has led to many exciting clinical candidates and chemical probes for human
bromodomains. Bromodomain motifs relevant for infectious disease are also now
being disclosed [42]. Increased structural biology efforts to study the bromodomains
as multidomain constructs both by NMR [72] and x-ray crystallography [23] will be
important contributions to the fields combined with our growing ability to study
these multidomain protein interactions with synthetic chromatin [2, 140]. Improvements with cryo-transmission electron microscopy (cryo-TEM) should also be
an enabling tool to study these large complexes. Additionally, as chemical probes
continue to be developed for bromodomains, in-cell engagement tools described
above, such as gene expression analysis, chromatin-based FRAP experiments, nanoBRET, and CETSA, will need to play significant roles to help validate molecular
mechanisms. With the wealth of biophysical methods and cellular tools available to
researchers, the chemical epigenetics field of bromodomain inhibitor development
should continue to innovate at an accelerated rate.
Compliance with Ethical Standards
Funding: This study was funded by the National Institute of General Medical Sciences of the
National Institutes under the award number R01GM121414 (W.C.K.P and P.D.Y). J.A.J. was
supported by a National Institutes of Health Biotechnology training grant 5T32GM008347-23.
Conflict of Interest: All authors declare that they have no conflicts of interest.
References
1. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature
403(6765):41–45. https://doi.org/10.1038/47412
2. Allis CD, Muir TW (2011) Spreading chromatin into chemical biology. Chembiochem
12(2):264–279. https://doi.org/10.1002/cbic.201000761
3. Phillips DM (1963) Presence of acetyl groups in histones. Biochem J 87(2):258. https://doi.
org/10.1042/bj0870258
4. Johns EW, Phillips DM, Simpson P, Butler JAW (1961) The electrophoresis of histones and
histone fractions on starch gel. Biochem J 80:189–192
5. Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation + methylation of histones + their
possible role in regulation of RNA synthesis. Proc Natl Acad Sci U S A 51(5):786–794.
https://doi.org/10.1073/pnas.51.5.786
6. Filippakopoulos P, Knapp S (2012) The bromodomain interaction module. FEBS Lett
586(17):2692–2704. https://doi.org/10.1016/j.febslet.2012.04.045
7. Li YY, Sabari BR, Panchenko T, Wen H, Zhao D, Guan HP, Wan LL, Huang H, Tang ZY,
Zhao YM, Roeder RG, Shi XB, Allis CD, Li HT (2016) Molecular coupling of histone
Crotonylation and active transcription by AF9 YEATS domain. Mol Cell 62(2):181–193.
https://doi.org/10.1016/j.molcel.2016.03.028
8. Fujimori DG, Conway SJ (2016) Editorial overview: chemical genetics and epigenetics. Curr
Opin Chem Biol 33:VI–VII. https://doi.org/10.1016/j.cbpa.2016.08.008
9. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, Morse EM, Keates T,
Hickman TT, Felletar I, Philpott M, Munro S, McKeown MR, Wang YC, Christie AL,
West N, Cameron MJ, Schwartz B, Heightman TD, La Thangue N, French CA, Wiest O,
Kung AL, Knapp S, Bradner JE (2010) Selective inhibition of BET bromodomains. Nature
468(7327):1067–1073. https://doi.org/10.1038/nature09504
Applied Biophysics for Bromodomain Drug Discovery
327
bromodomains. Bromodomain motifs relevant for infectious disease are also now
being disclosed [42]. Increased structural biology efforts to study the bromodomains
as multidomain constructs both by NMR [72] and x-ray crystallography [23] will be
important contributions to the fields combined with our growing ability to study
these multidomain protein interactions with synthetic chromatin [2, 140]. Improvements with cryo-transmission electron microscopy (cryo-TEM) should also be
an enabling tool to study these large complexes. Additionally, as chemical probes
continue to be developed for bromodomains, in-cell engagement tools described
above, such as gene expression analysis, chromatin-based FRAP experiments, nanoBRET, and CETSA, will need to play significant roles to help validate molecular
mechanisms. With the wealth of biophysical methods and cellular tools available to
researchers, the chemical epigenetics field of bromodomain inhibitor development
should continue to innovate at an accelerated rate.
Compliance with Ethical Standards
Funding: This study was funded by the National Institute of General Medical Sciences of the
National Institutes under the award number R01GM121414 (W.C.K.P and P.D.Y). J.A.J. was
supported by a National Institutes of Health Biotechnology training grant 5T32GM008347-23.
Conflict of Interest: All authors declare that they have no conflicts of interest.
References
1. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature
403(6765):41–45. https://doi.org/10.1038/47412
2. Allis CD, Muir TW (2011) Spreading chromatin into chemical biology. Chembiochem
12(2):264–279. https://doi.org/10.1002/cbic.201000761
3. Phillips DM (1963) Presence of acetyl groups in histones. Biochem J 87(2):258. https://doi.
org/10.1042/bj0870258
4. Johns EW, Phillips DM, Simpson P, Butler JAW (1961) The electrophoresis of histones and
histone fractions on starch gel. Biochem J 80:189–192
5. Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation + methylation of histones + their
possible role in regulation of RNA synthesis. Proc Natl Acad Sci U S A 51(5):786–794.
https://doi.org/10.1073/pnas.51.5.786
6. Filippakopoulos P, Knapp S (2012) The bromodomain interaction module. FEBS Lett
586(17):2692–2704. https://doi.org/10.1016/j.febslet.2012.04.045
7. Li YY, Sabari BR, Panchenko T, Wen H, Zhao D, Guan HP, Wan LL, Huang H, Tang ZY,
Zhao YM, Roeder RG, Shi XB, Allis CD, Li HT (2016) Molecular coupling of histone
Crotonylation and active transcription by AF9 YEATS domain. Mol Cell 62(2):181–193.
https://doi.org/10.1016/j.molcel.2016.03.028
8. Fujimori DG, Conway SJ (2016) Editorial overview: chemical genetics and epigenetics. Curr
Opin Chem Biol 33:VI–VII. https://doi.org/10.1016/j.cbpa.2016.08.008
9. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, Morse EM, Keates T,
Hickman TT, Felletar I, Philpott M, Munro S, McKeown MR, Wang YC, Christie AL,
West N, Cameron MJ, Schwartz B, Heightman TD, La Thangue N, French CA, Wiest O,
Kung AL, Knapp S, Bradner JE (2010) Selective inhibition of BET bromodomains. Nature
468(7327):1067–1073. https://doi.org/10.1038/nature09504
Applied Biophysics for Bromodomain Drug Discovery
327