Active Motif's Podcast

In this episode of the Epigenetics Podcast, we talked with Boyan Bonev from the HelmholtzZetrum in Munich about his work on neuroepigenetics, focusing on gene regulation, chromatin architecture, and primate epigenome evolution, This Episode focuses on Dr. Bonev’s recent research, particularly focusing on how chromatin architecture and gene regulation influence neural cell identity and function. He discusses his work investigating transcriptional activity in relation to chromatin insulation, highlighting a critical finding that induced expression of genes does not necessarily lead to chromatin insulation—a point that complicates prior assumptions about the relationship between gene expression and chromatin organization. This study aimed to determine the causal versus correlative aspects of chromatin architecture in brain development and links it to developmental processes and neurodevelopmental disorders. Building on his findings in gene regulation, Dr. Bonev elaborates on a significant study he conducted in h

In this episode of the Epigenetics Podcast, we talked with Dr. Eva Hörmanseder from the HelmholtzZentrum in Munich about her work on epigenetic mechanisms in cellular memory and gene regulation. In this episode, we delve into the fascinating world of cellular memory and gene regulation with Dr. Eva Hermanns-Eder from the Helmholtz Zentrum in Munich. Her research centers on how cells maintain their identity through the process of mitotic divisions, which is crucial for understanding both development and various diseases. We explore the role of chromatin dynamics and epigenetic modifications in switching genes on and off over time, which has significant implications for fields like cancer biology and regenerative medicine. The discussion starts with Dr. Hörmanseder's recent studies on epigenetic memories, particularly focusing on the concept of transcriptional memory in nuclear transfer embryos. She explains her work with H3K4 trimethylation, a crucial epigenetic mark associated with active transcription states

In this episode of the Epigenetics Podcast, we talked with Viviana Risca from Rockefeller University about her work on RICC-Seq and how it's used to probe DNA-DNA contacts in intact or fixed cells using ionizing radiation. This Interview covers Dr. Viviana Risca's cutting-edge methodologies, such as RICC-seq, which enables high-resolution analysis of chromatin structures without traditional cross-linking biases. We engage in a detailed discussion about how different techniques, such as RICC-seq and Micro-C, complement each other to provide robust insights into nucleosome interactions and chromatin dynamics. Dr. Risca articulates the challenges and innovations within her lab as it navigates through the complexities of chromatin mapping. The episode takes an exciting turn toward traversing the landscape of her future research directions, particularly studying the role of linker histones and other chromatin architectural proteins in regulating gene expression. Dr. Risca emphasizes the importance of understanding

In this episode of the Epigenetics Podcast, we talked with Geeta Narlikar from UCSF about her work on chromatin remodeling, Heterochromatin Protein 1, and the molecular mechanisms that influence the genome. The conversation starts with a pivotal paper from the early days of Dr. Narlikars research career, titled "Distinct Strategies to Make Nucleosomal DNA Accessible," focused on two ATP-dependent remodelers, BRG1 and SNF2H. Here, she notes that while both enzymes operate similarly, they generate different outputs and play distinct biological roles within the cell. The research revealed that BRG1 is more aggressive in altering nucleosome configuration, aligning with its role in transcription activation, while SNF2H showed a more refined approach in the formation of heterochromatin. Transitioning to her work at UCSF, she emphasized the importance of collaboration and mentoring within a research group. Her focus then shifted towards the ACF ATP-dependent chromatin assembly factor, hypothesizing how ACF measures

In this episode of the Epigenetics Podcast, we talked with Giacomo Cavalli from the Institute of Human Genetics in Montpellier about his work on critical aspects of epigenetic regulation, particularly the role of Polycomb proteins and chromatin architecture. We start the Interview by talking about Dr. Cavalli's work on Polycomb function in maintaining chromatin states and how it relates to gene regulation. He shares insights from his early lab experiences, where he aimed to understand the inheritance mechanisms of chromatin states through various models, including the FAB7 cellular memory module. The discussion uncovers how Polycomb proteins can silence gene expression and the complex interplay between different epigenetic factors that govern this process. Dr. Cavalli also addresses how he has investigated the recruitment mechanisms of Polycomb complexes, highlighting the roles of several DNA-binding proteins, including DSP-1 and GAGA factor, in this intricate regulatory landscape. He emphasizes the evolutio

