Biology subjects

Cakil, Z. V.

Publications and source records attributed to Cakil, Z. V..

3 recordsLinked to original sources

bioRxiv2026

Proteomics-Based Discovery of Symmetry-Specific Readers and Antireaders of 5-Formylcytosine in Mammalian DNA

5-methylcytosine (mC) and its oxidized derivatives are epigenetic modifications of mammalian DNA that play key roles in transcription, cell differentiation, and cancer. They predominantly occur within palindromic CpG dyads, creating multiple possible combinations across the two dyad strands, each representing a chemically distinct DNA major groove mark. Among the modifications, 5-formylcytosine (fC) interacts with a large number of proteins and has been associated with important roles in chromatin regulation. However, it is poorly understood whether nuclear proteins selectively recognize the symmetry of individual fC-containing CpG dyads. Here, we report the first proteome-wide interaction profiles of symmetric and asymmetric fC modifications in mammalian DNA. Our analysis spans several human and mouse cell lines and three DNA promoter probes containing CpG dyads with five distinct combinations of fC, C, and mC nucleobases. We identify a diverse set of fC reader proteins with distinct symmetry preferences, including transcription factors (e.g., MAX, HEY1, RFX5, SIX1, SIX2, and FOXJ3) and DNA repair proteins (MPG and TDG). Notably, some proteins act as fC readers or anti-readers depending on the sequence context, suggesting a role for fC in modulating their target selection. Our data reveal widespread symmetry-specific recognition of fC by mammalian proteins and provide a rich resource for studying its potential functions in chromatin regulation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=183 HEIGHT=200 SRC="FIGDIR/small/717454v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@10773borg.highwire.dtl.DTLVardef@103ced4org.highwire.dtl.DTLVardef@fff20eorg.highwire.dtl.DTLVardef@16c9678_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Mammalian Proteome Profiling Reveals Readers and Antireaders of Strand-Symmetric and -Asymmetric 5-Hydroxymethylcytosine-Modifications in DNA

The cytosine (C) modifications 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) are central regulatory elements of mammalian genomes. Both marks occur in dinucleotide contexts of double stranded DNA in either strand-symmetric or -asymmetric fashion, but it is still poorly understood how this symmetry information is selectively read out by the nuclear proteome as basis of potential symmetry-dependent regulation mechanisms. We report comparative enrichment/proteomics studies with promoter probes being strand-symmetrically or asymmetrically modified with C, mC and hmC, enabling a direct assessment of their reader profiles in the same sequence, tissue, and experimental contexts. We identify in human and mouse nuclear lysates a high number of tissue-specific readers for hmC-modified sequences that fall into distinct, probe-specific sub-groups, including members of important transcription factor classes and chromatin regulators. Among them, we discover the master regulators MYC and MAX that play central roles in cell (de)differentiation and cancer progression to read hmC in a sequence-dependent manner. We also find RFX5, a transcription factor critically involved in primary MHC class II deficiency to discriminate between specific hmC symmetries in CpG dyads. Our findings provide further support for the hypothesis that hmC symmetry information can provide distinct regulatory outputs, and provide a resource for studying the molecular mechanisms triggered by symmetric and asymmetric hmC modifications in chromatin regulation during development and disease.

biochemistry↗

bioRxiv2023

A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity

Proximity between proteins plays an essential and ubiquitous role in many biological processes. Molecular tools enabling to control and observe the proximity of proteins are essential for studying the functional role of physical distance between two proteins. Here we present CATCHFIRE (Chemically Assisted Tethering of CHimera by Fluorogenic Induced REcognition), a chemically induced proximity technology with intrinsic fluorescence imaging and sensing capabilities. CATCHFIRE relies on genetic fusion to small dimerizing domains that interact upon addition of fluorogenic inducers of proximity that fluoresce upon formation of the ternary assembly, allowing real-time monitoring of the chemically induced proximity. CATCHFIRE is rapid and fully reversible, and allows the control and tracking of protein localization, protein trafficking, organelle transport and cellular processes, opening new avenues for studying or controlling biological processes with high spatiotemporal resolution. Its fluorogenic nature allowed furthermore the design of innovative biosensors for the study of various processes, such as signal transduction and apoptosis.

cell biology↗