Epigenetics Podcast from Active Motif

scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)

Episode 100

May 17, 2023

In this episode of the Epigenetics Podcast, we caught up with Jop Kind from Hubrecht Institute to talk about his work on single cell DamID, EpiDamID, and Lamina Associated Domains (LADs).

Jop Kind started out developing single cell DamID (scDamID), based on the DamID technique. First, this technique was adapted to a microscopic readout which enabled them to follow the localisation of chromatin domains after cell division. Next, the lab expanded this technique into the NGS space and created genome-wide maps of nuclear lamina Interactions in single human cells. Since LADs are in a heterochromatic chromatin context, the lab expanded scDamID into the epigenetic space. They first combined it with a transcriptional readout. Later-on they developed EpiDamID, a method to target a diverse set of chromatin types by taking advantage of the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins.

Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon)

Episode 99

May 4, 2023

In this episode of the Epigenetics Podcast, we caught up with Charlotte Proudhon from the Institut for Environmental and Occupational Health in Rennes to talk about her work on circulating tumor DNA and circulating Epi-mutations as biomarkers in cancer.

Charlotte Proudhon started out her research career by investigating circulating tumor DNA (ctDNA). This kind of DNA is shed into the bloodstream by apoptotic tumor cells and can be analyzed after collection by a simple blood draw, which makes it a very useful biomarker for cancer. Using this approach cancers can be identified by their unique mutational fingerprint. However, soon the limitations of this approach became apparent and the fact that this ctDNA is actually shed into the bloodstream as nucleosomal particles was utilized by the Proudhon team and now the methylation fingerprint of the LINE-1 repeats is used as a biomarker for cancer diagnosis and monitoring of the success of a cancer treatment.

Epigenetic Landscapes During Cancer (Luciano Di Croce)

Episode 98

April 20, 2023

In this episode of the Epigenetics Podcast, we caught up with Luciano Di Croce from the Center of Genomic Regulation in Barcelona to talk about his work on epigenetic landscapes in cancer.

The Di Croce Lab focuses on the Polycomb Complex and its influence on diseases like cancer. Luciano Di Croce started out his research career investigating the oncogenic transcription factor PML-RAR. They could show that in leukemic cells knockdown of SUZ12, a key component of Polycomb repressive complex 2 (PRC2), reverts not only histone modification but also induces DNA de-methylation of PML-RAR target genes. More recently the team focused on two other Polycomb related proteins Zrf1 and PHF19 and were able to characterize some of their functions in gene targeting in different disease and developmental contexts.

Transgenerational Inheritance and Evolution of Epimutations (Peter Sarkies)

Episode 94

February 22, 2023

In this episode of the Epigenetics Podcast, we caught up with Peter Sarkies from University of Oxford Biochemistry to talk about his work on Transgenerational Inheritance of Epimutations.

The team in the Sarkies lab focuses on investigating the connections between epigenetic gene regulation and evolution. The lab performs evolution experiments in the nematode C. elegans to determine if evolution can be influenced by epigenetic differences between individuals in a given population when no changes in the underlying DNA sequence are observed. A second area of interest of the team is evolution of piRNAs, which are present in metazoans but have been lost in nematodes during evolution.

Genome Organization Mediated by RNA Polymerase II (Argyrys Papantonis)

Episode 90

December 14, 2022

In this episode of the Epigenetics Podcast, we caught up with Akis Papantonis from the University Medical Center Göttingen to talk about his work on genome organisation mediated by RNA Polymerase II.

The research of the Papantonis Laboratory focuses on investigating how environmental signalling stimuli are integrated by chromatin to control homeostatic to deregulated functional transitions. In more detail, the team is interested in how dynamic higher-order regulatory networks are influenced by the underlying linear DNA fiber. The ultimate goal of the laboratory is to understand general rules governing transcriptional and chromatin homeostasis and finally, how those rules might affect development, ageing or malignancies.

Bioinformatic Analysis in Epigenetics Research (Nick Pervolarakis)

Episode 87

November 3, 2022

In this episode of the Epigenetics Podcast, we caught up with Nick Pervolarakis from Active Motif to talk about bioinformatic analysis in epigenetics research.

While many “bench scientists” are familiar with the workflows of ChIP-Seq, ATAC-Seq and CUT&Tag, and even the preparation and analysis of the libraries, the steps between sequencing and fully analyzed data is sometimes thought of as a mystery known only to bioinformatic experts. Most of us have some understanding that the raw data is usually in a file format called a FASTQ. But how do we get from FASTQ files to peaks on a genome browser? This Podcast Episode will provide a peek behind the curtain of the informatic analysis we perform at Active Motif, as part of our end-to-end epigenetic services.

Anchor-Based Bisulfite Sequencing (Ben Delatte)

Episode 86

October 20, 2022

In this episode of the Epigenetics Podcast, we caught up with Ben Delatte Research Scientist at Active Motif to talk about his work on Anchor Based Bisulfite Sequencing.

Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling. However, this approach is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). ABBS captures accurate DNA methylation information in Escherichia coli and mammals, while requiring up to 10 times fewer sequencing reads than WGBS. ABBS interrogates the entire genome and is not restricted to the CpG islands assayed by methods like Reduced Representation Bisulfite Sequencing (RRBS). The ABBS protocol is simple and can be performed in a single day.

