Epigenetics Podcast
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Thursday Mar 13, 2025
Thursday Mar 13, 2025
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 chromatin's mechanical properties and how these influence cellular processes like transcriptional regulation, DNA replication, and cellular responses to damage.
We also explore her collaborative work that bridges the gap between basic research and clinical applications, particularly in cancer therapy. Dr. Risca shares insights into her investigations into how chromatin dynamics change during cell cycle arrest and their implications for cancer therapy resistance. Our discussion culminates in her reflections on the definition of epigenetics, framing it as the exploration of how cellular mechanisms encode and process information.
References
Risca VI, Denny SK, Straight AF, Greenleaf WJ. Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. Nature. 2017 Jan 12;541(7636):237-241. doi: 10.1038/nature20781. Epub 2016 Dec 26. PMID: 28024297; PMCID: PMC5526328.
Soroczynski J, Anderson LJ, Yeung JL, Rendleman JM, Oren DA, Konishi HA, Risca VI. OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization. bioRxiv [Preprint]. 2024 Jul 13:2024.07.11.602973. doi: 10.1101/2024.07.11.602973. PMID: 39026714; PMCID: PMC11257509.
Prescott, N. A., Biaco, T., Mansisidor, A., Bram, Y., Rendleman, J., Faulkner, S. C., Lemmon, A. A., Lim, C., Tiersky, R., Salataj, E., Garcia-Martinez, L., Borges, R. L., Morey, L., Hamard, P.-J., Koche, R. P., Risca, V. I., Schwartz, R. E., & David, Y. (2025). A nucleosome switch primes hepatitis B virus infection. Cell, S0092867425001023. https://doi.org/10.1016/j.cell.2025.01.033
Related Episodes
Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden)
Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman)
Effects of Non-Enzymatic Covalent Histone Modifications on Chromatin (Yael David)
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Thursday Feb 27, 2025
Thursday Feb 27, 2025
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 nucleosome distance—an inquiry that led to exciting insights regarding dynamic enzyme behavior. This includes findings that ACF operates not through a static ruler mechanism but rather through a kinetic mechanism, thus continuously adjusting nucleosome positioning based on DNA length during chromatin assembly.
Dr. Narlikar also delved into her studies on heterochromatin protein 1 (HP1), highlighting how HP1 recognizes methylation marks and assembles on chromatin to facilitate gene silencing. This segment of the discussion underscored her shift to studying phase separation and its implications in the organization of chromatin. Notably, her lab made significant advancements in understanding how HP1 forms phase-separated droplets, a finding that was independently corroborated by other laboratories, demonstrating the utility of collaborative scientific inquiry.
In discussing the nuances of chromatin dynamics, Dr. Narlikar also introduced her investigations into the INO80 complex, detailing its distinct mechanism for nucleosome movement compared to other remodelers. Each remodeling complex, as she elucidated, has unique catalytic capabilities while still utilizing similar biochemical foundations, highlighting the diverse regulatory roles these proteins play within cells.
References
Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A, Purcell TJ, Cooke R, Cheng Y, Narlikar GJ. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature. 2009 Dec 24;462(7276):1016-21. doi: 10.1038/nature08621. PMID: 20033039; PMCID: PMC2869534.
Canzio D, Liao M, Naber N, Pate E, Larson A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R, Schuck P, Cheng Y, Narlikar GJ. A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly. Nature. 2013 Apr 18;496(7445):377-81. doi: 10.1038/nature12032. Epub 2013 Mar 13. PMID: 23485968; PMCID: PMC3907283.
Sinha KK, Gross JD, Narlikar GJ. Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler. Science. 2017 Jan 20;355(6322):eaaa3761. doi: 10.1126/science.aaa3761. PMID: 28104838; PMCID: PMC5656449.
Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 2017 Jul 13;547(7662):236-240. doi: 10.1038/nature22822. Epub 2017 Jun 21. PMID: 28636604; PMCID: PMC5606208.
Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature. 2019 Nov;575(7782):390-394. doi: 10.1038/s41586-019-1669-2. Epub 2019 Oct 16. PMID: 31618757; PMCID: PMC7039410.
Related Episodes
Enhancers and Chromatin Remodeling in Mammary Gland Development (Camila dos Santos)
Heterochromatin Protein 1 and its Influence on the Structure of Chromatin (Serena Sanulli)
Heterochromatin and Phase Separation (Gary Karpen)
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Thursday Feb 13, 2025
Thursday Feb 13, 2025
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 evolution of our understanding of Polycomb recruitment, illustrating the multifactorial nature of this biological puzzle.
