Biology subjects

Tiedemann, R. L.

Publications and source records attributed to Tiedemann, R. L..

4 recordsLinked to original sources

bioRxiv2026

A feed-forward UHRF1 read-write mechanism supports H3 multi- mono-ubiquitination and DNA methylation maintenance at CpG-sparse regions

The epigenetic inheritance of mammalian DNA methylation requires DNMT1 and its E3 ligase cofactor UHRF1. At newly replicated chromatin, UHRF1 recognition of hemi-methylated DNA and histone H3 N-terminal tails directs catalysis of H3K14, H3K18, and/or H3K23 mono-ubiquitination to recruit DNMT1. While it is appreciated that UHRF1 can deposit multiple mono-ubiquitin marks on a single H3 tail and that DNMT1 recognizes this state through tandem ubiquitin interacting motifs, the mechanism that promotes successive ubiquitination and the biological function of multi-mono-ubiquitination are unknown. Here, we show that UHRF1 directly binds its mono-ubiquitinated H3 products through a previously uncharacterized LGDDSL loop in Tudor 2 of its tandem Tudor domain (TTD) to promote further ubiquitin deposition. Disruption of this ubiquitin reading activity impairs H3 multi-mono-ubiquitination and accelerates DNA methylation loss within late-replicating, CpG-sparse genomic regions that are characteristic of partially methylated domains (PMDs) in cancer and aging cells. These methylation defects overlap those observed by disruption of UHRF1 ubiquitin ligase activity, providing convergent evidence that both writing and reading of H3 ubiquitination support CpG-sparse DNA methylation maintenance. Together, these findings establish a feed-forward ubiquitin read-write mechanism that generates multi-mono-ubiquitinated H3 and safeguards DNMT1-dependent DNA methylation maintenance at vulnerable genomic regions of the mammalian methylome.

molecular biology↗

bioRxiv2025

Dual EZH1/2 inhibition enhances DNMT inhibitor efficacy in colon cancer through targeting H3K27me1

Abnormal DNA methylation patterning is a defining epigenetic hallmark of human cancer and is therapeutically targetable with DNA methyltransferase inhibitors (DNMTis). However, DNMTi-induced DNA hypomethylation promotes adaptive chromatin remodeling that limits molecular and therapeutic responses to these drugs. Here, we identify EZH1-dependent H3K27 mono-methylation (H3K27me1) as a previously unrecognized adaptive barrier to DNMTi response in colorectal cancer. While EZH2-selective inhibitors deplete H3K27me2 and H3K27me3, they preserve EZH1-dependent H3K27me1 at Polycomb-enriched genomic regions. In contrast, dual EZH1/2 inhibition eliminates all H3K27 methylation states and robustly synergizes with DNMTi to enhance transcriptional activation and growth suppression. Mechanistically, dual EZH1/2 inhibition induces a redistribution of p300/CBP-dependent H3K27 acetylation (H3K27ac), generating a therapy-associated bivalent chromatin state characterized by coexisting DNA methylation and H3K27ac. DNMT inhibition resolves this induced bivalency, enabling activation of tumor-suppressive transcriptional programs. At the same time, coordinated loss of H3K27me1 and gene-body DNA methylation, together with depletion of promoter-associated H3K27ac, suppresses MYC- and E2F-driven oncogenic transcription networks that define the cancer cell-intrinsic therapeutic response. Collectively, these findings establish EZH1-dependent H3K27me1 as a key mediator of adaptive epigenetic plasticity and provide mechanistic rationale for combining DNMT inhibitors with dual EZH1/2i inhibitors to reprogram chromatin and suppress oncogenic transcription in solid tumors. HighlightsO_LIEZH1-dependent H3K27me1 sustains an adaptive barrier to DNMT inhibitor response in colorectal cancer. C_LIO_LIDual EZH1/2 inhibition eliminates all H3K27 methylation states and remodels chromatin architecture. C_LIO_LIEZH inhibition induces a DNA methylation-H3K27ac bivalent chromatin state. C_LIO_LIDNMT and EZH1/2 co-inhibition reprograms enhancers and promoters to activate tumor-suppressive pathways. C_LIO_LICombination therapy suppresses MYC/E2F-driven oncogenic transcription, defining its cancer cell-intrinsic therapeutic efficacy. C_LI

cancer biology↗

bioRxiv2020

In silico APC/C substrate discovery reveals cell cycle degradation of chromatin regulators including UHRF1

The Anaphase-Promoting Complex/Cyclosome (APC/C) is an E3 ubiquitin ligase and critical regulator of cell cycle progression. Despite its vital role, it has remained challenging to globally map APC/C substrates. By combining orthogonal features of known substrates, we predicted APC/C substrates in silico. This analysis identified many known substrates and suggested numerous candidates. Unexpectedly, chromatin regulatory proteins are enriched among putative substrates and we show that several chromatin proteins bind APC/C, oscillate during the cell cycle and are degraded following APC/C activation, consistent with being direct APC/C substrates. Additional analysis revealed detailed mechanisms of ubiquitylation for UHRF1, a key chromatin regulator involved in histone ubiquitylation and DNA methylation maintenance. Disrupting UHRF1 degradation at mitotic exit accelerates G1-phase cell cycle progression and perturbs global DNA methylation patterning in the genome. We conclude that APC/C coordinates crosstalk between cell cycle and chromatin regulatory proteins. This has potential consequences in normal cell physiology, where the chromatin environment changes depending on proliferative state, as well as in disease.

cell biology↗

bioRxiv2019

siQ-ChIP:A reverse-engineered quantitative framework for ChIP-sequencing

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a key technique for mapping the distribution and relative abundance of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge regarding the ability to quantitatively plot ChIP-seq data, and as such, approaches making use of exogenous additives, or \"spike-ins\" have recently been developed. Relying on the fact that the IP step of ChIP-seq is a competitive binding reaction, we present a quantitative framework for ChIP-seq analysis that circumvents the need to modify standard sample preparation pipelines with spike-in reagents. We also introduce a visualization technique that, when paired with our formal developments, produces a much more rich characterization of sequencing data.

genomics↗