Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells

  • Cell Chem Biol. 2022 Aug 18;29(8):1273-1287.e8. doi: 10.1016/j.chembiol.2022.06.007.
Stuti Mehta  1 ,  Altantsetseg Buyanbat  1 ,  Yan Kai  1 ,  Ozge Karayel  2 ,  Seth Raphael Goldman  3 ,  Davide Seruggia  4 ,  Kevin Zhang  1 ,  Yuko Fujiwara  1 ,  Katherine A Donovan  5 ,  Qian Zhu  1 ,  Huan Yang  1 ,  Behnam Nabet  6 ,  Nathanael S Gray  7 ,  Matthias Mann  2 ,  Eric S Fischer  5 ,  Karen Adelman  3 ,  Stuart H Orkin  8
Affiliations
  • 1. Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA.
  • 2. Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Planegg, Germany.
  • 3. Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
  • 4. St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
  • 5. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
  • 6. Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
  • 7. Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
  • 8. Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Howard Hughes Medical Institute and Harvard Medical School, Boston, MA 02115, USA. Electronic address: [email protected].
PMID: 35839780 DOI: 10.1016/j.chembiol.2022.06.007
Abstract

Reactivation of fetal Hemoglobin expression by the downregulation of BCL11A is a promising treatment for β-hemoglobinopathies. A detailed understanding of BCL11A-mediated repression of γ-globin gene (HBG1/2) transcription is lacking, as studies to date used perturbations by shRNA or CRISPR-Cas9 gene editing. We leveraged the dTAG PROTAC degradation platform to acutely deplete BCL11A protein in erythroid cells and examined consequences by nascent transcriptomics, proteomics, chromatin accessibility, and histone profiling. Among 31 genes repressed by BCL11A, HBG1/2 and HBZ show the most abundant and progressive changes in transcription and chromatin accessibility upon BCL11A loss. Transcriptional changes at HBG1/2 were detected in <2 h. Robust HBG1/2 reactivation upon acute BCL11A depletion occurred without the loss of promoter 5-methylcytosine (5mC). Using targeted protein degradation, we establish a hierarchy of gene reactivation at BCL11A targets, in which nascent transcription is followed by increased chromatin accessibility, and both are uncoupled from promoter DNA methylation at the HBG1/2 loci.

Keywords
BCL11A; DNA methylation; PROTAC; chromatin accessibility; dTAG; erythropoiesis; globin regulation; nascent transcription; proteomics; sickle-cell disease, SCD; β-thalassemia.
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