Journal article

TINC-A Method to Dissect Regulatory Complexes at Single-Locus Resolution-Reveals an Extensive Protein Complex at the Nanog Promoter

Anja S Knaupp, Monika Mohenska, Michael R Larcombe, Ethan Ford, Sue Mei Lim, Kayla Wong, Joseph Chen, Jaber Firas, Cheng Huang, Xiaodong Liu, Nguyen Trung, Yu BY Sun, Melissa L Holmes, Pratibha Tripathi, Jahnvi Pflueger, Fernando J Rossello, Jan Schroder, Kathryn C Davidson, Christian M Nefzger, Partha P Das Show all

Stem Cell Reports | CELL PRESS | Published : 2020

Abstract

Cellular identity is ultimately dictated by the interaction of transcription factors with regulatory elements (REs) to control gene expression. Advances in epigenome profiling techniques have significantly increased our understanding of cell-specific utilization of REs. However, it remains difficult to dissect the majority of factors that interact with these REs due to the lack of appropriate techniques. Therefore, we developed TINC: TALE-mediated isolation of nuclear chromatin. Using this new method, we interrogated the protein complex formed at the Nanog promoter in embryonic stem cells (ESCs) and identified many known and previously unknown interactors, including RCOR2. Further interrogat..

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University of Melbourne Researchers

Grants

Awarded by National Health and Medical Research Council (NHMRC)


Awarded by NHMRC CDF


Awarded by ARC Future Fellowship


Awarded by ARC Center of Excellence program in Plant Energy Biology


Awarded by NHMRC Investigator grant


Awarded by NHMRC ECF


Funding Acknowledgements

This work was supported by a National Health and Medical Research Council (NHMRC) grant (APP1069830) to R.L. and J.M.P. J.M.P. and R.L. were supported by the Australian Research Council (ARC) Stem Cells Australia Special Initiative, an NHMRC CDF (APP1036587 to J.M.P.), an ARC Future Fellowship (FT120100862 to R.L. and FT180100674 to J.M.P.), and a Silvia and Charles Viertel Senior Medical Research Fellowship. R.L. was also supported by the ARC Center of Excellence program in Plant Energy Biology (CE140100008), HHMI International Research Scholarship, and NHMRC Investigator grant GNT1178460. A.S.K. was supported by an NHMRC ECF (APP1092280). We thank Flowcore, the MHTP Medical Genomics Facility, Micromon, the Monash Bioinformatics and Histology Platforms. This study used BPA-enabled/NCRIS-enabled infrastructure located at the Monash Proteomics and Metabolomics Facility led by R.B.S. The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. The PiggyBac vector and the OKMS MEFs were kindly provided by Andras Nagy.