In this episode of the Epigenetics Podcast, we caught up with Melissa Harrison from the University of Wisconsin-Madison to talk about her work on the “Pioneer” Transcription Factors - Zelda and Grainyhead - and their role at the maternal-to-zygotic transition.

The Harrison lab studies how differentiation and development are driven by coordinated changes in gene expression. To do this, the targets of choice are the transcription factors Zelda and Grainyhead that bind to the genome at specific and crucial points in development and differentiation. These specialised transcription factors have the ability to bind to DNA in the context of nucleosomes which defines regulatory elements and leads to subsequent binding of additional classical transcription factors. These properties allow pioneer factors to act at the top of gene regulatory networks and control developmental transitions.

References

Harrison, M. M., Botchan, M. R., & Cline, T. W. (2010). Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes. Developmental biology, 345(2), 248–255. https://doi.org/10.1016/j.ydbio.2010.06.026

Harrison, M. M., Li, X. Y., Kaplan, T., Botchan, M. R., & Eisen, M. B. (2011). Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS genetics, 7(10), e1002266. https://doi.org/10.1371/journal.pgen.1002266

McDaniel, S. L., Gibson, T. J., Schulz, K. N., Fernandez Garcia, M., Nevil, M., Jain, S. U., Lewis, P. W., Zaret, K. S., & Harrison, M. M. (2019). Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation. Molecular cell, 74(1), 185–195.e4. https://doi.org/10.1016/j.molcel.2019.01.014

McDaniel, S. L., & Harrison, M. M. (2019). Optogenetic Inactivation of Transcription Factors in the Early Embryo of Drosophila. Bio-protocol, 9(13), e3296. https://doi.org/10.21769/BioProtoc.3296

Larson, E.D., Komori, H., Gibson, T.J. et al. Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila. Nat Commun 12, 7153 (2021). https://doi.org/10.1038/s41467-021-27506-y

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Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret)

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In this episode of the Epigenetics Podcast, we caught up with Elena Gomez-Diaz from the Institute of Parasitology and Biomedicine López-Neyra at the Spanish National Research Council. She share with us her work on the Epigenetics in Human Malaria Parasites.

Elena Gómez-Díaz and her team are focusing on understanding how epigenetic processes are implicated in host-parasite interactions by regulating gene expression in the model of malaria. The team has started to investigate and uncover layers of chromatin regulation that control developmental transitions in Plasmodium falciparum, especially in the parts of the life cycle that take place in the mosquito. Furthermore, the lab has investigated epigenetic changes that are present in malaria-infected Anopheles mosquitos, this led to the identification of cis-regulatory elements and enhancer-promoter networks in response to infection.

References

Gómez-Díaz E, Rivero A, Chandre F, Corces VG. Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae. Front Genet. 2014 Aug 15;5:277. doi: 10.3389/fgene.2014.00277. PMID: 25177345; PMCID: PMC4133732.

Gómez-Díaz, E., Yerbanga, R., Lefèvre, T. et al. Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae. Sci Rep 7, 40655 (2017). https://doi.org/10.1038/srep40655

José Luis Ruiz, Juan J Tena, Cristina Bancells, Alfred Cortés, José Luis Gómez-Skarmeta, Elena Gómez-Díaz, Characterization of the accessible genome in the human malaria parasite. Plasmodium falciparum, Nucleic Acids Research, Volume 46, Issue 18, 12 October 2018, Pages 9414–9431, https://doi.org/10.1093/nar/gky643

Women in Malaria 2021: A Conference Premier. (2021). Trends in Parasitology, 37(7), 573–580. https://doi.org/10.1016/j.pt.2021.04.001

Twitter Account: https://twitter.com/womeninmalaria

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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.

References

Life in the FASTQ Lane

Bioinformatics Resource Center

Epigenetic Services

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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.

References

Chapin, N., Fernandez, J., Poole, J. et al. Anchor-based bisulfite sequencing determines genome-wide DNA methylation. Commun Biol 5, 596 (2022). https://doi.org/10.1038/s42003-022-03543-1

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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.

References

Siersbæk R, Rabiee A, Nielsen R, Sidoli S, Traynor S, Loft A, Poulsen LC, Rogowska-Wrzesinska A, Jensen ON, Mandrup S. Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell Rep. 2014 Jun 12;7(5):1443-1455. doi: 10.1016/j.celrep.2014.04.042. Epub 2014 May 22. PMID: 24857652.

