Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis

Authors: Catta-Preta, Rinaldo ^{1, 10, 11, 12, 13}, Lindtner, Susan ^{2, 10}, Ypsilanti, Athena ², Seban, Nicolas ¹, Price, James D. ², Abnousi, Armen ^{3, 14}, Su-Feher, Linda ¹, Wang, Yurong ¹, Cichewicz, Karol ¹, Boerma, Sally A. ¹, Juric, Ivan ³, Jones, Ian R. ^{8, 9}, Akiyama, Jennifer A. ⁴, Hu, Ming ³, Shen, Yin ^{8, 9}, Visel, Axel ^{4, 5, 7}, Pennacchio, Len A. ^{4, 5, 6}, Dickel, Diane E. ^{4, 15}, Rubenstein, John L.R. ^{2, ∗}, Nord, Alex S. ^{1, 16, ∗}

Source: In Developmental Cell 20 January 2025 60(2):288-304

Transcriptional network orchestrating regional patterning of cortical progenitors

Authors: Ypsilanti, Athena R., Pattabiraman, Kartik, Catta-Preta, Rinaldo, Golonzhka, Olga, Lindtner, Susan, Tang, Ke, Jones, Ian R., Abnousi, Armen, Juric, Ivan, Hu, Ming, Shen, Yin, Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Hawrylycz, Michael, Thompson, Carol L., Zeng, Hongkui, Barozzi, Iros, Nord, Alex S., Rubenstein, John L.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Dec . 118(51), 1-12.

Access URL: https://www.jstor.org/stable/27117501

Genome-wide fetalization of enhancer architecture in heart disease

Authors: Spurrell, Cailyn H., Barozzi, Iros, Kosicki, Michael, Mannion, Brandon J., Blow, Matthew J., Fukuda-Yuzawa, Yoko, Slaven, Neil, Afzal, Sarah Y., Akiyama, Jennifer A., Afzal, Veena, Tran, Stella, Plajzer-Frick, Ingrid, Novak, Catherine S., Kato, Momoe, Lee, Elizabeth A., Garvin, Tyler H., Pham, Quan T., Kronshage, Anne N., Lisgo, Steven, Bristow, James, Cappola, Thomas P., Morley, Michael P., Margulies, Kenneth B., Pennacchio, Len A., Dickel, Diane E., Visel, Axel

Source: In Cell Reports 20 September 2022 40(12)

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers.

Authors: Kosicki, Michael, Baltoumas, Fotis A, Kelman, Guy, Boverhof, Joshua, Ong, Yeongshnn, Cook, Laura E, Dickel, Diane E, Pavlopoulos, Georgios A, Pennacchio, Len A, Visel, Axel

Source: Nucleic Acids Research; 1/6/2025, Vol. 53 Issue D1, pD324-D330, 7p

Differential Etv2 threshold requirement for endothelial and erythropoietic development

Authors: Sinha, Tanvi, Lammerts van Bueren, Kelly, Dickel, Diane E., Zlatanova, Ivana, Thomas, Reuben, Lizama, Carlos O., Xu, Shan-Mei, Zovein, Ann C., Ikegami, Kohta, Moskowitz, Ivan P., Pollard, Katherine S., Pennacchio, Len A., Black, Brian L.

Source: In Cell Reports 31 May 2022 39(9)

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

Authors: Yu, Miao, Zemke, Nathan R., Chen, Ziyin, Juric, Ivan, Hu, Rong, Raviram, Ramya, Abnousi, Armen, Fang, Rongxin, Zhang, Yanxiao, Gorkin, David U., Li, Yang E., Zhao, Yuan, Lee, Lindsay, Mishra, Shreya, Schmitt, Anthony D., Qiu, Yunjiang, Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Hu, Ming, Ren, Bing

Source: Nature Structural and Molecular Biology; March 2025, Vol. 32 Issue: 3 p479-490, 12p

Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development.

Authors: Zhidong Liu, Ypsilanti, Athéna R., Markenscoff-Papadimitriou, Eirene, Dickel, Diane E., Sanders, Stephan J., Shan Dong, Pennacchio, Len A., Visel, Axel, Rubenstein, John L.

Source: Proceedings of the National Academy of Sciences of the United States of America; 10/1/2024, Vol. 121 Issue 40, p1-11, 51p

Subject Terms: TRANSCRIPTION factors, FETAL development, EPIGENOMICS, GENES, MICE

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder

Authors: Long, Hannah K., Osterwalder, Marco, Welsh, Ian C., Hansen, Karissa, Davies, James O.J., Liu, Yiran E., Koska, Mervenaz, Adams, Alexander T., Aho, Robert, Arora, Neha, Ikeda, Kazuya, Williams, Ruth M., Sauka-Spengler, Tatjana, Porteus, Matthew H., Mohun, Tim, Dickel, Diane E., Swigut, Tomek, Hughes, Jim R., Higgs, Douglas R., Visel, Axel, Selleri, Licia, Wysocka, Joanna

Source: In Cell Stem Cell 5 November 2020 27(5):765-783

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

Authors: Kvon, Evgeny Z., Zhu, Yiwen, Kelman, Guy, Novak, Catherine S., Plajzer-Frick, Ingrid, Kato, Momoe, Garvin, Tyler H., Pham, Quan, Harrington, Anne N., Hunter, Riana D., Godoy, Janeth, Meky, Eman M., Akiyama, Jennifer A., Afzal, Veena, Tran, Stella, Escande, Fabienne, Gilbert-Dussardier, Brigitte, Jean-Marçais, Nolwenn, Hudaiberdiev, Sanjarbek, Ovcharenko, Ivan, Dobbs, Matthew B., Gurnett, Christina A., Manouvrier-Hanu, Sylvie, Petit, Florence, Visel, Axel, Dickel, Diane E., Pennacchio, Len A.