As the conversation progresses, we explore Dr. Cavalli's fascinating research into the three-dimensional organization of the genome. He explains his contributions to mapping chromosomal interactions within Drosophila and the distinctions observed when performing similar studies in mammalian systems. Key findings regarding topologically associated domains (TADs) and their association with gene expression are presented, alongside the implications for our understanding of gene regulation in development and disease.
References
Déjardin, J., Rappailles, A., Cuvier, O., Grimaud, C., Decoville, M., Locker, D., & Cavalli, G. (2005). Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Nature, 434(7032), 533–538. https://doi.org/10.1038/nature03386
Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012). Three-dimensional folding and functional organization principles of the Drosophila genome. Cell, 148(3), 458–472. https://doi.org/10.1016/j.cell.2012.01.010
Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J. P., Tanay, A., & Cavalli, G. (2017). Multiscale 3D Genome Rewiring during Mouse Neural Development. Cell, 171(3), 557–572.e24. https://doi.org/10.1016/j.cell.2017.09.043
Szabo, Q., Donjon, A., Jerković, I., Papadopoulos, G. L., Cheutin, T., Bonev, B., Nora, E. P., Bruneau, B. G., Bantignies, F., & Cavalli, G. (2020). Regulation of single-cell genome organization into TADs and chromatin nanodomains. Nature genetics, 52(11), 1151–1157. https://doi.org/10.1038/s41588-020-00716-8
Related Episodes
BET Proteins and Their Role in Chromosome Folding and Compartmentalization (Kyle Eagen)
Long-Range Transcriptional Control by 3D Chromosome Structure (Luca Giorgetti)
Epigenetic Landscapes During Cancer (Luciano Di Croce)
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Thursday Jan 23, 2025
Thursday Jan 23, 2025
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 a discussion of his recent findings on histone lactylation and its implications in cellular metabolism, as well as the intricacies of epigenetic imprinting in stem cell biology.
Last but not least we touch upon Dr. Meyenn’s most recent study, published in Nature, investigating the epigenetic effects of obesity. He provides a detailed overview of how adipose tissue undergoes transcriptional and epigenetic rearrangements during weight fluctuations. The conversation highlights the notion of epigenetic memory in adipocytes, showing how obesity is not just a temporary state but leaves lasting cellular changes that can predispose individuals to future weight regain after dieting. This exploration opens avenues for potential therapeutic interventions aimed at reversing adverse epigenetic modifications.
References
von Meyenn, F., Iurlaro, M., Habibi, E., Liu, N. Q., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., Kroeze, L. I., Nesterova, T. B., Jansen, J. H., Xie, H., He, C., Reik, W., & Stunnenberg, H. G. (2016). Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Molecular cell, 62(6), 848–861. https://doi.org/10.1016/j.molcel.2016.04.025
Galle, E., Wong, C. W., Ghosh, A., Desgeorges, T., Melrose, K., Hinte, L. C., Castellano-Castillo, D., Engl, M., de Sousa, J. A., Ruiz-Ojeda, F. J., De Bock, K., Ruiz, J. R., & von Meyenn, F. (2022). H3K18 lactylation marks tissue-specific active enhancers. Genome biology, 23(1), 207. https://doi.org/10.1186/s13059-022-02775-y
Agostinho de Sousa, J., Wong, C. W., Dunkel, I., Owens, T., Voigt, P., Hodgson, A., Baker, D., Schulz, E. G., Reik, W., Smith, A., Rostovskaya, M., & von Meyenn, F. (2023). Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. Science advances, 9(39), eadg1936. https://doi.org/10.1126/sciadv.adg1936
Bonder, M. J., Clark, S. J., Krueger, F., Luo, S., Agostinho de Sousa, J., Hashtroud, A. M., Stubbs, T. M., Stark, A. K., Rulands, S., Stegle, O., Reik, W., & von Meyenn, F. (2024). scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood. Nature communications, 15(1), 7567. https://doi.org/10.1038/s41467-024-51833-5
Hinte, L. C., Castellano-Castillo, D., Ghosh, A., Melrose, K., Gasser, E., Noé, F., Massier, L., Dong, H., Sun, W., Hoffmann, A., Wolfrum, C., Rydén, M., Mejhert, N., Blüher, M., & von Meyenn, F. (2024). Adipose tissue retains an epigenetic memory of obesity after weight loss. Nature, 636(8042), 457–465. https://doi.org/10.1038/s41586-024-08165-7
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Nutriepigenetics: The Effects of Diet on Behavior (Monica Dus)
Epigenetic and Metabolic Regulation of Early Development (Jan Żylicz)
Effects of Environmental Cues on the Epigenome and Longevity (Paul Shiels)
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Thursday Jan 09, 2025
Thursday Jan 09, 2025
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 contemporaneous advancements in methods like Micro-C. The discussion highlighted the importance of understanding enzyme bias in chromatin studies and the need for meticulous experimental design to ensure the validity of biological interpretations.
