When they both come together in one paper and it’s in my favorite journal, Cell Stem Cell, you’ve got my full attention. My own lab is especially interested in the roles of histones and Myc in stem cells.
So when I saw a paper a paper from a team lead by Shunsuke Ishii at RIKEN on the roles of histones TH2A and TH2B (variants of H2A and H2B), I thought it was very cool.
The paper from Ishii’s team, Shinagawa, et al., is entitled Histone Variants Enriched in Oocytes Enhance Reprogramming to Induced Pluripotent Stem Cells.
They report that the histone variants TH2A and TH2B, which are highly expressed in testes, oocytes, and one-celled embryos, substantially boost the cellular reprogramming process to make iPS cells. There was almost no expression of the variants in MEFs (no surprise) but interestingly there was little expression of the variants in ES cells either. That’s more surprising.
A lot of factors can enhance reprogramming so why is this work exciting? What is particularly interesting here is that it seems that TH2A and TH2B function in a novel kind of way by globally opening chromatin structure (Figure 7). This may set the table for subsequent activity by other reprogramming factors.
Surprisingly, this new paper reports that TH2A and TH2B had no effect on the heterochromatic mark H3K9me3 so these variants must promote open chromatin through a mechanism not involving repression of heterochromatin that is enriched for H3K9me3. For comparison, Myc, which can also boost global chromatin openness at least in part by recruiting histone acetyltransferases, seems to inversely correlate with H3K9me3 based on Myc knockout studies.
The team did link up these histone variants to other epigenetic marks (emphasis mine) in ways that are fascinating even if still not entirely clear mechanistically:
A lack of maternal TH2A/TH2B disturbed activation of the paternal genome in zygotes. In zygotes lacking maternal TH2A/ TH2B, the levels of H3K4me3 on the paternal genome were much lower than those in the control WT zygotes. The levels of 5mC on the paternal genome in the zygotes lacking maternal TH2A/TH2B were higher than those in WT zygotes. In addition, the paternal genome in the zygotes lacking maternal TH2A/TH2B contained lower levels of 5hmC. These results suggest that in the absence of maternal TH2A/TH2B, paternal genome activation, which accompanies H3K4me3 and DNA demethylation, is defective. Consistent with these observations, the levels of H3K27me3 on the paternal genome were higher at the PN5 stage in zygotes lacking maternal TH2A/TH2B. H3K27me3 is a mark of repressive chromatin, and its formation is catalyzed by the enzymatic subunit Ezh2 in the Polycomb repressive complex 2 (PRC2) (Margueron and Reinberg, 2011). In WT zygotes, the H3K27me3 signals on the paternal genome started to increase at syngamy, after the PN5 stage, indicating that a loss of maternal TH2A/TH2B accelerates the formation of repressive chromatin in the paternal genome. In zygotes lacking maternal TH2A/TH2B, the level of H3K14ac on the maternal genome at PN0 was much lower than that of the control WT zygotes, but this decrease was recovered at PN2.
Note that when the authors add TH2A, TH2B, and Npm to their reprogramming cocktail they refer to those 3 factors together as “BAN”. A histone chaperone, nucleoplasmin (Npm), seems important as well. A phosphorylation-mimic form of Npm (P-Npm) enhanced reprogramming involving BAN.
It’s interesting that BAN plus Klf4 and Oct4 (referred to as KOBAN…made me think of Kurt Cobain) was sufficient for reprogramming.
With global chromatin opening factors like these histone variants and Myc, one of the tricky parts is looking at gene expression since it is possible for these factors to indirectly boost expression of many genes via their widespread chromatin activating function. However, the authors report some specific gene expression effects in Figure 5. They saw relatively discrete changes with BAN added to the mix with just a few hundred specific genes impacted. 22% overlapped with so-called “initiation” genes found previously to be turned on during early reprogramming.
They also used ChIP-Seq to identify the genomic location of TH2A and TH2B and found that its binding specifically to the X chromosome was greatly enriched during reprogramming, but what it is doing there and how that mechanism then feeds into reprogramming remain interesting open questions.
You can see their model above at the top of the post. One of their more notable conclusions is that the histone variants make cellular reprogramming more similar to SCNT:
the mechanism of reprogramming using TH2A/TH2B in conjunction with OKSM more closely resembles SCNT than conventional reprogramming and that TH2A/TH2B also play a functional role in reprogramming by SCNT.
TH2A and TH2B also seem to play roles in the global chromatin activity states of the maternal and paternal genomes. The authors further point out that another booster of reprogramming a couple years back, Glis1, is also enriched in expression in oocytes and zygotes.
Overall I thought this paper was very strong and opens up a lot of interesting mechanistic questions related to chromatin during reprogramming.