DUX4(HD2)-DNA(ERG) structure reveals new insight into DUX4-Responsive-Element.
DUX4(HD2)-DNA(ERG) structure reveals new insight into DUX4-Responsive-Element.
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DUX4HD2-DNAERG 结构揭示了对 DUX4 响应元件的新见解
DOI：
10.1038/s41375-018-0273-z
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发表时间：
2019-03
期刊：
影响因子：
11.4
通讯作者：
Meng G
中科院分区：
文献类型：
--
作者：
Dong X;Zhang H;Cheng N;Li K;Meng G
最近，我们报道了DUX 4 HD 2的2.6 nm晶体结构，其与源自野生型DUX 4 ChIP-seq分析的共有DREconsensus复合[1，2]。DREconsensus位点也存在于携带致癌DUX 4/IGH的白血病NALM 6和Reh细胞中（图1a和补充图1a）[3，4]。此外，GATXXGAT样、TGAT-ATTA样重复序列也经常与野生型DUX 4和DUX 4/IGH靶基因相关（图1a）。为了更深入地了解DUX 4-DRE相互作用的真实性质，我们已经确定了与来源于B-ALL患者RNA-seq和ChIP-seq分析的内源性ERG DNA序列结合的DUX 4 HD2的结构[3，4]。如前所述纯化重组DUX 4 HD2结构域[1]。与DUX 4 HD2- DREconsensus（2.6 nm）相比，HD2-DREERG晶体的衍射非常好（1.6 nm）。X射线数据采集统计详情见表1。对于结构测定，在PHASER [5]中实施的分子置换（MR）方法使用了改良的HD2结构（PDB代码：5 Z2 S和5 Z2 T）[1]，而不是DNA坐标。使用COOT [5]手动构建5′-TGATGAGATTA-3′/3′ACTACTCTAAT-5′的DNA双链体，然后使用PHENIX.REFINE [6]进行TLS精修。最终的R和Rfree因子分别为20.1%和20.7%。与先前的报道[1]一致，一个ERG DNA双链体可以与两个HD2分子结合（图1b）。与之前的2.6 kDa HD2-DREconsense结构不同，ERG DNA的电子密度图具有高质量（1.6 kDa，补充图1b），并允许清晰地登记ERG序列，5′-T1 GATGAGATT 11 -3′/3′-A1 CTACTC TAA 11 -5′。最后一对核苷酸T11和A11的电子密度图是无序的，因此不能用于模型构建。对于HD2分子，最终精制模型包含残基Arg 95至Gln 152。如前所述[1]，HD2结构域分别折叠成三个螺旋α1-α3的整体结构域。N末端的poly-Arg/Lys基序，垂直于螺旋α1，与DNA结合。在这种结构中，Arg 95和Arg 98侧链浸入小沟中。特别地，Arg 98与T1核苷酸的羟基形成氢键（图1c）。与之前的观察结果[1]一致，DUX 4 HD 2 DNAERG中R95 RKR 98的平均B因子为67.4 μ g，远高于结构的其余部分（40.3 μ g），重申了DUX 4驱动的反式激活的两步机制中的次要作用[1]。在目前的HD2-DNAERG结构中，QNR基序也是主要的DNA-代码-阅读模块（图1d-f）。先前的报告表明QNR可以结合共有TAAT重复序列[1]。令人惊讶的是，Asn 144和Arg 148与G2和A3核苷酸形成两对氢键（图1d）。同源异型盒超家族中的Asn 144位于大沟的中心。甲酰胺侧链与A3核苷酸形成两个氢键（分别为2.7和3.0 π）。与Asn 144侧链平行的是Arg 148胍头基，其又与G2核苷酸形成两个氢（分别为3.1和3.1个）。此外，在T1 GAT 4核苷酸周围的区域中，其富含带正电荷的残基，包括Arg 95、Arg 96、Lys 97、Arg 98、Arg 137、Trp 141、Arg 145、Arg 148和His 149（图1 e）。值得注意的是，在His 149中观察到的双侧链构型。
Recently, we have reported a 2.6 Å crystal structure of DUX4HD2 complexed with a consensus DREconsensus derived from the wild type DUX4 ChIP-seq analysis [1, 2] The DREconsensus site is also present in the leukemia NALM6 and Reh cells harboring oncogenic DUX4/IGHs (Fig. 1a and Supplementary Figure 1a) [3, 4]. Furthermore, the GATXXGAT-like, TGAT-ATTA-like repeats are also frequently associated with wild type DUX4 and DUX4/IGH target genes (Fig. 1a). In order to gain more insight into the true nature of DUX4-DRE interaction, we have determined the structure of DUX4 HD2 bound with endogeneous ERG DNA sequences derived from the B-ALL patient RNA-seq and ChIP-seq analysis [3, 4]. The recombinant DUX4 HD2 domain was purified as described before [1]. The crystal of HD2-DREERG diffracted remarkably well (1.6 Å) compared with that of DUX4HD2– DREconsensus (2.6 Å). The statistics detail of X-ray data collection is shown in Table 1. For structural determination, the refined HD2 structures (PDB codes: 5Z2S and 5Z2T) [1], but not DNA coordinates, were used for molecular replacement (MR) approach implemented in PHASER [5]. The DNA duplex of 5′-TGATGAGATTA-3′/3′ACTACTCTAAT-5′ were built manually using COOT [5], followed by TLS refinement using PHENIX.REFINE [6]. The final R and Rfree factors are 20.1 and 20.7%, respectively. Consistent with previous report [1], one ERG DNA duplex can bind to two HD2 molecules (Fig. 1b). Unlike the previous 2.6 Å HD2-DREconsensue structure, the electron density map of ERG DNA is of high quality (1.6 Å, Supplementary Figure 1b) and allows clear registration of ERG sequences, 5′-T1GATGAGATT11-3′/3′-A1CTACTC