We further explored exciting advancements in single-cell genomics, specifically Ramani's work on developing sci-Hi-C. This innovative technique leverages combinatorial indexing to allow high-resolution mapping of chromatin architecture at the single-cell level, a significant leap forward in understanding the complexities of gene regulation.
As we progress, Ramani detailed his transition from graduate student to independent investigator starting his own lab. He elaborated on the challenges and excitements associated with establishing his research focus in chromatin structure and function using advanced sequencing technologies. Employing various strategies, including the innovative SAMOSA assay, his research seeks to elucidate the mechanisms by which chromatin structure influences transcriptional regulation.
We also discussed the heterogeneity of chromatin and its implications for gene expression. Ramani provided a fascinating perspective on how variations in chromatin structure could affect gene activity, highlighting potential avenues for future research that aims to untangle the complex dynamics at play in both healthy and diseased states.
References
Ramani, V., Cusanovich, D., Hause, R. et al. Mapping 3D genome architecture through in situ DNase Hi-C. Nat Protoc 11, 2104–2121 (2016). https://doi.org/10.1038/nprot.2016.126
Nour J Abdulhay, Colin P McNally, Laura J Hsieh, Sivakanthan Kasinathan, Aidan Keith, Laurel S Estes, Mehran Karimzadeh, Jason G Underwood, Hani Goodarzi, Geeta J Narlikar, Vijay Ramani (2020) Massively multiplex single-molecule oligonucleosome footprinting eLife 9:e59404. https://doi.org/10.7554/eLife.59404
Abdulhay, N.J., Hsieh, L.J., McNally, C.P. et al. Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Nat Struct Mol Biol 30, 1571–1581 (2023). https://doi.org/10.1038/s41594-023-01093-6
Nanda, A.S., Wu, K., Irkliyenko, I. et al. Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. Nat Genet 56, 1300–1309 (2024). https://doi.org/10.1038/s41588-024-01748-0
Related Episodes
Epigenetic Mechanisms in Genome Regulation and Developmental Programming (James Hackett)
Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff)
Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman)
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Thursday Dec 19, 2024
Thursday Dec 19, 2024
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, we examined the intricate relationship between DNA methylation and Polycomb repression, discussing how these epigenetic mechanisms interact and the functional outcomes of their regulation. Dr. Greenberg's insights into his recent studies reveal a commitment to unraveling the complexities of enhancer-promoter interactions in the context of epigenetic regulation.
References
Greenberg, M. V., Ausin, I., Chan, S. W., Cokus, S. J., Cuperus, J. T., Feng, S., Law, J. A., Chu, C., Pellegrini, M., Carrington, J. C., & Jacobsen, S. E. (2011). Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics, 6(3), 344–354. https://doi.org/10.4161/epi.6.3.14242
Greenberg, M. V., Glaser, J., Borsos, M., Marjou, F. E., Walter, M., Teissandier, A., & Bourc'his, D. (2017). Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. Nature genetics, 49(1), 110–118. https://doi.org/10.1038/ng.3718
Greenberg, M., Teissandier, A., Walter, M., Noordermeer, D., & Bourc'his, D. (2019). Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency. eLife, 8, e44057. https://doi.org/10.7554/eLife.44057
Monteagudo-Sánchez, A., Richard Albert, J., Scarpa, M., Noordermeer, D., & Greenberg, M. V. C. (2024). The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation. Nucleic acids research, 52(18), 10934–10950. https://doi.org/10.1093/nar/gkae724
Richard Albert, J., Urli, T., Monteagudo-Sánchez, A., Le Breton, A., Sultanova, A., David, A., Scarpa, M., Schulz, M., & Greenberg, M. V. C. (2024). DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency. Nature structural & molecular biology, 10.1038/s41594-024-01405-4. Advance online publication. https://doi.org/10.1038/s41594-024-01405-4
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DNA Methylation and Mammalian Development (Déborah Bourc'his)
Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon)
Epigenetic Mechanisms in Genome Regulation and Developmental Programming (James Hackett)
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Thursday Dec 05, 2024
Thursday Dec 05, 2024
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 normal gene expression, and how R-loops exacerbate transcriptional silencing. Throughout her reflection on these discoveries, she emphasizes the importance of studying R-loops beyond merely being a transcriptional byproduct, but as players in gene regulation and potential contributors to disease pathology.
