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Supplemental Methods
Author(s) -
Daniël P. Melters,
Keith R. Bradnam,
Hugh A. Young,
Natalie Telis,
Michael R. May,
J. Graham Ruby,
Robert Sebra,
Paul Peluso,
John Eid,
David Rank,
José Fernando Garcia,
Joseph L. DeRisi,
Timothy Smith,
Christian Tobias,
Jeffrey Ross-Ibarra,
Ian F. Korf,
Simon W.-L. Chan
Publication year - 2007
Language(s) - English
DOI - 10.7554/elife.40613.018
cDNA encoding human TRIM24 from synthetic sources and used as templates to amplify the phd-bromodomain region using polymerase chain reaction (PCR) in the presence of Platinum® Pfx DNA polymerase (Invitrogen, UK). PCR products were purified (QIAquick PCR Purification Kit, Qiagen Ltd. UK) and further subcloned into a modified pET15 vector using NdeI/XhoI sites for expression as recombinant proteins with a His6 tag fused with small ubiquitin like modifier (SUMO)-1 fusion tag at the N terminus. Colonies from transformed plasmids DNA in competent E. coli BL21(DE3)-R3-pRARE2 cells (phageresistant derivative of BL21(DE3) strain), with a pRARE plasmid encoding rare codon tRNAs were grown overnight at 37 0C in 10 mL of Terrific broth medium (Sigma) with 100 μg/mL ampicillin and 34 μg/mL chloramphenicol. Cells were grown at 37 0C in TB from overnight cultures until A600 reached between 0.8-1.1, then the media was cooled and 0.2 mM isopropyl-β-D-thiogalactopyranoside (IPTG) was added to induce the protein expression at 18 0C for 16 hours plus an additional 0.1 mM ZnCl2. The bacteria were harvested by centrifugation (JLA 8,100 rotor Beckman Coulter Avanti J-20 XP centrifuge) and were frozen at -20 0C. Cell expressing His6-SUMO tagged TRIM24 protein was re-suspended in lysis buffer (20 mM Hepes pH 7.5, 500 mM NaCl, 20 mM Imidazole, 5% glycerol and 1 mM TCEP (Tris(2-carboxyethyl)phosphine hydrochloride) in the presence of protease inhibitors cocktail (1 μl/ml) and lysed using an EmulsiFlex-C5 high pressure homogenizer (Avestin-Mannheim, Germany) at 4 0C. The lysate was cleared by centrifugation (14,000 x g for 1 h at 4 0C). After centrifugation, the supernatant was loaded onto the nickel column and eluted in an imidazole linear gradient. The eluted proteins were collected and treated overnight with SENP1 (SUMO endoprotease-1) protease at 4oC to remove the N terminal tags. Digested protein was loaded onto a nickel column again to remove the cleaved 6His-SUMO tag and the hexahistidine expression tag SENP1 used. The flow through containing the untagged protein was collected and further dialysed and purified by an ion exchange chromatography (RESOURCE Q 6 ml GE Healthcare Life Sciences). Protein was eluted in a linear gradient of NaCl. Finally, a polishing step was performed through a size exclusion chromatography (HiLoad 16/600 Superdex 75 GE Healthcare Life Sciences). The correct mass and purity was confirmed by an Agilent 1100 Series LC/MSD TOF (Agilent Technologies Inc. – Palo Alto, CA).