In this episode of the Epigenetics Podcast, we talked with Ferdinand von Meyenn from ETH Zürich about his work on the interplay of nutrition, metabolic pathways, and epigenetic regulation. To start Dr. Meyenn recounts his pivotal research on DNA methylation in naive embryonic stem cells during his time with Wolf Reick. He explains the dynamics of global demethylation in naive stem cells, revealing the key enzymes involved and the unexpected findings surrounding UHF1—its role in maintaining DNA methylation levels and influencing the methylation landscape during early embryonic development. Dr. Meyenn then shares his perspective on the scientific transition to establishing his own lab at ETH. He reflects on his ambitions to merge the fields of metabolism and epigenetics, which is a recurring theme throughout his research. By investigating the interplay between metabolic changes and epigenetic regulation, he aims to uncover how environmental factors affect cellular dynamics across various tissues. This leads to

In this episode of the Epigenetics Podcast, we talked with Vijay Ramani from the Gladstone Institute about his work on Single-Molecule Adenine Methylated Oligonucleosome Sequencing Assay (SAMOSA). Our discussion starts with Vijay Ramani's impactful contributions to the field during his time in Jay Shendure's lab, where he worked on several innovative methods, including RNA proximity ligation. This project was conceived during his graduate studies, aiming to adapt techniques from DNA research to investigate RNA structures—a largely unexplored area at the time. We delved into the nuances of his experiences in graduate school, emphasizing how critical it was to have mentors who provided room for creativity and autonomy in experimental design. Dr. Ramani then shares insights about his foray into developing more refined methodologies, such as in-situ DNA Hi-C, a revolutionary protocol tailored for three-dimensional genomic mapping. He explained the rationale behind his projects, comparing the outcomes with contemp

In this episode of the Epigenetics Podcast, we talked with Maxim Greenberg from the Institute Jacob Monot about his work on epigenetic consequences of DNA methylation in development. In this interview we explore how Dr. Greenberg’s work at UCLA involved pioneering experiments on DNA methylation mechanisms and how this period was marked by significant collaborative efforts within a highly competitive yet supportive lab environment that ultimately lead to publications in high impact journals. His transition to a postdoctoral position at the Institut Curie with Deborah Bourc'his harnessed his expertise in mammalian systems, examining chromatin changes and the implications for embryonic development. Dr. Greenberg explained the nuances of his research, particularly how chromatin modifications during early development can influence gene regulatory mechanisms later in life, providing a compelling narrative about the potential long-term impacts of epigenetic changes that occur in utero. Throughout our conversation, w

In this episode of the Epigenetics Podcast, we talked with Natalia Gromak from the University of Oxford about her work on R-Loop biology in health and disease. In this interview Dr. Gromak delves into her significant research on transcription and RNA biology, particularly focusing on the molecular mechanisms involved at transcriptional pause sites. She describes her early work in understanding transcription termination and how her team investigated the role of specific RNA and DNA structures, including R-loops, that could influence polymerase progression. This exploration into R-loops—complexes formed by RNA and DNA interactions—was a key turning point in her research, as she and her colleagues identified their regulatory functions within the human genome. Discussion transitions into her findings regarding the implications of R-loops in diseases like Friedrich's ataxia and Fragile X syndrome. Dr. Gromak then elucidates how the pathological expansion of repeat sequences in these conditions interferes with norm

In this episode of the Epigenetics Podcast, we talked with Yadira Soto-Feliciano from MIT about her work on the Menin-MLL complex and the effect of small molecules on its stability in leukemia. We explore the pivotal moments that led her to cancer biology during her graduate studies, where her work included ground-breaking research on the role of the plant homeodomain Finger protein-6 (PHF-6) in leukemia. This work bridged the realms of chromatin accessibility, transcription factors, and cancer cell lineage, providing critical evidence for the concept of lineage plasticity in cancer biology—a topic that has gained significant traction in recent years. Dr. Soto-Feliciano discusses how advances in techniques like CRISPR and ChIP-sequencing have shaped her research, enabling deeper insights into the mechanisms underlying cancer cell identity. As our discussion transitions, Dr. Soto-Feliciano shares her experience in David Allis's lab, illustrating how the collaboration across diverse scientific disciplines enhan

