(2015) A plasmodium falciparum bromodomain protein regulates invasion gene expression.
Cell Host Microbe 17(6):741–751. https://doi.org/10.1016/j.chom.2015.05.009
20. Raha D, Hong M, Snyder M (2010) ChIP-seq: a method for global identification of regulatory
elements in the genome. Curr Protoc Mol Biol Chapter 21:Unit 21 19 21-14. https://doi.org/10.
1002/0471142727.mb2119s91
21. Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ,
Kharchenko PV, Garcia BA, Kuroda MI (2013) Chromatin proteins captured by ChIP-mass
spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 20
(2):202–209. https://doi.org/10.1038/nsmb.2477
22. Mohammed H, Taylor C, Brown GD, Papachristou EK, Carroll JS, D'Santos CS (2016) Rapid
immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes. Nat Protoc 11(2):316–326. https://doi.org/10.1038/nprot.2016.020
23. Cao Z, Lu C (2016) A microfluidic device with integrated sonication and immunoprecipitation
for sensitive epigenetic assays. Anal Chem 88(3):1965–1972. https://doi.org/10.1021/acs.
analchem.5b04707
24. Jafari R, Almqvist H, Axelsson H, Ignatushchenko M, Lundback T, Nordlund P, Martinez
Molina D (2014) The cellular thermal shift assay for evaluating drug target interactions in cells.
Nat Protoc 9(9):2100–2122. https://doi.org/10.1038/nprot.2014.138
25. Becher I, Werner T, Doce C, Zaal EA, Togel I, Khan CA, Rueger A, Muelbaier M, Salzer E,
Berkers CR, Fitzpatrick PF, Bantscheff M, Savitski MM (2016) Thermal profiling reveals
phenylalanine hydroxylase as an off-target of panobinostat. Nat Chem Biol 12(11):908–910.
https://doi.org/10.1038/nchembio.2185
26. McNulty DE, Bonnette WG, Qi H, Wang L, Ho TF, Waszkiewicz A, Kallal LA, Nagarajan RP,
Stern M, Quinn AM, Creasy CL, Su DS, Graves AP, Annan RS, Sweitzer SM, Holbert MA
(2018) A high-throughput dose-response cellular thermal shift assay for rapid screening of drug
target engagement in living cells, exemplified using SMYD3 and IDO1. SLAS Discov 23
(1):34–46. https://doi.org/10.1177/2472555217732014
27. Song Y, Madahar V, Liao J (2011) Development of FRET assay into quantitative and highthroughput screening technology platforms for protein-protein interactions. Ann Biomed Eng
39(4):1224–1234. https://doi.org/10.1007/s10439-010-0225-x
28. Alibhai D, Kelly DJ, Warren S, Kumar S, Margineau A, Serwa RA, Thinon E, Alexandrov Y,
Murray EJ, Stuhmeier F, Tate EW, Neil MA, Dunsby C, French PM (2013) Automated
fluorescence lifetime imaging plate reader and its application to Forster resonant energy transfer
readout of Gag protein aggregation. J Biophotonics 6(5):398–408. https://doi.org/10.1002/jbio.
201200185
29. Wade M, Mendez J, Coussens NP, Arkin MR, Glicksman MA (2004) Inhibition of proteinprotein interactions: cell-based assays. In: Sittampalam GS, Coussens NP, Brimacombe K et al
(eds) Assay guidance manual. Eli Lilly & Company and the National Center for Advancing
Translational Sciences, Bethesda
30. Bacart J, Corbel C, Jockers R, Bach S, Couturier C (2008) The BRET technology and its
application to screening assays. Biotechnol J 3(3):311–324. https://doi.org/10.1002/biot.
200700222
31. Machleidt T, Woodroofe CC, Schwinn MK, Mendez J, Robers MB, Zimmerman K, Otto P,
Daniels DL, Kirkland TA, Wood KV (2015) NanoBRET – a novel BRET platform for the
analysis of protein-protein interactions. ACS Chem Biol 10(8):1797–1804. https://doi.org/10.
1021/acschembio.5b00143
32. Hu F, Martin H, Martinez A, Everitt J, Erkanli A, Lee WT, Dewhirst M, Ramanujam N (2017)
Distinct angiogenic changes during carcinogenesis defined by novel label-free dark-field
imaging in a hamster cheek pouch model. Cancer Res 77(24):7109–7119. https://doi.org/10.