Siersbæk R, Baek S, Rabiee A, Nielsen R, Traynor S, Clark N, Sandelin A, Jensen ON, Sung MH, Hager GL, Mandrup S. Molecular architecture of transcription factor hotspots in early adipogenesis. Cell Rep. 2014 Jun 12;7(5):1434-1442. doi: 10.1016/j.celrep.2014.04.043. Epub 2014 May 22. PMID: 24857666; PMCID: PMC6360525.

Siersbæk R, Madsen JGS, Javierre BM, Nielsen R, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, Fraser P, Mandrup S. Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation. Mol Cell. 2017 May 4;66(3):420-435.e5. doi: 10.1016/j.molcel.2017.04.010. PMID: 28475875.

Rauch, A., Haakonsson, A.K., Madsen, J.G.S. et al. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet 51, 716–727 (2019). https://doi.org/10.1038/s41588-019-0359-1

Madsen, J.G.S., Madsen, M.S., Rauch, A. et al. Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells. Nat Genet 52, 1227–1238 (2020). https://doi.org/10.1038/s41588-020-0709-z

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In this episode of the Epigenetics Podcast, we caught up with Marco Trizzino from Thomas Jefferson University to talk about his work on transposable elements in gene regulation and evolution.

Marco Trizzino and his team focus on characterising transposable elements and how they affect gene regulation, evolution and ageing in primates. They could show that transposable elements that integrated into the genome turned into regulatory elements in the genome, like enhancers. They then contribute to regulation of processes like development or ageing, which could be among those factors that lead to increased brain development or longevity in great apes.

References

Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, Perry GH, Lynch VJ, Brown CD. Transposable elements are the primary source of novelty in primate gene regulation. Genome Res. 2017 Oct;27(10):1623-1633. doi: 10.1101/gr.218149.116. Epub 2017 Aug 30. PMID: 28855262; PMCID: PMC5630026.

Pagliaroli L, Porazzi P, Curtis AT, Scopa C, Mikkers HMM, Freund C, Daxinger L, Deliard S, Welsh SA, Offley S, Ott CA, Calabretta B, Brugmann SA, Santen GWE, Trizzino M. Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders. Nat Commun. 2021 Nov 9;12(1):6469. doi: 10.1038/s41467-021-26810-x. PMID: 34753942; PMCID: PMC8578637.

Tejada-Martinez D, Avelar RA, Lopes I, Zhang B, Novoa G, de Magalhães JP, Trizzino M. Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes. Mol Biol Evol. 2022 Feb 3;39(2):msab369. doi: 10.1093/molbev/msab369. PMID: 34971383; PMCID: PMC8837823.

Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors. Sruti Patoori, Samantha M. Barnada, Christopher Large, John I. Murray, Marco Trizzino. bioRxiv 2021.11.24.469877; doi: https://doi.org/10.1101/2021.11.24.469877

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

At the beginning of her career Marcela Sjöberg worked on Aurora B and Polycomb and how modifications placed by them modulate the binding of RNA Pol II. Later, her focus shifted to examine cytosine DNA methylation and hydroxymethylation changes in immune cells and how the epigenetic state of these marks varies between individuals and is reprogrammed for Metastable Epialleles in mouse. More recently, the laboratory is interested on how hydroxymethylation of transcription factor binding motifs influence binding and activity of the respective transcription factors in immune cells.

References

Sabbattini, P., Sjoberg, M., Nikic, S., Frangini, A., Holmqvist, P.-H., Kunowska, N., Carroll, T., Brookes, E., Arthur, S. J., Pombo, A., & Dillon, N. (2014). An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation. Molecular Biology of the Cell, 25(6), 904–915. https://doi.org/10.1091/mbc.e13-10-0628

Kazachenka, A., Bertozzi, T. M., Sjoberg-Herrera, M. K., Walker, N., Gardner, J., Gunning, R., Pahita, E., Adams, S., Adams, D., & Ferguson-Smith, A. C. (2018). Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance. Cell, 175(5), 1259-1271.e13. https://doi.org/10.1016/j.cell.2018.09.043

Westoby, J., Herrera, M.S., Ferguson-Smith, A.C. et al. Simulation-based benchmarking of isoform quantification in single-cell RNA-seq. Genome Biol 19, 191 (2018). https://doi.org/10.1186/s13059-018-1571-5

Viner, C., Johnson, J., Walker, N., Shi, H., Sjöberg, M., Adams, D. J., Ferguson-Smith, A. C., Bailey, T. L., & Hoffman, M. M. (2016). Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet [Preprint]. Bioinformatics. https://doi.org/10.1101/043794

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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 at the link below:  

https://www.nichd.nih.gov/research/atNICHD/Investigators/petros/data-sharing 

References

Datasets: https://www.nichd.nih.gov/research/atNICHD/Investigators/petros/data-sharing

Quattrocolo G, Fishell G, Petros TJ. Heterotopic Transplantations Reveal Environmental Influences on Interneuron Diversity and Maturation. Cell Rep. 2017 Oct 17;21(3):721-731. doi: 10.1016/j.celrep.2017.09.075. PMID: 29045839; PMCID: PMC5662128.

