1
|
Dhalluin C, Carlson JE, Zeng L, He C,
Aggarwal AK and Zhou MM: Structure and ligand of a histone
acetyltransferase bromodomain. Nature. 399:491–496. 1999.
View Article : Google Scholar : PubMed/NCBI
|
2
|
Belkina AC and Denis GV: BET domain
co-regulators in obesity, inflammation and cancer. Nat Rev Cancer.
12:465–477. 2012. View
Article : Google Scholar : PubMed/NCBI
|
3
|
Dey A, Chitsaz F, Abbasi A, Misteli T and
Ozato K: The double bromodomain protein Brd4 binds to acetylated
chromatin during interphase and mitosis. Proc Natl Acad Sci USA.
100:8758–8763. 2003. View Article : Google Scholar : PubMed/NCBI
|
4
|
Jang MK, Mochizuki K, Zhou M, Jeong HS,
Brady JN and Ozato K: The bromodomain protein Brd4 is a positive
regulatory component of P-TEFb and stimulates RNA polymerase
II-dependent transcription. Mol Cell. 19:523–534. 2005. View Article : Google Scholar : PubMed/NCBI
|
5
|
Jiang YW, Veschambre P, Erdjument-Bromage
H, Tempst P, Conaway JW, Conaway RC and Kornberg RD: Mammalian
mediator of transcriptional regulation and its possible role as an
end-point of signal transduction pathways. Proc Natl Acad Sci USA.
95:8538–8543. 1998. View Article : Google Scholar : PubMed/NCBI
|
6
|
Donner AJ, Ebmeier CC, Taatjes DJ and
Espinosa JM: CDK8 is a positive regulator of transcriptional
elongation within the serum response network. Nat Struct Mol Biol.
17:194–201. 2010. View Article : Google Scholar : PubMed/NCBI
|
7
|
Patel MC, Debrosse M, Smith M, Dey A,
Huynh W, Sarai N, Heightman TD, Tamura T and Ozato K: BRD4
coordinates recruitment of pause release Factor P-TEFb and the
pausing complex NELF/DSIF to regulate transcription elongation of
interferon-stimulated genes. Mol Cell Biol. 33:2497–2507. 2013.
View Article : Google Scholar : PubMed/NCBI
|
8
|
Liu W, Ma Q, Wong K, Li W, Ohgi K, Zhang
J, Aggarwal A and Rosenfeld MG: Brd4 and JMJD6-associated
anti-pause enhancers in regulation of transcriptional pause
release. Cell. 155:1581–1595. 2013. View Article : Google Scholar : PubMed/NCBI
|
9
|
Rahman S, Sowa ME, Ottinger M, Smith JA,
Shi Y, Harper JW and Howley PM: The Brd4 extraterminal domain
confers transcription activation independent of pTEFb by recruiting
multiple proteins, including NSD3. Mol Cell Biol. 31:2641–2652.
2011. View Article : Google Scholar : PubMed/NCBI
|
10
|
Yang Z, Yik JH, Chen R, He N, Jang MK,
Ozato K and Zhou Q: Recruitment of P-TEFb for stimulation of
transcriptional elongation by the bromodomain protein Brd4. Mol
Cell. 19:535–545. 2005. View Article : Google Scholar : PubMed/NCBI
|
11
|
Picaud S: Selective inhibition of BET
bromodomains. Nature. 468:1067–1073. 2010. View Article : Google Scholar : PubMed/NCBI
|
12
|
Nicodeme E, Jeffrey KL, Schaefer U, Beinke
S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H,
et al: Suppression of inflammation by a synthetic histone mimic.
Nature. 468:1119–1123. 2010. View Article : Google Scholar : PubMed/NCBI
|
13
|
Dawson MA, Prinjha RK, Dittmann A,
Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C,
Savitski MM, et al: Inhibition of BET recruitment to chromatin as
an effective treatment for MLL-fusion leukaemia. Nature.
