DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide.

Autor: Altemose N; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA., Maslan A; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Smith OK; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA., Sundararajan K; Department of Biochemistry, Stanford University, Stanford, CA, USA., Brown RR; Department of Biochemistry, Stanford University, Stanford, CA, USA., Mishra R; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA., Detweiler AM; Chan Zuckerberg Biohub, San Francisco, CA, USA., Neff N; Chan Zuckerberg Biohub, San Francisco, CA, USA., Miga KH; Department of Molecular & Cell Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Straight AF; Department of Biochemistry, Stanford University, Stanford, CA, USA. astraigh@stanford.edu., Streets A; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. astreets@berkeley.edu.; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA. astreets@berkeley.edu.; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. astreets@berkeley.edu.; Chan Zuckerberg Biohub, San Francisco, CA, USA. astreets@berkeley.edu.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2022 Jun; Vol. 19 (6), pp. 711-723. Date of Electronic Publication: 2022 Apr 08.
DOI: 10.1038/s41592-022-01475-6
Abstrakt: Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.
(© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
Externí odkaz: