BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

Matthew C. Canver, Elenoe C. Smith, Falak Sher, Luca Pinello, Neville E. Sanjana, Ophir Shalem, Diane D. Chen, Patrick G. Schupp, Divya S. Vinjamur, Sara P. Garcia, Sidinh Luc, Ryo Kurita, Yukio Nakamura, Yuko Fujiwara, Takahiro Maeda, Guo Cheng Yuan, Feng Zhang, Stuart H. Orkin, Daniel E. Bauer

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295 Citations (Scopus)

Abstract

Enhancers, critical determinants of cellular identity, are commonly recognized by correlative chromatin marks and gain-of-function potential, although only loss-of-function studies can demonstrate their requirement in the native genomic context. Previously, we identified an erythroid enhancer of human BCL11A, subject to common genetic variation associated with the fetal haemoglobin level, the mouse orthologue of which is necessary for erythroid BCL11A expression. Here we develop pooled clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 guide RNA libraries to perform in situ saturating mutagenesis of the human and mouse enhancers. This approach reveals critical minimal features and discrete vulnerabilities of these enhancers. Despite conserved function of the composite enhancers, their architecture diverges. The crucial human sequences appear to be primate-specific. Through editing of primary human progenitors and mouse transgenesis, we validate the BCL11A erythroid enhancer as a target for fetal haemoglobin reinduction. The detailed enhancer map will inform therapeutic genome editing, and the screening approach described here is generally applicable to functional interrogation of non-coding genomic elements.

Original languageEnglish
Pages (from-to)192-197
Number of pages6
JournalNature
Volume527
Issue number7577
DOIs
Publication statusPublished - Nov 12 2015

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Mutagenesis
Dissection
Fetal Hemoglobin
Guide RNA
Gene Transfer Techniques
Primates
Chromatin
Therapeutics

All Science Journal Classification (ASJC) codes

  • General

Cite this

Canver, M. C., Smith, E. C., Sher, F., Pinello, L., Sanjana, N. E., Shalem, O., ... Bauer, D. E. (2015). BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature, 527(7577), 192-197. https://doi.org/10.1038/nature15521

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. / Canver, Matthew C.; Smith, Elenoe C.; Sher, Falak; Pinello, Luca; Sanjana, Neville E.; Shalem, Ophir; Chen, Diane D.; Schupp, Patrick G.; Vinjamur, Divya S.; Garcia, Sara P.; Luc, Sidinh; Kurita, Ryo; Nakamura, Yukio; Fujiwara, Yuko; Maeda, Takahiro; Yuan, Guo Cheng; Zhang, Feng; Orkin, Stuart H.; Bauer, Daniel E.

In: Nature, Vol. 527, No. 7577, 12.11.2015, p. 192-197.

Research output: Contribution to journalArticle

Canver, MC, Smith, EC, Sher, F, Pinello, L, Sanjana, NE, Shalem, O, Chen, DD, Schupp, PG, Vinjamur, DS, Garcia, SP, Luc, S, Kurita, R, Nakamura, Y, Fujiwara, Y, Maeda, T, Yuan, GC, Zhang, F, Orkin, SH & Bauer, DE 2015, 'BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis', Nature, vol. 527, no. 7577, pp. 192-197. https://doi.org/10.1038/nature15521
Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Nov 12;527(7577):192-197. https://doi.org/10.1038/nature15521
Canver, Matthew C. ; Smith, Elenoe C. ; Sher, Falak ; Pinello, Luca ; Sanjana, Neville E. ; Shalem, Ophir ; Chen, Diane D. ; Schupp, Patrick G. ; Vinjamur, Divya S. ; Garcia, Sara P. ; Luc, Sidinh ; Kurita, Ryo ; Nakamura, Yukio ; Fujiwara, Yuko ; Maeda, Takahiro ; Yuan, Guo Cheng ; Zhang, Feng ; Orkin, Stuart H. ; Bauer, Daniel E. / BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. In: Nature. 2015 ; Vol. 527, No. 7577. pp. 192-197.
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