478:529–533. 2011. View Article : Google Scholar : PubMed/NCBI
|
14
|
Zuber J, Shi J, Wang E, Rappaport AR,
Herrmann H, Sison EA, Magoon D, Qi J, Blatt K, Wunderlich M, et al:
RNAi screen identifies Brd4 as a therapeutic target in acute
myeloid leukaemia. Nature. 478:524–528. 2011. View Article : Google Scholar : PubMed/NCBI
|
15
|
Delmore JE, Issa GC, Lemieux ME, Rahl PB,
Shi J, Jacobs HM, Kastritis E, Gilpatrick T, Paranal RM, Qi J, et
al: BET bromodomain inhibition as a therapeutic strategy to target
c-Myc. Cell. 146:904–917. 2011. View Article : Google Scholar : PubMed/NCBI
|
16
|
Mertz JA, Conery AR, Bryant BM, Sandy P,
Balasubramanian S, Mele DA, Bergeron L and Sims RJ III: Targeting
MYC dependence in cancer by inhibiting BET bromodomains. Proc Natl
Acad Sci USA. 108:16669–16674. 2011. View Article : Google Scholar : PubMed/NCBI
|
17
|
Chapuy B, McKeown MR, Lin CY, Monti S,
Roemer MG, Qi J, Rahl PB, Sun HH, Yeda KT, Doench JG, et al:
Discovery and characterization of super-enhancer-associated
dependencies in diffuse large B cell lymphoma. Cancer Cell.
24:777–790. 2013. View Article : Google Scholar : PubMed/NCBI
|
18
|
Knoechel B, Roderick JE, Williamson KE,
Zhu J, Lohr JG, Cotton MJ, Gillespie SM, Fernandez D, Ku M, Wang H,
et al: An epigenetic mechanism of resistance to targeted therapy in
T cell acute lymphoblastic leukemia. Nat Genet. 46:364–370. 2014.
View Article : Google Scholar : PubMed/NCBI
|
19
|
Puissant A, Frumm SM, Alexe G, Bassil CF,
Qi J, Chanthery YH, Nekritz EA, Zeid R, Gustafson WC, Greninger P,
et al: Targeting MYCN in neuroblastoma by BET bromodomain
inhibition. Cancer Discov. 3:308–323. 2013. View Article : Google Scholar : PubMed/NCBI
|
20
|
Bandopadhayay P, Bergthold G, Nguyen B,
Schubert S, Gholamin S, Tang Y, Bolin S, Schumacher SE, Zeid R,
Masoud S, et al: BET bromodomain inhibition of MYC-amplified
medulloblastoma. Clin Cancer Res. 20:912–925. 2014. View Article : Google Scholar : PubMed/NCBI
|
21
|
Lockwood WW, Zejnullahu K, Bradner JE and
Varmus H: Sensitivity of human lung adenocarcinoma cell lines to
targeted inhibition of BET epigenetic signaling proteins. Proc Natl
Acad Sci USA. 109:19408–19413. 2012. View Article : Google Scholar : PubMed/NCBI
|
22
|
Asangani IA, Dommeti VL, Wang X, Malik R,
Cieslik M, Yang R, Escara-Wilke J, Wilder-Romans K, Dhanireddy S,
Engelke C, et al: Therapeutic targeting of BET bromodomain proteins
in castration-resistant prostate cancer. Nature. 510:278–282. 2014.
View Article : Google Scholar : PubMed/NCBI
|
23
|
Lovén J, Hoke HA, Lin CY, Lau A, Orlando
DA, Vakoc CR, Bradner JE, Lee TI and Young RA: Selective inhibition
of tumor oncogenes by disruption of super-enhancers. Cell.
153:320–334. 2013. View Article : Google Scholar : PubMed/NCBI
|
24
|
Whyte WA, Orlando DA, Hnisz D, Abraham BJ,
Lin CY, Kagey MH, Rahl PB, Lee TI and Young RA: Master
transcription factors and mediator establish super-enhancers at key
cell identity genes. Cell. 153:307–319. 2013. View Article : Google Scholar : PubMed/NCBI
|
25
|
Di Micco R, Fontanals-Cirera B, Low V,
Ntziachristos P, Yuen SK, Lovell CD, Dolgalev I, Yonekubo Y, Zhang
G, Rusinova E, et al: Control of embryonic stem cell identity by
BRD4-dependent transcriptional elongation of
super-enhancer-associated pluripotency genes. Cell Rep. 9:234–247.
2014. View Article : Google Scholar : PubMed/NCBI
|
26
|
Hnisz D, Abraham BJ, Lee TI, Lau A,
Saint-André V, Sigova AA, Hoke HA and Young RA: Super-enhancers in
the control of cell identity and disease. Cell. 155:934–947. 2013.
View Article : Google Scholar : PubMed/NCBI
|
27
|
Wu SY, Lee AY, Lai HT, Zhang H and Chiang
CM: Phospho switch triggers Brd4 chromatin binding and activator
recruitment for gene-specific targeting. Mol Cell. 49:843–857.
2013. View Article : Google Scholar : PubMed/NCBI
|
28
|
Brown JD, Lin CY, Duan Q, Griffin G,
Federation A, Paranal RM, Bair S, Newton G, Lichtman A, Kung A, et
al: NF-κB directs dynamic super enhancer formation in inflammation
and atherogenesis. Mol Cell. 56:219–231. 2014. View Article : Google Scholar : PubMed/NCBI
|
29
|
Bolger AM, Lohse M and Usadel B:
Trimmomatic: A flexible trimmer for Illumina sequence data.
Bioinformatics. 30:2114–2120. 2014. View Article : Google Scholar : PubMed/NCBI
|
30
|
Langmead B, Trapnell C, Pop M and Salzberg
SL: Ultrafast and memory-efficient alignment of short DNA sequences
to the human genome. Genome Biol. 10:R252009. View Article : Google Scholar : PubMed/NCBI
|
31
|
Thorvaldsdottir H, Robinson JT and Mesirov
JP: Integrative Genomics Viewer (IGV): High-performance genomics
data visualization and exploration. Brief Bioinform. 14:178–192.
2013. View Article : Google Scholar : PubMed/NCBI
|
32
|
Zhang Y, Liu T, Meyer CA, Eeckhoute J,
Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W and
Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome Biol.
9:R372008. View Article : Google Scholar : PubMed/NCBI
|
33
|
Heinz S, Benner C, Spann N, Bertolino E,
Lin YC, Laslo P, Cheng JX, Murre C, Singh H and Glass CK: Simple
combinations of lineage-determining transcription factors
prime-regulatory elements required for macrophage and B cell
identities. Mol Cell. 38:576–589. 2010. View Article : Google Scholar : PubMed/NCBI
|
34
|
Gautier L, Cope L, Bolstad BM and Irizarry
RA: affy-analysis of Affymetrix GeneChip data at the probe level.
Bioinformatics. 20:307–315. 2004. View Article : Google Scholar : PubMed/NCBI
|
35
|
Irizarry RA, Bolstad BM, Collin F, Cope
LM, Hobbs B and Speed TP: Summaries of Affymetrix GeneChip probe
level data. Nucleic Acids Res. 31:e152003. View Article : Google Scholar : PubMed/NCBI
|
36
|
Irizarry RA, Hobbs B, Collin F,
Beazer-Barclay YD, Antonellis KJ, Scherf U and Speed TP:
Exploration, normalization, and summaries of high density
oligonucleotide array probe level data. Biostatistics. 4:249–264.
2003. View Article : Google Scholar : PubMed/NCBI
|
37
|
Gentleman RC, Carey VJ, Bates DM, Bolstad
B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al:
Bioconductor: Open software development for computational biology
and bioinformatics. Genome Biol. 5:R802004. View Article : Google Scholar : PubMed/NCBI
|
38
|
Subramanian A, Tamayo P, Mootha VK,
Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub
TR, Lander ES and Mesirov JP: Gene set enrichment analysis: A
knowledge-based approach for interpreting genome-wide expression
profiles. Proc Natl Acad Sci USA. 102:15545–15550. 2005. View Article : Google Scholar : PubMed/NCBI
|
39
|
Barski A, Cuddapah S, Cui K, Roh TY,
Schones DE, Wang Z, Wei G, Chepelev I and Zhao K: High-resolution
profiling of histone methylations in the human genome. Cell.
