Single-cell profiling of transcriptome and histone modifications with EpiDamID

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Single-cell profiling of transcriptome and histone modifications with EpiDamID
 
Rang, Franka J.; de Luca, Kim L.; de Vries, Sandra S.; Valdes-Quezada, Christian; Boele, Ellen; Nguyen, Phong D.; Guerreiro, Isabel; Sato, Yuko; Kimura, Hiroshi; Bakkers, Jeroen; Kind, Jop
(2022) Molecular Cell, volume 82, issue 10, pp. 1956 - 1970.e14
(Article)
Abstract
Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities ... read more
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Keywords: Animals, Chromatin/genetics, Histone Code, Histones/genetics, Mice, Protein Processing, Post-Translational, Transcriptome, Zebrafish/genetics, Journal Article, Research Support, Non-U.S. Gov't
DOI: https://doi.org/10.1016/j.molcel.2022.03.009
ISSN: 1097-2765
Publisher: Cell Press
Note: Funding Information: We would like to thank the members of the Kind laboratory for their helpful comments and suggestions. In particular, we thank Koos Rooijers for providing input and support on the computational work. This work was funded by an ERC Starting grant ( ERC-StG 678423-EpiID ) to J.K. The Oncode Institute is partially funded by the KWF Dutch Cancer Society. I.G. is supported by an EMBO Long-Term Fellowship ALTF1214-2016 , Swiss National Science Fund grant P400PB_186758 and NWO-ENW Veni grant VI.Veni.202.073 . P.D.N. is supported by an EMBO Long-Term Fellowship ALTF1129-2015 , HFSPO Fellowship ( LT001404/2017-L ) and an NWO-ZonMW Veni grant ( 016.186.017-3 ). The laboratory of J.B. is supported by the Netherlands Cardiovascular Research Initiative , an initiative with support of the Dutch Heart Foundation and Hartekind , CVON2019-002 OUTREACH . The laboratory of H.K. is supported by MEXT/JSPS KAKENHI ( JP18H05527 , JP20K06484 , and JP21H04764 ) and Japan Science and Technology Agency ( JPMJCR16G1 and JPMJCR20S6 ). We additionally thank the Hubrecht Sorting Facility, the Hubrecht Imaging Center, and the Utrecht Sequencing Facility (USEQ), subsidized by the University Medical Center Utrecht. Funding Information: We would like to thank the members of the Kind laboratory for their helpful comments and suggestions. In particular, we thank Koos Rooijers for providing input and support on the computational work. This work was funded by an ERC Starting grant (ERC-StG 678423-EpiID) to J.K. The Oncode Institute is partially funded by the KWF Dutch Cancer Society. I.G. is supported by an EMBO Long-Term Fellowship ALTF1214-2016, Swiss National Science Fund grant P400PB_186758 and NWO-ENW Veni grant VI.Veni.202.073. P.D.N. is supported by an EMBO Long-Term Fellowship ALTF1129-2015, HFSPO Fellowship (LT001404/2017-L) and an NWO-ZonMW Veni grant (016.186.017-3). The laboratory of J.B. is supported by the Netherlands Cardiovascular Research Initiative, an initiative with support of the Dutch Heart Foundation and Hartekind, CVON2019-002 OUTREACH. The laboratory of H.K. is supported by MEXT/JSPS KAKENHI (JP18H05527, JP20K06484, and JP21H04764) and Japan Science and Technology Agency (JPMJCR16G1 and JPMJCR20S6). We additionally thank the Hubrecht Sorting Facility, the Hubrecht Imaging Center, and the Utrecht Sequencing Facility (USEQ), subsidized by the University Medical Center Utrecht. Conceptualization: F.J.R. K.L.d.L. S.S.d.V. and J.K. Data curation & Validation: F.J.R. K.L.d.L. and S.S.d.V. Formal analysis & Software: F.J.R. Funding acquisition & Project administration: J.K. Investigation & Methodology: K.L.d.L. and S.S.d.V. designed and performed all experiments unless noted otherwise. C.V.Q. and E.B. designed and generated knock-in mouse ESC lines. P.D.N. performed all zebrafish experiments, with assistance from I.G. and S.S.d.V. Resources: Y.S. and H.K. Supervision: J.B. and J.K. Visualization: F.J.R. and K.L.d.L. Writing – original draft: F.J.R. K.L.d.L. and J.K. Writing – review & editing: all authors. The authors declare no competing interests. One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in science. One or more of the authors of this paper self-identifies as a member of the LGBTQ+ community. Publisher Copyright: © 2022 The Author(s)
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