Peter Zeller
YOU?
Author Swipe
View article: Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation
Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation Open
The regulation of gene expression is governed at multiple levels of chromatin organization. However, how gene regulation is co-ordinated remains relatively unexplored. Here we develop Dam&ChIC, a method that enables retrospective and multi…
View article: sortChIC [version without A-tailing] v1
sortChIC [version without A-tailing] v1 Open
This is an adaptation of single-cell sortChIC (Zeller et al., 2023), in which we omit A-tailing and use blunt-end adapters for ligation/barcoding. We made this version to enable benchmarking during development of Dam&ChIC (Kefalopoulou et …
View article: Dam&ChIC in bulk v1
Dam&ChIC in bulk v1 Open
Bulk Dam&ChIC is an adaptation of single-cell Dam&ChIC (Kefalopoulou et al., 2025) tailored to sorted populations of cells (e.g. 20c-10000c). The protocol doesn't require the specialized robotic liquid handlers used in its single-cell vers…
View article: Dam&ChIC collection: Methods developed and implemented by Kefalopoulou et al., 2025 v1
Dam&ChIC collection: Methods developed and implemented by Kefalopoulou et al., 2025 v1 Open
This collection includes a detailed protocol for Dam&ChIC, developed by Kefalopoulou et al., 2025. Additionally, it includes previously developed methods that were implemented in the study, such as sortChIC and scDam&T-seq.
View article: FACS to measure epitopes in CellTrace-multiplexed samples v1
FACS to measure epitopes in CellTrace-multiplexed samples v1 Open
This assay enables measurements of epitope abundance via FACS in samples that have been (optionally) multiplexed with Cell-Tracer dyes. It uses the same sample preparation procedure of sortChIC and Dam&ChIC, followed by FACS-based detectio…
View article: Dam&ChIC v1
Dam&ChIC v1 Open
Dam&ChIC is a single-cell chromatin profiling method that allows for multifactorial and retrospective measurements of chromatin factors. It builds-upon and integrates scDamID and sortChIC, which are both methods for profiling of chromatin …
View article: sortChIC in bulk [version without A-tailing] v1
sortChIC in bulk [version without A-tailing] v1 Open
Bulk sortChIC is an adaptation of single-cell sortChIC (Zeller et al., 2023, Gaza et al., 2024) tailored to sorted populations of cells (e.g. 20c-10000c). The protocol doesn't require the specialized robotic liquid handlers used in its sin…
View article: Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation
Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation Open
Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates ‘gastruloids’, self-organising complex structures that display an anteroposterior organisation of cell types derived from all three germ la…
View article: An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC
An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC Open
Translocation renal cell carcinoma (tRCC) is a rare, aggressive kidney cancer primarily occurring in children. They are genetically defined by translocations involving MiT/TFE gene family members TFE3 or TFEB. The biology underlying tRCC d…
View article: Shining a light on cell biology of the nucleus with single-cell sequencing
Shining a light on cell biology of the nucleus with single-cell sequencing Open
From the preservation of genomic integrity to the regulation of RNA translation, nearly all cellular processes are regulated in a cell context-dependent manner. To fully understand the context-specific function of involved nuclear processe…
View article: Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development
Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development Open
Establishing a cell-type-specific chromatin landscape is crucial for the maintenance of cell identity during embryonic development. However, our knowledge of how this landscape is set during vertebrate embryogenesis has been limited, due t…
View article: Detection of histone modifications and full-length transcriptome in single cells identifies sequential epigenetic perceptiveness to lineage commitment
Detection of histone modifications and full-length transcriptome in single cells identifies sequential epigenetic perceptiveness to lineage commitment Open
Epigenetic mechanisms, including histone modifications, are key regulators of transcription and influence cellular differentiation. To uncover the interplay between histone modifications and transcription, we developed T-ChIC (Transcriptom…
View article: Stem cell culture conditions affect in vitro differentiation potential and efficiency of mouse gastruloid development
Stem cell culture conditions affect in vitro differentiation potential and efficiency of mouse gastruloid development Open