In this episode of the Epigenetics Podcast, we talked with Mary Anne Jelinek Associate Director of R&D at Active Motif about writing and reviewing grants in academia and industry. Learn from Dr. Jelinek’s years of experience writing and reviewing grants and get her best advice and insight for success. Hear about similarities and differences in preparing grants in academia vs. biotech or other industry settings. Key insights include: Finding Grant opportunities that exist for different sectors and countries, from the familiar ones like NIH and NSF in the United States grant funding offered by NATO for member countries.  Learn about grants targeted to small businesses and specific allocation of resources intended to foster and promote innovation and entrepreneurship and how to navigate confidentiality when writing grants in industry, being mindful of conflict of interest and best practices.  Coming up with ideas is easy – but how do you find institutes interested in funding those research areas? Get tips on

In this episode of the Epigenetics Podcast, we talked with Carl Wu from John's Hopkins University about his work on nucleosome remodeling, histone variants, and the role of single-molecule imaging in gene regulation. Our discussion starts with Carl Wu sharing his first significant milestones, a paper in "Cell" and the serendipitous discovery of DNA hypersensitive sites, which transformed our understanding of chromatin accessibility and its implications for gene regulation. As we delve into Dr. Wu’s specific areas of research, he elaborates on the biochemistry of nucleosome remodeling and the intricate role of chromatin remodeling enzymes like NURF. We discuss how these enzymes employ ATP hydrolysis to reposition nucleosomes, making DNA accessible for transcription. He then explains the collaborative relationship between chromatin remodelers and transcription factors, showcasing the fascinating interplay that governs gene expression and regulatory mechanisms. The conversation takes a deeper turn as we explore

In this episode of the Epigenetics Podcast, we talked with Mitinori Saitou from Kyoto University about his work on germ cell development, focusing on proteins like BLIMP1 and PRDM14, reprogramming iPSCs, and his vision to address infertility and genetic disorders through epigenetic insights. To start our discussion, Dr. Saitou shares the foundation of his research, which centers on the mechanisms of germ cell development across various species, including mice, non-human primates, and humans. He provides insight into his early work examining the roles of two key proteins: BLIMP1 and PRDM14. These proteins are essential for germline specification in mammals, and their functions are unveiled through detailed exploration of knockout models. In particular, Dr. Saitou elucidates the critical events in germ cell specification, highlighting how disruptions to the functions of these proteins lead to significant impairments in development. As the conversation deepens, we discuss Dr. Saitou’s groundbreaking advances in

In this episode of the Epigenetics Podcast, we talked with Karine Le Roch from the University of California at Riverside about her work on malaria chromatin structure and its transcriptional regulation. In this Interview Dr. Le Roch discusses her investigation of post-transcriptional controls and nucleosome positioning in Plasmodium falciparum, employing next-generation sequencing and chromatin profiling methods. Karin emphasizes how these methodologies contribute to a comprehensive understanding of gene regulation beyond mere transcription initiation, emphasizing the significance of mRNA binding proteins and their role in stabilizing gene transcripts for translation. This exploration of the interaction between chromatin structure, transcriptional dynamics, and post-transcriptional regulation reveals a multidimensional perspective of gene expression. Transitioning to her lab’s focus on high-throughput genomic technologies, we discuss how Karin and her team are uncovering conserved and species-specific genomic

In this episode of the Epigenetics Podcast, we talked with Bas van Steensel from the Netherlands Cancer Institute about his work on characterizing chromatin at the Nuclear Lamina. The Interview starts with discussing Bas van Steensel's significant contributions to understanding genome-nuclear lamina interactions. Bas detailed the development of the DAM-ID technique during his postdoctoral studies, which provided a novel way to map genome-wide occupancy and identify Lamina-Associated Domains (LADs). He elaborated on how LADs reveal a distinct domain architecture, often correlating with gene expression levels. This prompted an exploration of the dynamics of these domains during differentiation processes, allowing insights into how gene activation and repression are influenced by their positioning relative to the nuclear lamina. The conversation highlighted the intricate relationship between chromatin dynamics and gene regulation, with Bas sharing compelling findings on how LADs behave during cell differentiatio