1158/0008-5472.CAN-17-1058
33. Tollefsbol TO (2011) Advances in epigenetic technology. Methods Mol Biol 791:1–10. https://
doi.org/10.1007/978-1-61779-316-5_1
556
C. Dell’Aversana et al.
Cell Host Microbe 17(6):741–751. https://doi.org/10.1016/j.chom.2015.05.009
20. Raha D, Hong M, Snyder M (2010) ChIP-seq: a method for global identification of regulatory
elements in the genome. Curr Protoc Mol Biol Chapter 21:Unit 21 19 21-14. https://doi.org/10.
1002/0471142727.mb2119s91
21. Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ,
Kharchenko PV, Garcia BA, Kuroda MI (2013) Chromatin proteins captured by ChIP-mass
spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 20
(2):202–209. https://doi.org/10.1038/nsmb.2477
22. Mohammed H, Taylor C, Brown GD, Papachristou EK, Carroll JS, D'Santos CS (2016) Rapid
immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes. Nat Protoc 11(2):316–326. https://doi.org/10.1038/nprot.2016.020
23. Cao Z, Lu C (2016) A microfluidic device with integrated sonication and immunoprecipitation
for sensitive epigenetic assays. Anal Chem 88(3):1965–1972. https://doi.org/10.1021/acs.
analchem.5b04707
24. Jafari R, Almqvist H, Axelsson H, Ignatushchenko M, Lundback T, Nordlund P, Martinez
Molina D (2014) The cellular thermal shift assay for evaluating drug target interactions in cells.
Nat Protoc 9(9):2100–2122. https://doi.org/10.1038/nprot.2014.138
25. Becher I, Werner T, Doce C, Zaal EA, Togel I, Khan CA, Rueger A, Muelbaier M, Salzer E,
Berkers CR, Fitzpatrick PF, Bantscheff M, Savitski MM (2016) Thermal profiling reveals
phenylalanine hydroxylase as an off-target of panobinostat. Nat Chem Biol 12(11):908–910.
https://doi.org/10.1038/nchembio.2185
26. McNulty DE, Bonnette WG, Qi H, Wang L, Ho TF, Waszkiewicz A, Kallal LA, Nagarajan RP,
Stern M, Quinn AM, Creasy CL, Su DS, Graves AP, Annan RS, Sweitzer SM, Holbert MA
(2018) A high-throughput dose-response cellular thermal shift assay for rapid screening of drug
target engagement in living cells, exemplified using SMYD3 and IDO1. SLAS Discov 23
(1):34–46. https://doi.org/10.1177/2472555217732014
27. Song Y, Madahar V, Liao J (2011) Development of FRET assay into quantitative and highthroughput screening technology platforms for protein-protein interactions. Ann Biomed Eng
39(4):1224–1234. https://doi.org/10.1007/s10439-010-0225-x
28. Alibhai D, Kelly DJ, Warren S, Kumar S, Margineau A, Serwa RA, Thinon E, Alexandrov Y,
Murray EJ, Stuhmeier F, Tate EW, Neil MA, Dunsby C, French PM (2013) Automated
fluorescence lifetime imaging plate reader and its application to Forster resonant energy transfer
readout of Gag protein aggregation. J Biophotonics 6(5):398–408. https://doi.org/10.1002/jbio.
201200185
29. Wade M, Mendez J, Coussens NP, Arkin MR, Glicksman MA (2004) Inhibition of proteinprotein interactions: cell-based assays. In: Sittampalam GS, Coussens NP, Brimacombe K et al
(eds) Assay guidance manual. Eli Lilly & Company and the National Center for Advancing
Translational Sciences, Bethesda
30. Bacart J, Corbel C, Jockers R, Bach S, Couturier C (2008) The BRET technology and its
application to screening assays. Biotechnol J 3(3):311–324. https://doi.org/10.1002/biot.
200700222
31. Machleidt T, Woodroofe CC, Schwinn MK, Mendez J, Robers MB, Zimmerman K, Otto P,
Daniels DL, Kirkland TA, Wood KV (2015) NanoBRET – a novel BRET platform for the
analysis of protein-protein interactions. ACS Chem Biol 10(8):1797–1804. https://doi.org/10.
1021/acschembio.5b00143
32. Hu F, Martin H, Martinez A, Everitt J, Erkanli A, Lee WT, Dewhirst M, Ramanujam N (2017)
Distinct angiogenic changes during carcinogenesis defined by novel label-free dark-field
imaging in a hamster cheek pouch model. Cancer Res 77(24):7109–7119. https://doi.org/10.
1158/0008-5472.CAN-17-1058
33. Tollefsbol TO (2011) Advances in epigenetic technology. Methods Mol Biol 791:1–10. https://
doi.org/10.1007/978-1-61779-316-5_1
556
C. Dell’Aversana et al.