Whether you learn through hitting the books or traveling the globe – speaking two languages has many advantages. Now, a study into the basis of gene expression regulation reports how bilingual “read-write” proteins that “speak” two epigenetic languages can help us to learn about the complex mechanisms controlling sequence-independent heritable gene silencing.
The dynamic duo of Andy H. Yuan and Danesh Moazed (Harvard Medical School) took a molecular engineering approach in yeast cells naturally lacking H3K9me in a reduced-complexity attempt to understand the principles behind establishing/maintaining silent chromatin domains controlled by this heterochromatin-associated histone modification. This study employed an artificially introduced genomic domain and engineered bilingual “read-write” proteins, which they discovered to form an interdependent positive feedback loop that suffices to establish, maintain, and support the inheritance of sequence-independent silent chromatin.
Let’s hear more about how bilingual “read-write” proteins form heritable silent chromatin from Yuan and Moazed:
- A chimeric protein comprising the bacterial tetracycline repressor TetR fused to the catalytic domain of the SUV39H2 H3K9 methyltransferase (TetR-SET) prompts the deposition of H3K9me at an exogenously integrated locus with ten tandem tet operators upstream of a reporter gene (ADE2) in yeast cells
- Epigenetic silencing of ADE2 by TetR-SET leads to red pigment accumulation from the growth media (and vice versa) while inhibiting TetR binding reduces H3K9me2 via the dilution of parental histones during proliferation
- H3K9me can recruit HP1 to silent chromatin; here, a bilingual protein with a H4K16-specific HDAC fused to HP1 – Sir2Sp-HP1 – decreases ADE2 expression and prompts red pigmentation accumulation in TetR-SET-containing cells via the binding of Sir2Sp-HP1 to H3K9me
- The generation of a chimeric protein comprised of the HDAC Sir3 (which recognizes unmodified H4K16) fused to a catalytic domain of human SUV39H2 – Sir3-SET – creates a similar bilingual chimera to Sir2Sp-HP1
- Sir3-SET binds deacetylated H4K16 to induce H3K9me while Sir2Sp-HP1 binds H3K9me to induce H4K16 deacetylation
- Together, these bilingual read-write proteins establish/maintain reporter silencing, suggestive of an interdependent positive feedback loop supporting DNA sequence-independent heritable gene silencing
- Transposon mutagenesis screens reveals the involvement of DNA replication in the regulation of this system, which suggests the sensitivity of the positive feedback loop to asymmetric parental histone transfer
The authors of this horizon-expanding bilingual study highlight the importance of read-write mechanisms in silent chromatin domain assembly and the transfer of “silent information” between histone proteins over multiple generations in a replication-coupled parental histone transfer-dependent manner. The authors hope to study gene silencing-associated mechanisms of increased complexity and additional memory-conferring cellular processes next. To learn more about how bilingual read-write proteins underpin establishing and maintaining heritable silent chromatin domains, see PNAS, January 2024.