Epigenetics Podcast by Active Motif
Active Motif
Categories: Science & Medicine
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In this episode of the Epigenetics Podcast, we talked with Sarah Marzi from the UK Dementia Research Institute at Imperial College London about her work on epigenetic changes in Alzheimer's Disease, and comparing CUT&Tag to ENCODE ChIP-Seq using limited cell samples. The interview discusses Sarah Marzi's work on ChIP-Seq experiments and their significance in understanding Alzheimer's disease from an epigenetic perspective. The discussion touches on the widespread dysregulation and changes in acetylation, particularly in genes associated with Alzheimer's risk, providing insights into potential links between epigenetic insults and disease onset. Moving on to the technical aspects of the study, the interview examines the strategic use of CUT&Tag. It explores the challenges and optimizations involved in accurately profiling limited cell samples. The dialogue also compares CUT&Tag to ENCODE ChIP-Seq, highlighting the complexities of peak calling and data interpretation across different methodologies. References Kumsta, R., Marzi, S., Viana, J. et al. Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1. Transl Psychiatry 6, e830 (2016). https://doi.org/10.1038/tp.2016.95 Marzi, S. J., Schilder, B. M., Nott, A., Frigerio, C. S., Willaime‐Morawek, S., Bucholc, M., Hanger, D. P., James, C., Lewis, P. A., Lourida, I., Noble, W., Rodriguez‐Algarra, F., Sharif, J., Tsalenchuk, M., Winchester, L. M., Yaman, Ü., Yao, Z., The Deep Dementia Phenotyping (DEMON) Network, Ranson, J. M., & Llewellyn, D. J. (2023). Artificial intelligence for neurodegenerative experimental models. Alzheimer’s & Dementia, 19(12), 5970–5987. https://doi.org/10.1002/alz.13479 Marzi, S. J., Leung, S. K., Ribarska, T., Hannon, E., Smith, A. R., Pishva, E., Poschmann, J., Moore, K., Troakes, C., Al-Sarraj, S., Beck, S., Newman, S., Lunnon, K., Schalkwyk, L. C., & Mill, J. (2018). A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nature Neuroscience, 21(11), 1618–1627. https://doi.org/10.1038/s41593-018-0253-7 Hu, D., Abbasova, L., Schilder, B. M., Nott, A., Skene, N. G., & Marzi, S. J. (2022). CUT&Tag recovers up to half of ENCODE ChIP-seq peaks in modifications of H3K27 [Preprint]. Genomics. https://doi.org/10.1101/2022.03.30.486382 Related Episodes When is a Peak a Peak? (Claudio Cantù) Development of Integrative Machine Learning Tools for Neurodegenerative Diseases (Enrico Glaab) DNA Methylation Alterations in Neurodegenerative Diseases (Paula Desplats) Contact Epigenetics Podcast on X Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Epigenetics Podcast on Threads Active Motif on X Active Motif on LinkedIn Email: podcast@activemotif.com
Previous episodes
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123 - Comparing CUT&Tag to ENCODE ChIP-Seq in Alzheimer's Disease Samples (Sarah Marzi)Thu, 18 Apr 2024 - 0h
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122 - The Role of Hat1p in Chromatin Assembly (Mark Parthun)Thu, 04 Apr 2024 - 0h
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121 - The Impact of Paternal Diet on Offspring Metabolism (Upasna Sharma)Thu, 21 Mar 2024 - 0h
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120 - H3K36me3, H4K16ac and Cryptic Transcription in Ageing (Weiwei Dang)Thu, 07 Mar 2024 - 0h
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119 - Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman)Thu, 22 Feb 2024 - 0h
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118 - MLL Proteins in Mixed-Lineage Leukemia (Yali Dou)Thu, 08 Feb 2024 - 0h
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117 - Sex-biased Imprinting and DNA Regulatory Landscapes During Reprogramming (Sam Buckberry)Thu, 25 Jan 2024 - 0h
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116 - BET Proteins and Their Role in Chromosome Folding and Compartmentalization (Kyle Eagen)Thu, 11 Jan 2024 - 0h
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115 - Epigenetic Underpinnings of Human Addiction (Francesca Telese & Jessica Zhou)Thu, 21 Dec 2023 - 0h
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114 - H3K79 Methylation, DOT1L, and FOXG1 in Neural Development (Tanja Vogel)Thu, 30 Nov 2023 - 0h
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113 - Function of Insulators in 3D Genome Folding (Maria Gambetta)Thu, 16 Nov 2023 - 0h
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112 - Contribution of the Estrogen Receptor to Breast Cancer Progression (Jason Carroll)Thu, 02 Nov 2023 - 0h
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111 - Inheritance of Transcriptional Memory by Mitotic Bookmarking (Sheila Teves)Thu, 19 Oct 2023 - 0h
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110 - Differential Methylated Regions in Autism Spectrum Disorders (Janine La Salle)Thu, 05 Oct 2023 - 0h
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109 - DNA Damage in Longevity and Ageing (Björn Schumacher)Thu, 21 Sep 2023 - 0h
