Long-range single-molecule mapping of chromatin accessibility in eukaryotes
| Autor: | Anshul Kundaje, Georgi K. Marinov, Jan M. Skotheim, Nicholas A. Sinnott-Armstrong, William J. Greenleaf, Zohar Shipony, Matthew P. Swaffer |
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| Rok vydání: | 2019 |
| Předmět: |
Chromatin Immunoprecipitation
Adenosine Computational biology DNA Fragmentation Saccharomyces cerevisiae Biology Biochemistry Methylation Article Cell Line 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Nucleosome Humans Promoter Regions Genetic Molecular Biology Transcription factor 030304 developmental biology 0303 health sciences High-Throughput Nucleotide Sequencing Cell Biology Methyltransferases DNA Methylation Chromatin Nucleosomes CpG site chemistry DNA methylation DNA fragmentation CpG Islands Nanopore sequencing Chromatin immunoprecipitation Functional genomics 030217 neurology & neurosurgery DNA Biotechnology Protein Binding |
| Zdroj: | Nat Methods |
| ISSN: | 1548-7105 |
| Popis: | Active regulatory elements in eukaryotes are typically characterized by an open, nucleosome-depleted chromatin structure; mapping areas of open chromatin has accordingly emerged as a widely used tool in the arsenal of modern functional genomics. However, existing approaches for profiling chromatin accessibility are limited by their reliance on DNA fragmentation and short read sequencing, which leaves them unable to provide information about the state of chromatin on larger scales or reveal coordination between the chromatin state of individual distal regulatory elements. To address these limitations, we have developed a method for profiling accessibility of individual chromatin fibers at multi-kilobase length scale (SMAC-seq, or Single-Molecule long-read Accessible Chromatin mapping sequencing assay), enabling the simultaneous, high-resolution, single-molecule assessment of the chromatin state of distal genomic elements. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases (CpG and GpC 5-methylcytosine (5mC) and N6-methyladenosine (m6A) enzymes) and the ability of long-read single-molecule nanopore sequencing to directly read out the methylation state of individual DNA bases. Applying SMAC-seq to the budding yeast Saccharomyces cerevisiae, we demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule protection footprints of nucleosomes and transcription factors, and quantify the correlation between the chromatin states of distal genomic elements. |
| Databáze: | OpenAIRE |
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