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lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

View ORCID ProfileKaveh Daneshvar, M. Behfar Ardehali, Isaac A. Klein, Arcadia J. Kratkiewicz, Chan Zhou, Amin Mahpour, Brett M. Cook, Wenyang Li, Joshua V. Pondick, Sean P. Moran, Richard A. Young, Robert E. Kingston, Alan C. Mullen
doi: https://doi.org/10.1101/547513
Kaveh Daneshvar
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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  • ORCID record for Kaveh Daneshvar
M. Behfar Ardehali
3Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA 02114, USA
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Isaac A. Klein
5Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
6Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
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Arcadia J. Kratkiewicz
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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Chan Zhou
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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Amin Mahpour
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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Brett M. Cook
7Optical Biosystems, Inc. Santa Clara, CA 95050, USA
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Wenyang Li
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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Joshua V. Pondick
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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Sean P. Moran
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
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Richard A. Young
5Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
8Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Robert E. Kingston
3Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA 02114, USA
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Alan C. Mullen
1Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
2Harvard Medical School, Boston, MA 02115, USA
9Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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  • For correspondence: acmullen@mgh.harvard.edu
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Abstract

Gene programs that control differentiation are regulated through the interplay between DNA, RNA, and protein. Cooperation among these fundamental cellular components can occur through highly structured interactions connecting domains formed by specific sequences of nucleotides, ribonucleotides, and/or amino acids and also through the assembly of biomolecular condensates. Here, we show that endoderm differentiation is regulated through the interaction of the long noncoding (lnc) RNA DIGIT and the bromodomain and extra-terminal (BET) domain family protein BRD3. BRD3 forms phase-separated condensates that contain DIGIT, occupies enhancers of endoderm transcription factors, and is required for endoderm differentiation. Purified BRD3 binds to acetylated histone H3 lysine 18 (H3K18ac) in vitro and occupies regions of the genome enriched in H3K18ac during endoderm differentiation, including the key transcription factors that regulate endoderm differentiation. DIGIT is also enriched in regions of H3K18ac, and depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings support a model where cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest a broader role for protein-lncRNA phase-separated condensates as regulators of transcription in development.

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Posted February 12, 2019.
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lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation
Kaveh Daneshvar, M. Behfar Ardehali, Isaac A. Klein, Arcadia J. Kratkiewicz, Chan Zhou, Amin Mahpour, Brett M. Cook, Wenyang Li, Joshua V. Pondick, Sean P. Moran, Richard A. Young, Robert E. Kingston, Alan C. Mullen
bioRxiv 547513; doi: https://doi.org/10.1101/547513
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lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation
Kaveh Daneshvar, M. Behfar Ardehali, Isaac A. Klein, Arcadia J. Kratkiewicz, Chan Zhou, Amin Mahpour, Brett M. Cook, Wenyang Li, Joshua V. Pondick, Sean P. Moran, Richard A. Young, Robert E. Kingston, Alan C. Mullen
bioRxiv 547513; doi: https://doi.org/10.1101/547513

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