129:823–837. 2007. View Article : Google Scholar : PubMed/NCBI
|
40
|
Rahl PB and Young RA: MYC and
transcription elongation. Cold Spring Harb Perspect Med.
4:a0209902014. View Article : Google Scholar : PubMed/NCBI
|
41
|
Zhou VW, Goren A and Bernstein BE:
Charting histone modifications and the functional organization of
mammalian genomes. Nat Rev Genet. 12:7–18. 2011. View Article : Google Scholar : PubMed/NCBI
|
42
|
Claudio JO, Masih-Khan E, Tang H,
Gonçalves J, Voralia M, Li ZH, Nadeem V, Cukerman E,
Francisco-Pabalan O, Liew CC, et al: A molecular compendium of
genes expressed in multiple myeloma. Blood. 100:2175–2186. 2002.
View Article : Google Scholar : PubMed/NCBI
|
43
|
Whitfield TW, Wang J, Collins PJ,
Partridge EC, Aldred SF, Trinklein ND, Myers RM and Weng Z:
Functional analysis of transcription factor binding sites in human
promoters. Genome Biol. 13:R502012. View Article : Google Scholar : PubMed/NCBI
|
44
|
Jelinek DF, Aagaard-Tillery KM, Arendt BK,
Arora T, Tschumper RC and Westendorf JJ: Differential human
multiple myeloma cell line responsiveness to interferon-alpha.
Analysis of transcription factor activation and interleukin 6
receptor expression. J Clin Invest. 99:447–456. 1997. View Article : Google Scholar : PubMed/NCBI
|
45
|
Otsuki T, Yamada O, Sakaguchi H, Tomokuni
A, Wada H, Yawata Y and Ueki A: Human myeloma cell apoptosis
induced by interferon-alpha. Br J Haematol. 103:518–529. 1998.
View Article : Google Scholar : PubMed/NCBI
|
46
|
Mccoull W, Cheung T, Anderson E, Barton P,
Burgess J, Byth K, Cao Q, Castaldi MP, Chen H, Chiarparin E, et al:
Development of a novel B-cell lymphoma 6 (BCL6) PROTAC to provide
insight into small molecule targeting of BCL6. ACS Chem Biol.
13:3131–3141. 2018. View Article : Google Scholar : PubMed/NCBI
|
47
|
Rodriguez EF, Chowsilpa S and Maleki Z:
insulinoma-associated protein 1 immunostain: A diagnostic tool for
pulmonary small cell carcinoma in cytology. Acta Cytol. 62:333–338.
2018. View Article : Google Scholar : PubMed/NCBI
|
48
|
Chen C, Breslin MB and Lan MS: Sonic
hedgehog signaling pathway promotes INSM1 transcription factor in
neuroendocrine lung cancer. Cell Signal. 46:83–91. 2018. View Article : Google Scholar : PubMed/NCBI
|
49
|
Gabay M, Li Y and Felsher DW: MYC
activation is a hallmark of cancer initiation and maintenance. Cold
Spring Harb Perspect Med. 4(pii): a0142412014. View Article : Google Scholar : PubMed/NCBI
|
50
|
Vogler M: BCL2A1: The underdog in the BCL2
family. Cell Death Differ. 19:67–74. 2012. View Article : Google Scholar : PubMed/NCBI
|
51
|
Shi J and Vakoc CR: The mechanisms behind
the therapeutic activity of BET bromodomain inhibition. Mol Cell.
54:728–736. 2014. View Article : Google Scholar : PubMed/NCBI
|
52
|
Anand P, Brown JD, Lin CY, Qi J, Zhang R,
Artero PC, Alaiti MA, Bullard J, Alazem K, Margulies KB, et al: BET
bromodomains mediate transcriptional pause release in heart
failure. Cell. 154:569–582. 2013. View Article : Google Scholar : PubMed/NCBI
|
53
|
Lamoureux F, Baud'huin M, Rodriguez
Calleja L, Jacques C, Berreur M, Rédini F, Lecanda F, Bradner JE,
Heymann D and Ory B: Selective inhibition of BET bromodomain
epigenetic signalling interferes with the bone-associated tumour
vicious cycle. Nat Commun. 5:35112014. View Article : Google Scholar : PubMed/NCBI
|