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108 - The Impact of Chromatin Modifiers on Disease Development and Progression (Capucine van Rechem)Thu, 07 Sep 2023 - 0h
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107 - Long-Range Transcriptional Control by 3D Chromosome Structure (Luca Giorgetti)Thu, 24 Aug 2023 - 0h
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106 - Transgenerational Inheritance and Epigenetic Imprinting in Plants (Mary Gehring)Thu, 10 Aug 2023 - 0h
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105 - When is a Peak a Peak? (Claudio Cantù)Thu, 27 Jul 2023
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104 - Analysis of 3D Chromatin Structure Using Super-Resolution Imaging (Alistair Boettiger)Thu, 13 Jul 2023 - 0h
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103 - Gene Dosage Alterations in Evolution and Ageing (Claudia Keller Valsecchi)Thu, 29 Jun 2023 - 0h
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102 - Structural Analysis of Nucleosomes During Transcription (Lucas Farnung)Thu, 15 Jun 2023 - 0h
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101 - DNA Methylation Alterations in Neurodegenerative Diseases (Paula Desplats)Thu, 01 Jun 2023 - 0h
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100 - scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)Wed, 17 May 2023 - 0h
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99 - Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon)Thu, 04 May 2023 - 0h
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98 - Epigenetic Landscapes During Cancer (Luciano Di Croce)Thu, 20 Apr 2023 - 0h
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97 - Formation of CenH3-deficient Kinetochores (Ines Drinnenberg)Thu, 06 Apr 2023 - 0h
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96 - Effects of Environmental Cues on the Epigenome and Longevity (Paul Shiels)Thu, 23 Mar 2023 - 0h
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95 - The Epigenetics of Human Sperm Cells (Sarah Kimmins)Thu, 09 Mar 2023 - 0h
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94 - Transgenerational Inheritance and Evolution of Epimutations (Peter Sarkies)Thu, 23 Feb 2023 - 0h
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93 - Transcription Elongation Control by the Paf1 Complex (Karen Arndt)Thu, 09 Feb 2023 - 0h
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92 - Molecular Mechanisms of Chromatin Modifying Enzymes (Karim-Jean Armache)Thu, 26 Jan 2023 - 0h
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91 - The Role of PHF13 in Chromatin and Transcription (Sarah Kinkley)Thu, 12 Jan 2023 - 0h
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90 - Genome Organization Mediated by RNA Polymerase II (Argyrys Papantonis)Thu, 15 Dec 2022 - 0h
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89 - The Role of Pioneer Factors Zelda and Grainyhead at the Maternal-to-Zygotic Transition (Melissa Harrison)Thu, 01 Dec 2022 - 0h
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88 - Epigenetics in Human Malaria Parasites (Elena Gómez-Diaz)Thu, 17 Nov 2022 - 0h
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87 - Bioinformatic Analysis in Epigenetics Research (Nick Pervolarakis)Thu, 03 Nov 2022 - 0h
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86 - Anchor-Based Bisulfite Sequencing (Ben Delatte)Thu, 20 Oct 2022 - 0h
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85 - Enhancer Communities in Adipocyte Differentiation (Susanne Mandrup)Thu, 06 Oct 2022 - 0h
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84 - Transposable Elements in Gene Regulation and Evolution (Marco Trizzino)Thu, 22 Sep 2022 - 0h
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83 - Hydroxymethylation Landscape in Immunecells (Marcela Sjöberg)Thu, 08 Sep 2022 - 0h
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82 - Single Cell Epigenomics in Neuronal Development (Tim Petros)Thu, 25 Aug 2022 - 0h
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81 - Oncohistones as Drivers of Pediatric Brain Tumors (Nada Jabado)Thu, 11 Aug 2022 - 0h
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80 - Characterization of Epigenetic States in the Oligodendrocyte Lineage (Gonçalo Castelo-Branco)Thu, 28 Jul 2022 - 0h
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79 - Multiple challenges of ATAC-Seq, Points to Consider (Yuan Xue)Thu, 14 Jul 2022 - 0h
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78 - The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn)Thu, 30 Jun 2022 - 0h
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77 - Epigenetic Clocks and Biomarkers of Ageing (Morgan Levine)Thu, 23 Jun 2022 - 0h
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76 - Epigenetic and Metabolic Regulation of Early Development (Jan Żylicz)Thu, 09 Jun 2022 - 0h
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75 - Multiple challenges of CUT&Tag (Cassidee McDonough, Kyle Tanguay)Thu, 26 May 2022 - 0h
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74 - The Role of Histone Dopaminylation and Serotinylation in Neuronal Plasticity (Ian Maze)Thu, 12 May 2022 - 0h
