University of Massachusetts Medical School Faculty Publications
UMMS Affiliation
Department of Molecular, Cell, and Cancer Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
3-21-2018
Document Type
Article Preprint
Disciplines
Cell Biology | Cells | Developmental Biology | Embryonic Structures | Genomics
Abstract
Major cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small cell populations within developing embryos. To understand how TFs regulate cell fate it is important to identify their genomic binding sites in these populations. However, current methods cannot profile TFs genome-wide at or near the single cell level. Here we adapt the CUT&RUN method to profile chromatin proteins in low cell numbers, mapping TF-DNA interactions in single cells and individual pre-implantation embryos for the first time. Using this method, we demonstrate that the pluripotency TF NANOG is significantly more dependent on the SWI/SNF family ATPase BRG1 for association with its genomic targets in vivo than in cultured cells, a finding that could not have been made using traditional approaches. Ultra-low input CUT&RUN (uliCUT&RUN) enables interrogation of TF binding from low cell numbers, with broad applicability to rare cell populations of importance in development or disease.
Keywords
pluripotency, stem cells, embryos, genomics
Rights and Permissions
The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
DOI of Published Version
10.1101/286351
Source
bioRxiv 286351; doi: https://doi.org/10.1101/286351. Link to preprint on bioRxiv service.
Journal/Book/Conference Title
bioRxiv
Repository Citation
Hainer, Sarah J.; Boskovic, Ana; Rando, Oliver J.; and Fazzio, Thomas G., "Profiling of pluripotency factors in individual stem cells and early embryos" (2018). University of Massachusetts Medical School Faculty Publications. 1506.
https://escholarship.umassmed.edu/faculty_pubs/1506
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Included in
Cell Biology Commons, Cells Commons, Developmental Biology Commons, Embryonic Structures Commons, Genomics Commons