TAA11-5′. The electron density map of the last pair of nucleotides, T11 and A11, are disordered and hence not available for model building. For the HD2 molecules, the final refined models contain residues Arg95 to Gln152. As reported before [1], the HD2 domain folds into a global domain of three helices, α1–α3, respectively. The Nterminal poly-Arg/Lys motif, perpendicular to the helix α1, engages the DNA binding. In this structure, the Arg95 and Arg98 side-chains dip into the minor groove. In particular, Arg98 forms a hydrogen bond with the hydroxyl group of T1 nucleotide (Fig. 1c). Consistent with previous observation [1], the average B factor of R95RKR98 in DUX4HD2DNAERG is 67.4 Å , much higher than the rest of the structure (40.3 Å), reiterating a secondary role in the twostep mechanism of DUX4-driven transactivation [1]. In current HD2-DNAERG structure, the QNR motif is also the major DNA-code-reading module (Figure 1d–f). The previous report suggests QNR can bind to the consensus TAAT repeat [1]. To our surprise, the Asn144 and Arg148 form two pairs of hydrogen bond with the G2 and A3 nucleotide (Fig. 1d). The invariant Asn144 among homeobox superfamily lies in the heart of the major groove. The carboxamide side-chain form two hydrogen bonds with the A3 nucleotide (2.7 and 3.0 Å, respectively). In parallel with Asn144 side chain lies the Arg148 guanidinium head group, which in turn forms two hydrogen with the G2 nucleotide (3.1 and 3.1 Å, respectively). Besides, in the region surrounding T1GAT4 nucleotides, it is enriched with positively charged residues including Arg95, Arg96, Lys97, Arg98, Arg137, Trp141, Arg145, Arg148 and His149 (Fig. 1e). Of note, the dual side-chain configuration observed in His149 These authors contributed equally: Xue Dong, Hao Zhang, Nuo Cheng
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DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH
影响因子：
30.8
作者：
Zhang, Jinghui;McCastlain, Kelly;Yoshihara, Hiroki;Xu, Beisi;Chang, Yunchao;Churchman, Michelle L.;Wul, Gang;Li, Yongjin;Wei, Lei;Iacobucci, Ilaria;Liu, Yu;Qu, Chunxu;Wen, Ji;Edmonsonl, Michael;Payne-Turner, Debbie;Kaufmann, Kerstin B.;Takayanagi, Shin-ichiro;Wienholds, Erno;Waanders, Esme;Ntziachristos, Panagiotis;Bakogianni, Sofia;Wang, Jingjing;Aifantis, Iannis;Roberts, Kathryn G.;Ma, Jing;Song, Guangchun;Easton, John;Mulder, Heather L.;Chen, Xiang;Newman, Scott;Ma, Xiaotu;Rusch, Michael;Gupta, Pankaj;Boggs, Kristy;Vadodaria, Bhavin;Dalton, James;Liu, Yanling;Valentine, Marcus L.;Ding, Li;Lu, Charles;Fulton, Robert S.;Fulton, Lucinda;Tabib, Yashodhan;Ochoa, Kerri;Devidas, Meenakshi;Pei, Deqing;Cheng, Cheng;Yang, Jun;Evans, William E.;Relling, Mary V.;Pui, Ching-Hon;Jeha, Sima;Harvey, Richard C.;Chen, I-Ming L.;Willman, Cheryl L.;Marcucci, Guido;Bloomfield, Clara D.;Kohlschmidt, Jessica;Mrozek, Krzysztof;Paietta, Elisabeth;Tallman, Martin S.;Stock, Wendy;Foster, Matthew C.;Racevskis, Janis;Rowe, Jacob M.;Luger, Selina;Kornblau, Steven M.;Shurtleff, Sheila A.;Raimondi, Susana C.;Mardis, Elaine R.;Wilson, Richard K.;Dick, John E.;Hunger, Stephen P.;Loh, Mignon L.;Downing, James R.;Mullighan, Charles G.
通讯作者：
Mullighan, Charles G.
DUX4/IGH驱动的反式激活的结构基础
影响因子：
11.4
作者：
Dong X;Zhang W;Wu H;Huang J;Zhang M;Wang P;Zhang H;Chen Z;Chen SJ;Meng G
通讯作者：
Meng G
影响因子：
4.9
作者：
Zhang Y;Lee JK;Toso EA;Lee JS;Choi SH;Slattery M;Aihara H;Kyba M
通讯作者：
Kyba M
DOI：
10.1107/s0907444994003112
发表时间：
1994-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
BAILEY, S
通讯作者：
BAILEY, S