TALEN outperforms Cas9 in editing heterochromatin target sites

Surbhi Jain, Saurabh Shukla, Che Yang, Meng Zhang, Zia Fatma, Manasi Lingamaneni, Shireen Abesteh, Stephan Thomas Lane, Xiong Xiong, Yuchuan Wang, Charles M. Schroeder, Paul R. Selvin, Huimin Zhao

Research output: Contribution to journalArticlepeer-review


Genome editing critically relies on selective recognition of target sites. However, despite recent progress, the underlying search mechanism of genome-editing proteins is not fully understood in the context of cellular chromatin environments. Here, we use single-molecule imaging in live cells to directly study the behavior of CRISPR/Cas9 and TALEN. Our single-molecule imaging of genome-editing proteins reveals that Cas9 is less efficient in heterochromatin than TALEN because Cas9 becomes encumbered by local searches on non-specific sites in these regions. We find up to a fivefold increase in editing efficiency for TALEN compared to Cas9 in heterochromatin regions. Overall, our results show that Cas9 and TALEN use a combination of 3-D and local searches to identify target sites, and the nanoscopic granularity of local search determines the editing outcomes of the genome-editing proteins. Taken together, our results suggest that TALEN is a more efficient gene-editing tool than Cas9 for applications in heterochromatin.
Original languageEnglish (US)
Article number606
JournalNature communications
Issue number1
StatePublished - Dec 2021

ASJC Scopus subject areas

  • General Physics and Astronomy
  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology


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