TY - JOUR
T1 - DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers
AU - Umeyama, Taichi
AU - Ito, Takashi
N1 - Funding Information:
We appreciate the technical assistance from The Research Support Center, Research Center for Human Disease Modeling, Kyushu University Graduate School of Medical Sciences. We thank Satoshi Okada for critical reading of the manuscript. This work was partly supported by JSPS KAKENHI ( 24651226 , 16K14642 , 17H06305 ) and AMED CREST ( 16gm0510008h0305 ).
Publisher Copyright:
© 2017 The Author(s)
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 -