By aggregating low numbers of mouse embryonic stem cells (mESCs) followed by exposure to Wnt activation, structures termed gastruloids are produced that display an anteroposterior organisation of cell types derived from all three germ laye…
View article: Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation
Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation Open
The regulation of gene expression is governed at multiple levels of chromatin organization. However, how coordination is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that enables time-resolved and multifactori…
View article: An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying translocation RCC
An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying translocation RCC Open
Translocation renal cell carcinoma (tRCC) is a rare, aggressive type of kidney cancer primarily occurring in children. They are genetically defined by translocations involving MiT/TFE gene family members, TFE3 or, in rare cases, TFEB. The …
View article: Evaluation Tests of Metal Oxide Varistors for DC Circuit Breakers
Evaluation Tests of Metal Oxide Varistors for DC Circuit Breakers Open
With emerging technologies and products in power semiconductors and ultrafast mechanical switches, direct-current circuit breakers (DCCBs) have been developing rapidly. Yet the metal-oxide varistors (MOVs), being the indispensable DCCB com…
View article: Deconvolving multiplexed histone modifications in single cells
Deconvolving multiplexed histone modifications in single cells Open
Recent advances have enabled mapping of histone modifications in single cells 1–12 , but current methods are constrained to profile only one histone modification per cell. Here we present an integrated experimental and computational framew…
View article: Hierarchical chromatin regulation during blood formation uncovered by single-cell sortChIC
Hierarchical chromatin regulation during blood formation uncovered by single-cell sortChIC Open
SUMMARY Post-translational histone modifications modulate chromatin packing to regulate gene expression. How chromatin states, at euchromatic and heterochromatic regions, underlie cell fate decisions in single cells is relatively unexplore…
View article: Argonaute NRDE-3 and MBT domain protein LIN-61 redundantly recruit an H3K9me3 HMT to prevent embryonic lethality and transposon expression
Argonaute NRDE-3 and MBT domain protein LIN-61 redundantly recruit an H3K9me3 HMT to prevent embryonic lethality and transposon expression Open
The establishment and maintenance of chromatin domains shape the epigenetic memory of a cell, with the methylation of histone H3 lysine 9 (H3K9me) defining transcriptionally silent heterochromatin. We show here that the C. elegans SET-25 (…
View article: Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression
Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression Open
Caenorhabditis elegans has two histone H3 Lys9 methyltransferases, MET-2 (SETDB1 homolog) and SET-25 (G9a/SUV39H1 related). In worms, we found simple repeat sequences primarily marked by H3K9me2, while transposable elements and silent tiss…
View article: H3K9me is dispensable for C. elegans development but essential for genome integrity
H3K9me is dispensable for C. elegans development but essential for genome integrity Open
Epigenetic mechanisms as key regulators of chromatin biology have been the focus of intensive research over the past 20 years. It has become clear that epigenetic pathways play a major role in the pathology of numerous diseases ranging fro…
View article: The Importance of Satellite Sequence Repression for Genome Stability
The Importance of Satellite Sequence Repression for Genome Stability Open
Up to two-thirds of eukaryotic genomes consist of repetitive sequences, which include both transposable elements and tandemly arranged simple or satellite repeats. Whereas extensive progress has been made toward understanding the danger of…
View article: Differential use of autophagy by primary dendritic cells specialized in cross-presentation
Differential use of autophagy by primary dendritic cells specialized in cross-presentation Open
Antigen-presenting cells survey their environment and present captured antigens bound to major histocompatibility complex (MHC) molecules. Formation of MHC-antigen complexes occurs in specialized compartments where multiple protein traffic…
View article: Differential use of autophagy by primary dendritic cells specialized in cross-presentation
Differential use of autophagy by primary dendritic cells specialized in cross-presentation Open
Antigen-presenting cells survey their environment and present captured antigens bound to major histocompatibility complex (MHC) molecules. Formation of MHC-antigen complexes occurs in specialized compartments where multiple protein traffic…