genome stability and contribute to the tumor-suppressor function of SETD2. Thus, to understand its role in disease, it is important to understand and dissect the multiple roles of SETD2 within the cell. In this review we discuss how histone methylation by Set2/SETD2 has led the way in connecting histone modifications in active regions of the genome to chromatin functions and how SETD2 is leading the way to showing that we also have to look beyond histones to truly understand the physiological role of an ‘epigenetic’ writer enzyme in normal cells and in disease.

show abstract

Section: Regulation Of Set2/setd2 Activity and Substrate Recognitionmentioning

confidence: 99%

SETD2: from chromatin modifier to multipronged regulator of the genome and beyond

Molenaar

Leeuwen

2022

Cell. Mol. Life Sci.

View full text Add to dashboard Cite

show abstract

“…H2BK123ub is important for nucleosome stability during transcription elongation in vivo, likely in coordination with the histone chaperone FACT, and poses an energetic barrier to RNAPII in vitro (5)(6)(7)(8). Through a crosstalk mechanism, H2BK123ub is required for the di-and tri-methylation of H3K4 and H3K79 via the Set1 and Dot1 methyltransferases, respectively (9)(10)(11)(12)(13). In turn, H3K4me2 and H3K4me3 recruit histone acetyltransferase and deacetylase complexes, further modulating chromatin accessibility (14)(15)(16).…”

Section: Introductionmentioning

confidence: 99%

Paf1 complex subunit Rtf1 stimulates H2B ubiquitylation by interacting with the highly conserved N-terminal helix of Rad6

Fetian

McShane

Horan

et al. 2022

Preprint

View full text Add to dashboard Cite

Histone modifications coupled to transcription elongation play important roles in regulating the accuracy and efficiency of gene expression. The mono-ubiquitylation of a conserved lysine in H2B (K123 inSaccharomyces cerevisiae; K120 in humans) occurs co-transcriptionally and is required for initiating a histone modification cascade on active genes. H2BK123 ubiquitylation (H2BK123ub) requires the RNA polymerase II (RNAPII)-associated Paf1 transcription elongation complex (Paf1C). Through its Histone Modification Domain (HMD), the Rtf1 subunit of Paf1C directly interacts with the ubiquitin conjugase Rad6, leading to the stimulation of H2BK123ubin vivoandin vitro. To understand the molecular mechanisms that target Rad6 to its histone substrate, we identified the site of interaction for the HMD on Rad6. Usingin vitrocrosslinking followed by mass spectrometry, we localized the primary contact surface for the HMD to the highly conserved N-terminal helix of Rad6. Using a combination of genetic and biochemical experiments, we identified separation-of-function mutations inS. cerevisiae RAD6that greatly impair H2BK123 ubiquitylation but not other Rad6 functions. Finally, by employing RNA-sequencing as a sensitive approach for comparing mutant phenotypes, we show that mutating either side of the proposed Rad6-HMD interface yields strikingly similar transcriptome profiles that extensively overlap with those of a mutant that lacks the site of ubiquitylation in H2B. Our results fit a model in which a specific interface between a transcription elongation factor and a ubiquitin conjugase guides substrate selection toward a highly conserved chromatin target during active gene expression.Significance StatementTranscription by RNAPII is tightly coordinated with mechanisms that control chromatin structure. Disruption of this interplay leads to deleterious effects on gene expression and genome architecture. Proteins that associate with RNAPII during transcription elongation play an important role in coupling histone modifications to active transcription. Paf1C, a conserved member of the RNAPII active elongation complex, is required for the ubiquitylation of histone H2B, a modification with effects on nucleosome stability and the methylation and acetylation state of chromatin. Here, we provide new insights into how a conserved domain in Paf1C, which we previously showed to be necessary and sufficient for Paf1C-mediated stimulation of H2B ubiquitylation, interacts with the ubiquitin conjugase for H2B thereby guiding its specificity.

show abstract

“…Disrupting the interaction impairs the enzyme activity both in vitro and in vivo. 24,42,43 Our study shows that SET8 contains an arginine-rich motif. SET8 single residue mutation R192A reduces the SET8-nucleosome interaction in vitro and impairs the SET8 activity in vivo.…”

Section: Discussionmentioning

confidence: 65%

“…The Dot1 residues R278, R282 and Set1 residues R821, R824, R828, R829 interact with the acidic patch. Disrupting the interaction impairs the enzyme activity both in vitro and in vivo 24,42,43 . Our study shows that SET8 contains an arginine‐rich motif.…”

Section: Discussionmentioning

confidence: 74%

Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8

et al. 2022

View full text Add to dashboard Cite

Histone H4 lysine 20 monomethylation (H4K20me1) plays a crucial role in multiple processes including DNA damage repair, DNA replication, and cell cycle control. Histone methyltransferase SET8 (previously named PR‐Set7/KMT5A) mediates the chromatin deposition of H4K20me1, but how SET8 recognizes and modifies H4 in the context of the nucleosome is not fully understood. Here, we developed a simple chemical modification approach for H4K20 substitution by using the lysine analog S‐ethyl‐L‐cysteine (Ecx). Substitution of H4K20 with H4Ecx20 improves the stability of the SET8‐nucleosome complex, allowing us to determine the cryo‐EM structure at 3.2 Å resolution. Structural analyses show that SET8 directly interacts with the H4 tail and the H2A‐H2B acidic patch to ensure nucleosome binding. SET8 residues R339, K341, K351 make contact with nucleosomal DNA at the super helical location 2 (SHL2). Substitution of SET8 DNA‐binding residues with alanines decreases the SET8‐nucleosome interaction and impairs the methyltransferase activity. Disrupting the binding between SET8 R192 and H2A‐H2B acidic patch decreases the cellular level of H4K20me1. Together, these results reveal a near‐atomic resolution structure of SET8‐bound nucleosome and provide insights into the SET8‐mediated H4K20 recognition and modification. The lysine‐to‐Ecx substitution approach can be applied to the study of other methyltransferases.

show abstract

Structural Paradigms in the Recognition of the Nucleosome Core Particle by Histone Lysine Methyltransferases

Cited by 8 publications

References 95 publications

SETD2: from chromatin modifier to multipronged regulator of the genome and beyond

SETD2: from chromatin modifier to multipronged regulator of the genome and beyond

Paf1 complex subunit Rtf1 stimulates H2B ubiquitylation by interacting with the highly conserved N-terminal helix of Rad6

Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8

Contact Info

Product

Resources

About