Abstract
Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Umeyama and Ito develop DMS-seq for nuclear isolation-free genomic footprinting by exploiting the cell-permeable nature of dimethyl sulfate (DMS). DMS-seq detects trans-acting factors bound to cis-regulatory elements, as well as non-canonical chromatin particles in nucleosome-free regions. It also has the unique potential to directly locate nucleosome centers.
| Original language | English |
|---|---|
| Pages (from-to) | 289-300 |
| Number of pages | 12 |
| Journal | Cell Reports |
| Volume | 21 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - Oct 3 2017 |
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All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
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DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. / Umeyama, Taichi; Ito, Takashi.
In: Cell Reports, Vol. 21, No. 1, 03.10.2017, p. 289-300.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers
AU - Umeyama, Taichi
AU - Ito, Takashi
PY - 2017/10/3
Y1 - 2017/10/3
N2 - Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Umeyama and Ito develop DMS-seq for nuclear isolation-free genomic footprinting by exploiting the cell-permeable nature of dimethyl sulfate (DMS). DMS-seq detects trans-acting factors bound to cis-regulatory elements, as well as non-canonical chromatin particles in nucleosome-free regions. It also has the unique potential to directly locate nucleosome centers.
AB - Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Umeyama and Ito develop DMS-seq for nuclear isolation-free genomic footprinting by exploiting the cell-permeable nature of dimethyl sulfate (DMS). DMS-seq detects trans-acting factors bound to cis-regulatory elements, as well as non-canonical chromatin particles in nucleosome-free regions. It also has the unique potential to directly locate nucleosome centers.
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U2 - 10.1016/j.celrep.2017.09.035
DO - 10.1016/j.celrep.2017.09.035
M3 - Article
C2 - 28978481
AN - SCOPUS:85030663641
VL - 21
SP - 289
EP - 300
JO - Cell Reports
JF - Cell Reports
SN - 2211-1247
IS - 1
ER -