The episode also covers her innovative work in characterizing the R-loop interactome through various experimental techniques. She highlights the complexity of R-loop dynamics, including the discovery of protein factors that interact with R-loops and could influence their stability and regulatory functions. Furthermore, she discusses the exciting intersection of RNA modifications, such as m6A, which plays a role in R-loop regulation and presents new avenues for research, particularly pertaining to how disease-specific modifications might alter R-loop behavior.
References
Cristini, A., Groh, M., Kristiansen, M. S., & Gromak, N. (2018). RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage. Cell reports, 23(6), 1891–1905. https://doi.org/10.1016/j.celrep.2018.04.025
Abakir, A., Giles, T. C., Cristini, A., Foster, J. M., Dai, N., Starczak, M., Rubio-Roldan, A., Li, M., Eleftheriou, M., Crutchley, J., Flatt, L., Young, L., Gaffney, D. J., Denning, C., Dalhus, B., Emes, R. D., Gackowski, D., Corrêa, I. R., Jr, Garcia-Perez, J. L., Klungland, A., … Ruzov, A. (2020). N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nature genetics, 52(1), 48–55. https://doi.org/10.1038/s41588-019-0549-x
Related Episodes
DNA Replication, Transcription and R-loops (Stephan Hamperl)
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Thursday Nov 21, 2024
Thursday Nov 21, 2024
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 enhanced her understanding of chromatin biology and generated significant insights into the mechanics of epigenetic regulation. Highlighting a recent 2023 publication, we unpack her findings related to the conserved molecular switch between MLL1 and MLL3 complexes. These discoveries revealed how the application of small-molecule inhibitors of the menin-MLL interaction can alter gene expression and affect leukemia cells’ responses to treatments.
We also touch on the operational dynamics within her lab at MIT, established during challenging times marked by the pandemic. Yadira is dedicated to fostering a collaborative and respectful environment among her team, comprised of PhD candidates and research technicians, all sharing a commitment to unraveling the complexities of chromatin regulation. She emphasizes the significance of understanding chromatin scaffold proteins and their role in regulating gene expression and genome organization.
References
Soto-Feliciano, Y. M., Bartlebaugh, J. M. E., Liu, Y., Sánchez-Rivera, F. J., Bhutkar, A., Weintraub, A. S., Buenrostro, J. D., Cheng, C. S., Regev, A., Jacks, T. E., Young, R. A., & Hemann, M. T. (2017). PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes & development, 31(10), 973–989. https://doi.org/10.1101/gad.295857.117
Soto-Feliciano, Y. M., Sánchez-Rivera, F. J., Perner, F., Barrows, D. W., Kastenhuber, E. R., Ho, Y. J., Carroll, T., Xiong, Y., Anand, D., Soshnev, A. A., Gates, L., Beytagh, M. C., Cheon, D., Gu, S., Liu, X. S., Krivtsov, A. V., Meneses, M., de Stanchina, E., Stone, R. M., Armstrong, S. A., … Allis, C. D. (2023). A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition. Cancer discovery, 13(1), 146–169. https://doi.org/10.1158/2159-8290.CD-22-0416
Zhu, C., Soto-Feliciano, Y. M., Morris, J. P., Huang, C. H., Koche, R. P., Ho, Y. J., Banito, A., Chen, C. W., Shroff, A., Tian, S., Livshits, G., Chen, C. C., Fennell, M., Armstrong, S. A., Allis, C. D., Tschaharganeh, D. F., & Lowe, S. W. (2023). MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer. eLife, 12, e80854. https://doi.org/10.7554/eLife.80854
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MLL Proteins in Mixed-Lineage Leukemia (Yali Dou)
Targeting COMPASS to Cure Childhood Leukemia (Ali Shilatifard)
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