Cellular Memory Laboratory

Outline

Our laboratory's principal objective is to understand the molecular mechanism of epigenetic gene regulation and the role of epigenetics in health and disease. To address these topics, we take multidisciplinary approaches, including molecular biology, biochemistry, cell biology, structural biology and mouse molecular genetics

Recent Research Topic

Histone methyltransferase ESET silences endogenous retrovirus

Fig. 1 Molecular mechanism of transcriptional repression of ESET to ERVs in mouse ES cells

Repetitive sequences that do not code for genes make up at least 50% of the genome of mammals, including humans. Most repetitive sequences are derived from transposable elements that can move around within the genomes and endogenous retroviruses (ERVs) are retrotransposable elements with long terminal repeats (LTRs), a family of transposable elements, and account for up to 8% of the human genome.

Some mouse retrotransposable elements are still active and transposition of ERVs induces approximately 10% of mutations in mice. Organisms have various inhibiting mechanisms to prevent these selfish genes from entering and amplifying. Transcriptional repression of ERVs is one of such mechanisms. DNA methylation plays an important role in the silencing expression of ERVs incorporated into the host's genome (proviruses) and proviral expression increases when LTR DNA methylation decreases. On the other hand, in cell lines derived from early embryos including embryonic carcinoma (EC) and embryonic stem (ES) cells, it was found 30 or more years ago that these cells had a specific DNA-methylation-independent mechanism for silencing proviral expression. However, the details of the mechanism remain unclear.

We showed that histone H3 lysine 9 (H3K9) methyltransferase ESET/SETDB1 plays a very important role in the proviral silencing mechanism that functions specifically in cells of the early embryogenesis [T. Matsui, et al. Nature 2010, 464, 927]. ESET has the activity of methylating a specific histone amino acid (H3K9). Analysis using ES cell system in which genes coding for ESET were selectively knocked out (KO) showed that ERV expression was significantly increased by ESET deletion. It was also shown that H3K9 in LTR-promoter regions of ERVs were ESET-dependently trimethylated. It was confirmed that ESET was introduced to proviral LTR regions by a molecule named Kruppel-associated box protein 1 (KAP1). Furthermore, it was shown that proviral silencing in ES cells was associated with the activity of ESET histone methylation but not always required DNA methylation. Based on the above, it was suggested that ESET was involved in proviral silencing independently of DNA methylation in cells of the early embryogenesis, in which DNA methylation drastically changes.

Furthermore, we performed deep RNA sequencing analysis of ESET KO ES cells and found that ~15% of upregulated genes in ESET deficient ES cells were induced in association with derepression of promoter-proximal ERVs, half in the context of “chimeric” transcripts that initiated within these retroelements and spliced to genic exons [MM. Karimi, et al. Cell Stem Cell 2011, 8, 676]. Thus, SETDB1 plays a previously unappreciated yet critical role in inhibiting aberrant gene transcription by suppressing the expression of proximal ERVs.

Fig. 2 ERV chimaeric transcripts identified exclusively in the Eset KOES cells

Fig. 3 Histone Methyltransferases G9a/GLP are involved in various biological processes

Fig. 2

Reproduced, with permission, from MM. Karimi, et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs, Cell Stem Cell 2011, 8, 676. © (2012) Elsevier