Biology subjects

Wille, C. K.

Publications and source records attributed to Wille, C. K..

4 recordsLinked to original sources

bioRxiv2022

Antagonistic H3K79me-H3K9ac crosstalk determines elongation at housekeeping genes to promote pluripotency

Pluripotent embryonic stem cells (ESCs) have a transcriptionally permissive chromatin environment enriched for gene activation-associated histone modifications as compared to somatic cells. A striking exception is DOT1L-mediated H3K79 methylation that is considered a positive regulator of transcription. Here we find that ESCs maintain low H3K79 methylation to facilitate RNA polymerase II (RNAPII) elongation for greater nascent transcription. Inhibiting DOT1L during the reprogramming of somatic to induced pluripotent stem cells (iPSCs) enables ESC-like RNAPII and transcriptional status. Mechanistically, DOT1L inhibition causes a local gain of histone acetylation at genes that lose the most H3K79me, which unexpectedly are ubiquitously expressed genes that perform essential functions in every cell, rather than lineage specifying genes. Maintenance of this elevated histone acetylation is required for the enhanced conversion to iPSCs upon DOT1L inhibition. Remarkably, increasing global DOT1L or site-specific tethering of DOT1L is sufficient to decrease H3K9ac in ESCs. We discover a high H3ac-low H3K79me epigenetic mechanism that promotes transcription elongation at ubiquitously expressed genes to enforce pluripotent cell identity.

developmental biology↗

bioRxiv2020

Dot1L interaction partner AF10 safeguards cell identity during the acquisition of pluripotency

Histone 3 Lysine 79 methylation (H3K79me) is enriched on gene bodies proportional to gene expression levels, and serves as a strong barrier for reprogramming of somatic cells to induced pluripotent stem cells (iPSCs). DOT1L is the sole histone methyltransferase that deposits all three orders - mono, di, and tri methylation - at H3K79. Here we leverage genetic and chemical approaches to parse the specific functions of the higher orders of H3K79me in maintaining cell identity. DOT1L interacts with AF10 (Mllt10) which recognizes unmodified H3K27 and boosts higher order H3K79 methylation. AF10 deletion evicts higher order H3K79me2/3, and reorganizes H3K79me1 to the transcription start site, to facilitate iPSC formation in the absence of steady state transcriptional changes. Instead, AF10 loss redistributes RNA polymerase II to a uniquely pluripotent pattern at highly expressed, rapidly transcribed housekeeping genes. Taken together, we reveal a mechanism for higher order histone methylation located at the gene body in reinforcing cell identity.

genetics↗

bioRxiv2019

Depletion of H3K79 methylation specifically enhances reprogramming to pluripotency but not transdifferentiation

The ability of pluripotent stem cells to be poised to differentiate into any somatic cell type is partly derived from a unique chromatin structure that is depleted for transcriptional elongation associated epigenetic modifications, primarily H3K79 methylation. Inhibiting the H3K79 methyltransferase, Dot1L, increases the efficiency of reprogramming somatic cells to induced pluripotent stem cells (iPSCs) most potently at the mid-point of the process. Surprisingly, despite the enrichment of H3K79me2 on thousands of actively transcribed genes, Dot1L inhibition (Dot1Li) results in few changes in steady state mRNA levels during reprogramming. Dot1Li spuriously upregulates genes not involved in pluripotency and does not shutdown the somatic program. Depletion of the few genes that are downregulated, such as Nfix, enhances reprogramming efficiency in cooperation with Dot1Li. Contrary to the prevalent view, Dot1Li promotes iPSC generation beyond early phases of reprogramming such as the mesenchymal to epithelial transition and from already epithelial cell types including keratinocytes. Significantly, Dot1L inhibition does not enhance lineage conversion to neurons or muscle cells. Taken together, our results indicate that H3K79me is not a universal barrier of cell fate transitions but specifically protects somatic cells from reverting to the pluripotent state.

developmental biology↗

bioRxiv2019

Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence

S-adenosylmethionine (SAM) is the methyl-donor substrate for DNA and histone methyltransferases that regulate cellular epigenetic states. This metabolism-epigenome link enables the sensitization of chromatin methylation to altered SAM abundance. However, a chromatin-wide understanding of the adaptive/responsive mechanisms that allow cells to actively protect epigenetic information during life-experienced fluctuations in SAM availability are unknown. We identified a robust response to SAM depletion that is highlighted by preferential cytoplasmic and nuclear de novo mono-methylation of H3 Lys 9 (H3K9) at the expense of global losses in histone di- and tri-methylation. Under SAM-depleted conditions, de novo H3K9 mono-methylation preserves heterochromatin stability and supports global epigenetic persistence upon metabolic recovery. This unique chromatin response was robust across the mouse lifespan and correlated with improved metabolic health, supporting a significant role for epigenetic adaptation to SAM depletion in vivo. Together, these studies provide the first evidence for active epigenetic adaptation and persistence to metabolic stress.

biochemistry↗