Dongjin R Lee, Christopher Rhodes, Apratim Mitra, Yajun Zhang, Dragan Maric, Ryan K Dale, Timothy J Petros (2022) Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain eLife 11:e71864 https://doi.org/10.7554/eLife.71864

Rhodes, C. T., Thompson, J. J., Mitra, A., Asokumar, D., Lee, D. R., Lee, D. J., Zhang, Y., Jason, E., Dale, R. K., Rocha, P. P., & Petros, T. J. (2022). An epigenome atlas of neural progenitors within the embryonic mouse forebrain. Nature communications, 13(1), 4196. https://doi.org/10.1038/s41467-022-31793-4

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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 remodeled 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.

References

Schwartzentruber, J., Korshunov, A., Liu, X. Y., Jones, D. T., Pfaff, E., Jacob, K., Sturm, D., Fontebasso, A. M., Quang, D. A., Tönjes, M., Hovestadt, V., Albrecht, S., Kool, M., Nantel, A., Konermann, C., Lindroth, A., Jäger, N., Rausch, T., Ryzhova, M., Korbel, J. O., … Jabado, N. (2012). Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature, 482(7384), 226–231. https://doi.org/10.1038/nature10833

Kleinman, C. L., Gerges, N., Papillon-Cavanagh, S., Sin-Chan, P., Pramatarova, A., Quang, D. A., Adoue, V., Busche, S., Caron, M., Djambazian, H., Bemmo, A., Fontebasso, A. M., Spence, T., Schwartzentruber, J., Albrecht, S., Hauser, P., Garami, M., Klekner, A., Bognar, L., Montes, J. L., … Jabado, N. (2014). Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nature genetics, 46(1), 39–44. https://doi.org/10.1038/ng.2849

Papillon-Cavanagh, S., Lu, C., Gayden, T., Mikael, L. G., Bechet, D., Karamboulas, C., Ailles, L., Karamchandani, J., Marchione, D. M., Garcia, B. A., Weinreb, I., Goldstein, D., Lewis, P. W., Dancu, O. M., Dhaliwal, S., Stecho, W., Howlett, C. J., Mymryk, J. S., Barrett, J. W., Nichols, A. C., … Jabado, N. (2017). Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Nature genetics, 49(2), 180–185. https://doi.org/10.1038/ng.3757

Chen, C., Deshmukh, S., Jessa, S., Hadjadj, D., Lisi, V., Andrade, A. F., Faury, D., Jawhar, W., Dali, R., Suzuki, H., Pathania, M., A, D., Dubois, F., Woodward, E., Hébert, S., Coutelier, M., Karamchandani, J., Albrecht, S., Brandner, S., De Jay, N., … Jabado, N. (2020). Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell, 183(6), 1617–1633.e22. https://doi.org/10.1016/j.cell.2020.11.012

Chaouch, A., Berlandi, J., Chen, C., Frey, F., Badini, S., Harutyunyan, A. S., Chen, X., Krug, B., Hébert, S., Jeibmann, A., Lu, C., Kleinman, C. L., Hasselblatt, M., Lasko, P., Shirinian, M., & Jabado, N. (2021). Histone H3.3 K27M and K36M mutations de-repress transposable elements through perturbation of antagonistic chromatin marks. Molecular cell, 81(23), 4876–4890.e7. https://doi.org/10.1016/j.molcel.2021.10.008

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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.

References

Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science. 2022 Feb 11;375(6581):681-686. doi: 10.1126/science.abg7216. Epub 2022 Feb 10. PMID: 35143307.

Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Cell-type specialization is encoded by specific chromatin topologies. Nature. 2021 Nov;599(7886):684-691. doi: 10.1038/s41586-021-04081-2. Epub 2021 Nov 17. PMID: 34789882; PMCID: PMC8612935.

Bartosovic M, Kabbe M, Castelo-Branco G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat Biotechnol. 2021 Jul;39(7):825-835. doi: 10.1038/s41587-021-00869-9. Epub 2021 Apr 12. PMID: 33846645; PMCID: PMC7611252.

Marek Bartosovic, Gonçalo Castelo-Branco. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. bioRxiv. 2022.03.08.483459; doi: https://doi.org/10.1101/2022.03.08.483459

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