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Epigenetics: Plasticity Versus Inheritability

Research Summary

Bing Zhu is investigating how epigenetic information is inherited during mitotic division and how chromatin-modifying enzymes respond to the chromatin environment, which ultimately determines the epigenetic landscape in eukaryotic cells.

In my laboratory, the ultimate goal is to understand how we can qualify to be successful multicellular organisms. Successful multicellular organisms are required to achieve two simple tasks: (1) Cells should be able to alter their fate to generate distinct cell types for different functions, in a process termed differentiation; and (2) cells and their progenies should be able to maintain their fate when differentiation is no longer required at the postmitotic stages or during proliferation.

DNA is unarguably the carrier of genetic information. However, DNA sequence alone cannot explain how hundreds of cell types in a complex multicellular organism such as a human individual can possess distinct transcription programs, while sharing the same genetic information. This is believed to be achieved by fine-tuning our genetic information with so-called "epigenetic" systems. To fulfill the two basic tasks challenging multicellular organisms, epigenetic systems must simultaneously offer dual characteristics: plasticity and inheritability. Plasticity allows the transformation of one genome into hundreds of epigenomes and transcriptomes, whereas inheritability permits the maintenance of every single epigenome and its corresponding transcriptome.

Mitotic Inheritance of Histone-Modification-Based Epigenetic Information
Several histone modifications have been shown to be critical in classic epigenetic phenomena, including position-effect variegation, Polycomb silencing, and dosage compensation. However, how newly deposited histones acquire these modifications during and after DNA replication remains unclear.

In addition to histone-modification-based epigenetic inheritance, there are two well-studied biological phenomena in which information is transmitted across cell division: the inheritance of genetic information through the DNA sequence and the inheritance of epigenetic information encoded by CpG methylation. Semiconservative DNA replication and sister chromatid segregation ensure the faithful duplication and partition of genetic information. Similarly, symmetric CpG methylations are segregated in a semiconservative way and are faithfully reestablished on the newly synthesized DNA strand by a templated copying event. Therefore, semiconservative partitioning of the histone H3/H4 tetramers followed by templated modification-copying events provides a tempting model for the inheritance of histone modifications during mitotic divisions. However, this model relies on two critical assumptions: (1) inheritable histone modifications are required to exist in a symmetric manner within mononucleosomes and (2) histone H3/H4 tetramers undergo semiconservative segregation during DNA replication-dependent chromatin assembly.

We designed two sets of experiments (Figures 1 and 2) to specifically address the assumptions listed above and reported that neither of these two assumptions exists as a general principle. Therefore, modification copying within the same nucleosomes cannot be the general mechanism governing mitotic epigenetic inheritance. These studies ruled out a seemingly attractive model, provoking further studies toward alternative models.

To establish alternative models for histone-modification-based epigenetic inheritance, we need to know how newly deposited histones acquire their modifications. We took advantage of the stable isotope-based quantitative mass spectrometry to monitor the reestablishment of lysine methylation on newly deposited histones throughout the cell cycle. We discovered that histone methylation levels are transiently reduced during S phase and are gradually reestablished during subsequent cell-cycle stages. However, despite the recovery of overall methylation levels before the next S phase, the methylation levels of parental and newly incorporated histones differ significantly, suggesting even the most "epigenetic" modifications, such as trimethylation at H3K9 and H3K27, are not faithfully duplicated at near-mononucleosome resolution. Finally, we proposed a "buffer model" (Figure 3) that unifies the imprecise inheritance of histone methylation and the faithful maintenance of underlying gene silencing.

Enzymatic Activity Regulation of the Chromatin-Modifying Enzymes
Another important direction in my laboratory is to study the biochemical regulation of chromatin-modifying enzymes. Despite the exponentially increasing number of studies about chromatin-modifying enzymes, the mechanistic regulation of these enzymes is poorly understood. Therefore, we are interested in understanding the molecular mechanisms behind activation and antagonization of chromatin-modifying enzymes. We believe that such mechanistic studies will provide critical information about how the patterns of epigenetic modifications are established and maintained and about how the chromatin modifiers respond to environmental cues.

Our studies in this direction are currently focused on (but not limited to) regulation of the H3K27 methyltransferase Polycomb repressive complex 2 (PRC2), which is pivotal in epigenetic transcriptional regulation, as it is involved in Polycomb silencing, dosage compensation, and cell-lineage specification. From the literature, PRC2 is known to facilitate the spreading of H3K27 methylation along the chromatin and to create a regional repressive environment. However, two important questions remain: (1) How does PRC2-mediated H3K27-methylation spreading become restrained, and (2) how does PRC2 become de novo–activated at genes that just ceased transcription and lead to eventual repression?

Using quantitative mass spectrometry, we discovered that H3 histones that are unmethylated at H3K36 are almost inevitably methylated at H3K27, except for newly deposited H3 histones. On the other hand, H3K27 trimethylation rarely coexists with H3K36 di- or trimethylation on the same H3 polypeptides, suggesting that H3K36 methylation may repress H3K27-specific histone methyltransferase or vice versa. Using biochemical approaches, we discovered that H3K36 methylation can indeed inhibit PRC2-mediated H3K27 methylation. We also discovered that the Trithorax group protein Ash1, which is known to antagonize PRC2 function in vivo, is indeed a histone methyltransferase that is specific to H3K36 dimethylation. This study identified one chromatin component, H3K36 methylation, which antagonizes PRC2 function by directly inhibiting its enzymatic activity. More recently, we also discovered a novel mechanism that permits the de novo allosteric activation of PRC2.

In contrast with studies that aim to identify the chromatin-modifying enzymes or to understand the transcriptional regulation and recruitment of the chromatin-modifying enzymes, studies on regulation of the direct activity of chromatin-modifying enzymes are underrepresented. However, we believe this is an important direction for chromatin biology, not only because of mechanistic insights that can be derived from such studies, but also because we believe that a mechanistic understanding will contribute to guided small-molecule-inhibitor design for chromatin-modifying enzymes. This goal is particularly important because many chromatin-modifying enzymes, such as histone deacetylases (HDACs) and, more recently, PRC2, are being considered as potential drug targets.

Finally, chromatin events are believed to be able to respond to environmental cues, but studies in this direction are quite limited. We reason that signaling events may directly impact the enzymatic activities of chromatin-modifying enzymes and influence their underlying biological processes, and we believe that our focus on understanding the activation and inhibition of chromatin-modifying enzymes will eventually contribute to an important direction—from signaling to chromatin.

These projects are funded in part by grants from the Chinese Ministry of Science and Technology and the Beijing Municipal Science and Technology Commission.

As of January 17, 2012