In this episode of the Epigenetics Podcast, we caught up with Vladimir Teif from the University of Essex to talk about his work on nucleosome positioning in development and disease. Vladimir's research has been pivotal in understanding nucleosome positioning and its implications for cell differentiation, particularly in embryonic stem cells and cancer. We discuss his groundbreaking studies that first mapped nucleosome positions in various cell types and how these findings led to uncovering the intricate relationships between nucleosome stability, transcription factors, and DNA modifications such as methylation. This understanding has immense significance for cancer diagnostics, where knowing the spatial arrangement of nucleosomes could influence how aggressive a cancer type might be, or how a patient might respond to treatment. Transitioning from foundational research to clinical applications, Vladimir elaborates on his exciting work with liquid biopsies. By analyzing cell-free DNA from blood plasma, research

In this episode of the Epigenetics Podcast, we talked with Johnathan Whetstine from Fox Chase Cancer Center about his work on how histone demethylases affect gene expression and cancer cell stability. The Interview start by discussing a pivotal paper from Jonathan's lab in 2010, where they identified a role for the KDM4A histone demethylase in replication timing and cell cycle progression. They elaborate on the discoveries made regarding the link between histone marks, replication timing, and gene expression control. Jonathan explains the impact of microRNAs on regulating KDM4A and how protein turnover rates can influence cellular responses to treatments like mTOR inhibitors. Further, they explore the causal relationship between histone marks and replication timing, demonstrating how alterations in epigenetic regulation can affect genome stability. Jonathan shares insights from his latest research on H3K9 methylation balance at the MLL-KM2A locus, elucidating how these epigenetic modifications regulate amplif

In this episode of the Epigenetics Podcast, we talked with Christa Buecker from the Max Perutz Laboratories in Vienna about her work on transcriptional regulation during early embryonic development. Dr. Buecker unravels the differences between naive and primed pluripotency states, showcasing how OCT4 relocalization and enhancer chromatin landscapes play pivotal roles during this transition. The conversation delves into the intricate interplay of transcription factors like OCT4 and OTX2, shedding light on their collaborative efforts in regulating gene expression during differentiation. Dr. Buecker then shares insights from her study on enhancer elements controlling FGF5 expression and discusses the surprising revelation that individual enhancers show no intrinsic activity but work together in a super additive fashion. She also touches upon her research on IRF1's connection to the gene regulatory network and its role in protecting cells against viral infections. The conversation shifts to Dr. Buecker's current

In this episode of the Epigenetics Podcast, we talked with Claire Rougeulle from the Epigenetics and Cell Fate Center at Université Paris City about her work on gene expression control, the intricacies of X-chromosome inactivation, and the potential of non-coding RNAs in this process. In this episode Claire Rougeulle explains her discoveries regarding the transcription regulation of XIST by factors like YY1 and the erosion of X-chromosome inactivation in human pluripotent stem cells. She shares the complexity of distinguishing between epigenetics and transcriptional regulation, highlighting the challenges in studying allelic expression of X-chromosomes at the single-cell level. The Episode further explores Claire's findings on the XACT locus regulation, evolution from retroviruses, and its potential role in preventing X-chromosome silencing. Claire also shares her future research focus on understanding X-inactivation establishment in humans and the transition from XIST attenuating to silencing X-chromosomes a

In this episode of the Epigenetics Podcast, we talked with James Hackett from the EMBL in Rome about his work on epigenetic mechanisms in genome regulation and developmental programming. One of James Hackett's significant studies focused on DNA methylation and genome defense mechanisms in the germline, exploring the role of chromatin modifications in mammalian gene regulation. He delves into investigating the erasure of DNA methylation in the germline, highlighting the key role of the TET-enzymes in demethylation processes. Dr. Hackett shares insights from his research on pluripotent stem cells, where he mapped genome-wide DNA methylation and hydroxymethylation in different pluripotent states. He discusses the impact of extrinsic conditions on pluripotent states and the biases observed in lineage preferences. Furthermore, the discussion delves into the development of a CRISPR screening tool to study cell fate transitions, particularly focusing on the genetic factors contributing to germline specification. He