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(*denotes co-first authorship, † denotes co-corresponding authors)

Active RNA synthesis patterns nuclear condensates (preprint)
S.F. Banani*, A. Goychuk*, P. Natarajan*, M.M. Zheng*, G. Dall’Agnese,  J.E. Henninger†, M. Kardar†,  R.A. Young†, A.K. Chakraborty†. bioRxiv, doi: 10.1101/2024.10.12.614958 (2024)

An RNA-centric view of transcription and genome organization.
J.E. Henninger & R.A. Young. Molecular Cell, doi: 10.1016/j.molcel.2024.08.021 (2024)

Transcription factors interact with RNA to regulate genes.
O. Oksuz*, J. E. Henninger*, R. Warneford-Thomson, M. M. Zheng, H. Erb, A. Vancura, K. J. Overholt, S. W. Hawken, S. F. Banani, R. Lauman, L. N. Reich, A. L. Robertson, N. M. Hannett, T. I. Lee, L. I. Zon, R. Bonasio, R. A. Young,  Molecular Cell, doi: 10.1016/j.molcel.2023.06.012 (2023).

Genetic variation associated with condensate dysregulation in disease.
S. F. Banani*, L. K. Afeyan*, S. W. Hawken*, J. E. Henninger, A. Dall’Agnese, V. E. Clark, J. M. Platt, O. Oksuz, N. M. Hannett, I. Sagi, T. I. Lee, R. A. Young, Developmental Cell, doi: 10.1016/j.devcel.2022.06.010 (2022).

RNA in formation and regulation of transcriptional condensates.
P. A. Sharp, A. K. Chakraborty, J. E. Henninger, R. A. Young, RNA, doi: 10.1261/rna.078997.121 (2022).

Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis.
S. Avagyan*, J. E. Henninger*, W. P. Mannherz, M. Mistry, J. Yoon, S. Yang, M. C. Weber, J. L. Moore, L. I. Zon, Science, doi:10.1126/science.aba9304 (2021).

RNA-mediated feedback control of transcriptional condensates.
J. E. Henninger*, O. Oksuz*, K. Shrinivas*, I. Sagi, G. LeRoy, M. M. Zheng, J. O. Andrews, A. V. Zamudio, C. Lazaris, N. M. Hannett, T. I. Lee, P. A. Sharp, I. I. Cissé, A. K. Chakraborty, R. A. Young, Cell 10.1016/j.cell.2020.11.030 (2021).

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.
Y. E. Guo*, J. C. Manteiga*, J. E. Henninger, B. R. Sabari, A. Dall’Agnese, N. M. Hannett, J.-H. Spille, L. K. Afeyan, A. V. Zamudio, K. Shrinivas, B. J. Abraham, A. Boija, T.-M. Decker, J. K. Rimel, C. B. Fant, T. I. Lee, I. I. Cisse, P. A. Sharp, D. J. Taatjes, R. A. Young, Nature, 10.1038/s41586-019-1464-0 (2019).

Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development.
J. Henninger, B. Santoso, S. Hans, E. Durand, J. Moore, C. Mosimann, M. Brand, D. Traver, L. Zon, Nature Cell Biology, 10.1038/ncb3444 (2017).