TY - JOUR
T1 - Elucidating the temporal dynamics of chromatin-associated protein release upon DNA digestion by quantitative proteomic approach
AU - Dutta, Bamaprasad
AU - Adav, Sunil S.
AU - Koh, Cheng Gee
AU - Lim, Sai Kiang
AU - Meshorer, Eran
AU - Sze, Siu Kwan
N1 - Funding Information:
This work is supported by grants from Nanyang Technological University ( RG 157/06 , RG 61/06 and RG 51/10 ).
PY - 2012/9/18
Y1 - 2012/9/18
N2 - Chromatin is a highly dynamic well organized nucleoprotein complex of DNA and proteins that controls DNA-dependent processes such as transcription, replication, repair and many others. Chromatin structure is regulated by various chromatin associated proteins, post-translational modifications of histones and DNA methylation, but a complete picture of structural changes in chromatin architecture is unclear due to the lack of comprehensive data of chromatin-associated proteins and their bindings to different chromatin regions. This study temporally released chromatin-associated proteins by DNase I and MNase treatment and profiled them by exponentially modified protein abundance index (emPAI) based label-free quantitative proteomics. We identified 694 high confidence proteins, with 160 known chromatin-associated proteins. Identified proteins were functionally classified into histones, non-histones involved in architectural maintenance, proteins involved in DNA replication and repair, transcription machinery, transcription regulation, other chromatin proteins, cell cycle proteins and several novel proteins. Numerous proteins presumed to be chromatin associated were identified and their chromatin interactions were explored. The comprehensive differential chromatin bound proteome might expand our knowledge of the proteins that were associated with different chromatin regions, which could be very useful in elucidating chromatin biology.
AB - Chromatin is a highly dynamic well organized nucleoprotein complex of DNA and proteins that controls DNA-dependent processes such as transcription, replication, repair and many others. Chromatin structure is regulated by various chromatin associated proteins, post-translational modifications of histones and DNA methylation, but a complete picture of structural changes in chromatin architecture is unclear due to the lack of comprehensive data of chromatin-associated proteins and their bindings to different chromatin regions. This study temporally released chromatin-associated proteins by DNase I and MNase treatment and profiled them by exponentially modified protein abundance index (emPAI) based label-free quantitative proteomics. We identified 694 high confidence proteins, with 160 known chromatin-associated proteins. Identified proteins were functionally classified into histones, non-histones involved in architectural maintenance, proteins involved in DNA replication and repair, transcription machinery, transcription regulation, other chromatin proteins, cell cycle proteins and several novel proteins. Numerous proteins presumed to be chromatin associated were identified and their chromatin interactions were explored. The comprehensive differential chromatin bound proteome might expand our knowledge of the proteins that were associated with different chromatin regions, which could be very useful in elucidating chromatin biology.
KW - Chromatin
KW - Chromatin associated proteins
KW - DNase I
KW - EmPAI
KW - LC-MS/MS
KW - MNase
UR - http://www.scopus.com/inward/record.url?scp=84865571448&partnerID=8YFLogxK
U2 - 10.1016/j.jprot.2012.06.030
DO - 10.1016/j.jprot.2012.06.030
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C2 - 22796351
AN - SCOPUS:84865571448
SN - 1874-3919
VL - 75
SP - 5493
EP - 5506
JO - Journal of Proteomics
JF - Journal of Proteomics
IS - 17
ER -