TY - JOUR
T1 - Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly
AU - Chereji, Rǎzvan V.
AU - Bharatula, Vasudha
AU - Elfving, Nils
AU - Blomberg, Jeanette
AU - Larsson, Miriam
AU - Morozov, Alexandre V.
AU - Broach, James R.
AU - Björklund, Stefan
N1 - Funding Information:
R.V.C. thanks Ho Sung Rhee and Bongsoo Park for helpful discussions regarding the ChIP-exo experiments. We are grateful to the staff at the KBC Proteomics Facility, Umeå University for assistance with the LC–MS analysis. Bioinformatic support by BILS (Bioinformatics Infrastructure for Life Sciences) is gratefully acknowledged. We also thank Dr Bruce Goode for providing us with the HA-tagged Arp35 strain. This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih. gov). The Department of Health specifically disclaims responsibility for any analyses, interpretations or conclusions.
Funding Information:
Swedish Cancer Society (to to S.B.); Swedish Research Council; Knut and Alice Wallenberg Foundation; National Institutes of Health [GM076562]; Pennsylvania Department of Health using Tobacco CURE funds (to J.R.B., in part); Intramural Research Program of the NIH (to R.V.C.). Funding for open access charge: The Swedish Cancer Society and the Swedish Research Council. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2017.
PY - 2017/9/1
Y1 - 2017/9/1
N2 - Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3″-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization.
AB - Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3″-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization.
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U2 - 10.1093/nar/gkx491
DO - 10.1093/nar/gkx491
M3 - Article
C2 - 28575439
AN - SCOPUS:85032877707
VL - 45
SP - 8806
EP - 8821
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 15
ER -