Source: In Cell 19 March 2020 180(6):1262-1271

Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons

Authors: Lindtner, Susan, Catta-Preta, Rinaldo, Tian, Hua, Su-Feher, Linda, Price, James D., Dickel, Diane E., Greiner, Vanille, Silberberg, Shanni N., McKinsey, Gabriel L., McManus, Michael T., Pennacchio, Len A., Visel, Axel, Nord, Alex S., Rubenstein, John L.R.

Source: In Cell Reports 20 August 2019 28(8):2048-2063

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

Authors: Hashimoto, Hisayuki, Wang, Zhaoning, Garry, Glynnis A., Malladi, Venkat S., Botten, Giovanni A., Ye, Wenduo, Zhou, Huanyu, Osterwalder, Marco, Dickel, Diane E., Visel, Axel, Liu, Ning, Bassel-Duby, Rhonda, Olson, Eric N.

Source: In Cell Stem Cell 3 July 2019 25(1):69-86

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Authors: Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., Dickel, Diane E.

Source: In Cell Reports 14 May 2019 27(7):2241-2247

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons

Authors: McClymont, Sarah A., Hook, Paul W., Soto, Alexandra I., Reed, Xylena, Law, William D., Kerans, Samuel J., Waite, Eric L., Briceno, Nicole J., Thole, Joey F., Heckman, Michael G., Diehl, Nancy N., Wszolek, Zbigniew K., Moore, Cedric D., Zhu, Heng, Akiyama, Jennifer A., Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Ross, Owen A., Beer, Michael A., McCallion, Andrew S.

Source: In The American Journal of Human Genetics 6 December 2018 103(6):874-892

Ultraconserved Enhancers Are Required for Normal Development

Authors: Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth A., Harrington, Anne N., Pham, Quan T., Garvin, Tyler H., Kato, Momoe, Osterwalder, Marco, Akiyama, Jennifer A., Afzal, Veena, Rubenstein, John L.R., Pennacchio, Len A., Visel, Axel

Source: In Cell 25 January 2018 172(3):491-499

Genomic Patterns of De Novo Mutation in Simplex Autism

Authors: Turner, Tychele N., Coe, Bradley P., Dickel, Diane E., Hoekzema, Kendra, Nelson, Bradley J., Zody, Michael C., Kronenberg, Zev N., Hormozdiari, Fereydoun, Raja, Archana, Pennacchio, Len A., Darnell, Robert B., Eichler, Evan E.

Source: In Cell 19 October 2017 171(3):710-722

The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome

Authors: Spurrell, Cailyn H., Dickel, Diane E., Visel, Axel

Source: In Cell 17 November 2016 167(5):1163-1166

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

Authors: Kvon, Evgeny Z., Kamneva, Olga K., Melo, Uirá S., Barozzi, Iros, Osterwalder, Marco, Mannion, Brandon J., Tissières, Virginie, Pickle, Catherine S., Plajzer-Frick, Ingrid, Lee, Elizabeth A., Kato, Momoe, Garvin, Tyler H., Akiyama, Jennifer A., Afzal, Veena, Lopez-Rios, Javier, Rubin, Edward M., Dickel, Diane E., Pennacchio, Len A., Visel, Axel

Source: In Cell 20 October 2016 167(3):633-642

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

Authors: He, Yupeng, Gorkin, David U., Dickel, Diane E., Nery, Joseph R., Castanon, Rosa G., Lee, Ah Young, Shen, Yin, Visel, Axel, Pennacchio, Len A., Ren, Bing, Ecker, Joseph R.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Feb . 114(9), E1633-E1640.

Access URL: https://www.jstor.org/stable/26479515

Fishing for Function in the Human Gene Pool

Authors: Barozzi, Iros, Visel, Axel, Dickel, Diane E.

Source: In Trends in Genetics July 2016 32(7):392-394

Single-cell, whole-embryo phenotyping of mammalian developmental disorders.

Authors: Huang, Xingfan, Henck, Jana, Qiu, Chengxiang, Sreenivasan, Varun K. A., Balachandran, Saranya, Amarie, Oana V., Hrabě de Angelis, Martin, Behncke, Rose Yinghan, Chan, Wing-Lee, Despang, Alexandra, Dickel, Diane E., Duran, Madeleine, Feuchtinger, Annette, Fuchs, Helmut, Gailus-Durner, Valerie, Haag, Natja, Hägerling, Rene, Hansmeier, Nils, Hennig, Friederike, Marshall, Cooper

Source: Nature; Nov2023, Vol. 623 Issue 7988, p772-781, 10p