Enhancer Communities in Adipocyte Differentiation (Susanne Mandrup)

Episode 85

October 6, 2022

In this episode of the Epigenetics Podcast, we caught up with Susanne Mandrup from the University of Southern Denmark to talk about her work on the role of enhancer communities in adipocyte differentiation.

The Laboratory of Susanne Mandrup focuses on the effect of enhancers and enhancer communities on the differentiation of mesenchymal stem cell into adipocytes and osteoblasts. The team has shown that there is significant cross-talk between enhancers and that these form communities of highly interconnected enhancers. Inactive enhancers are then activated by association with these pre-existing enhancer networks to facilitate gene expression in adipocyte differentiation.

Hydroxymethylation Landscape in Immune Cells (Marcela Sjöberg)

Episode 83

September 8, 2022

In this episode of the Epigenetics Podcast, we caught up with Marcela Sjöberg from the University of Chile to talk about her work on the hydroxymethylation landscape in immune cells.

At the beginning of her career Marcela Sjöberg worked on Polycomb and how modifications placed by this complex modulate the binding of RNA Pol II. Later, her focus shifted to hydroxymethylated cytosine and how it is involved in the inheritance of Metastable Epialleles in mouse. More recently, the laboratory is interested in transcription factor binding motifs and how hydroxymethylation of those binding motifs modulates the binding and activity of the respective transcription factors.

Single Cell Epigenomics in Neuronal Development (Tim Petros)

Episode 82

August 25, 2022

In this episode of the Epigenetics Podcast, we caught up with Tim Petros from the Eunice Kennedy Shriver National Institute of Child Health and Human Development at the NIH to talk about his work on Single Cell Epigenomics in Neuronal Development.

The Petros lab focuses on “interneurons”, their diversity and how environmental signals interact to generate this diversity. This subgroup of neurons comprise about 20% of neutrons in the brain, however, they are the primary source of inhibition. Furthermore, interneurons are critical components in modulating information flow throughout the nervous system. The Petros lab seeks to uncover the genetic programs that lead to the incredible diversity in interneurons, as well as how the local environment influences this process.

To lay a foundation for this and to provide a data-base for other researchers the Petros lab generated an epigenome atlas of neural progenitor cells of the mouse brain. This data includes scRNA-Seq, snATAC-Seq, CUT&Tag (H3K4me3, H3K27me3), CUT&RUN (H3K27ac), Hi-C and Capture-C. This data can be downloaded from the NIH website.

Oncohistones as Drivers of Pediatric Brain Tumors (Nada Jabado)

Episode 81

August 11, 2022

In this episode of the Epigenetics Podcast, we caught up with Nada Jabado from McGill University to talk about her work on oncohistones as drivers of Pediatric Brain Tumors.

Nada Jabado and her team were amongst the first to identify mutations in Histone 3.3 Tails which lead to differentially remodelled chromatin in pediatric glioblastoma. Mutations that occur include the Lysine at position 27 and the Glycine at position 34. If those residues are mutated it will influence the equilibrium of chromatin associated proteins like the Polycomb Repressive Complex (PRC) and hence domains of heterochromatin will be shifted. This, in turn, will lead to differential gene expression and development of developmental disorders or cancer.

Characterization of Epigenetic States in the Oligodendrocyte Lineage (Gonçalo Castelo-Branco)

Episode 80

July 28, 2022

In this episode of the Epigenetics Podcast, we caught up with Goncalo Castelo-Branco from the Karolinska Institute to talk about his work on the characterization of epigenetic states in the Oligodendrocyte Lineage.

The group from Gonçalo Castelo-Branco’s lab focuses on characterizing epigenetic states of oligodendrocytes, with the aim to understand their contribution to diseases like multiple sclerosis. To do this the group used single-cell RNA-Seq to identify sub-populations of oligodendrocytes. Furthermore, the team pioneered improvements in CUT&Tag and applied it to the single-cell space, as well as developing spatial CUT&Tag. More recently they used nanobodies in an optimised version of single cell CUT&Tag that allows simultaneous probing of three epigenomic modalities at single-cell resolution, using nanobody-Tn5 fusion proteins. The three modalities encompass chromatin accessibility as measured via ATAC-Seq and two histone post-transcriptional modifications.

MacroH2A Function in Development and Disease (Emily Bernstein)

Episode 63

December 1, 2021

In this episode of the Epigenetics Podcast, we caught up with Emily Bernstein from Icahn School of Medicine at Mount Sinai to talk about her work on MacroH2A function and the role of Polycomb proteins in its epigenetic regulation, and how this affects stem cell development and disease.

The Bernstein Lab focuses on histone variants, in particular the H2A variant macroH2A. Chromatin architecture is influenced by the composition of the nucleosome and, hence, exchanging the core histones for histone variants can have a major impact on chromatin structure. MacroH2A variants are the most unique histone variants due to a 30kDa non-histone domain (macro domain) at their C-termini. This macro domain likely confers important functions to macroH2A variants, which have important regulatory roles in the cell. Among other things, the Bernstein Lab has shown that macroH2A is enriched at a critical set of Utx target genes whose expression is critical for the early stages of induced pluripotency, and that macroH2A plays a role as a barrier to tumorigenesis.