Crystal Structure of the ENT Domain of Human EMSY

Chavali, G.B.; Ekblad, Caroline; Basu, Balaka Piku; Brissett, Nigel C.; Veprintsev, Dmitry B.; Hughes-Davies, Luke; Kouzarides, Tony; Itzhaki, Laura S.; Doherty, Aidan J.

doi:10.1016/j.jmb.2005.05.047

Cited by 23 publications

(22 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2) (29). The structure of the EMSY ENT domain was recently solved, and it revealed that EMSY forms homodimers through its ENT domain (25). As expected, given the high sequence identity, the RIF1 ENT domain mediates RIF1 homodimer formation (SI Fig.…”

Section: Discussionsupporting

confidence: 53%

“…Whereas the ENT domain of RIF1 homodimerizes in yeast (SI Fig. 8), as is the case for the EMSY ENT domain (25), neither the ENT nor the AGENT domain of RIF1 is sufficient for the interaction with R, suggesting that multiple regions in RIF1 are involved (data not shown). Together, these results provide evidence for the interaction of a bHLH domain with an ENT/AGENET-containing protein.…”

Section: Identification Of Rif1 As An Ent Domain Protein That Specifimentioning

confidence: 83%

See 1 more Smart Citation

The basic helix–loop–helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor

Hernandez

Feller

Morohashi³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The control of anthocyanin accumulation in maize by the cooperation of the basic helix-loop-helix (bHLH) protein R with the MYB transcription factor C1 provides one of the best examples of plant combinatorial transcriptional control. Establishing the function of the bHLH domain of R has remained elusive, and so far no proteins that interact with this conserved domain have been identified. We show here that the bHLH domain of R is dispensable for the activation of transiently expressed genes yet is essential for the activation of the endogenous genes in their normal chromatin environment. The activation of A1, one of the anthocyanin biosynthetic genes, is associated with increased acetylation of histone 3 (H3) at K9/K14 in the promoter region to which the C1/R complex binds. We identified R-interacting factor 1 (RIF1) as a nuclear, AGENET domain-containing EMSY-like protein that specifically interacts with the bHLH region of R. Knockdown experiments show that RIF1 is necessary for the activation of the endogenous promoters but not of transiently expressed genes. ChIP experiments established that RIF1 is tethered to the regulatory region of the A1 promoter by the C1/R complex. Together, these findings describe a function for the bHLH domain of R in linking transcriptional regulation with chromatin functions by the recruitment of an EMSY-related factor.anthocyanin ͉ BRCA2 ͉ chromatin T he evolution of multicellular organisms was accompanied by an increase in the complexity of gene regulatory mechanisms, reflected in the dramatic expansion of transcription factor families and in the intricate interactions between regulatory proteins and cis-regulatory elements in what is commonly known as combinatorial transcriptional control. Superimposed on this complexity is the understanding that histone modifications and chromatin structure are intimately linked to the regulatory activity of many transcription factors (1). Establishing the interactions between combinatorial gene regulation and histone functions thus poses a problem of significant biological importance.The basic helix-loop-helix (bHLH) family of transcription factors is among the largest in animals and plants (2). bHLH domains are characterized by the presence of an Ϸ18-residue hydrophilic basic helix followed by two amphipathic ␣-helices separated by a loop (3, 4). When present, basic regions contribute to the binding of bHLH factors to DNA, through cisregulatory elements, termed E-boxes, with the CANNTG consensus, whereas HLH motifs participate in homodimer or heterodimer formation (4). Maize R was the first plant bHLH transcription factor described (5). R belongs to a small gene family, which includes B, and R/B specify anthocyanin pigmentation in different plant tissues (6). They participate in the transcriptional regulation of the anthocyanin pathway genes through the cooperation with the R2R3-MYB transcription factor C1 or its paralog, PL1 (7). C1 and R/B physically interact through the MYB domain of C1 and the N-terminal region of R (which does not contai...

show abstract

Section: Discussionsupporting

confidence: 53%

Section: Identification Of Rif1 As An Ent Domain Protein That Specifimentioning

confidence: 83%

The basic helix–loop–helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor

Hernandez

Feller

Morohashi³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The remarkable relationship between CC s and mean phase error is shown in Fig. 2 as stages of DDM refinement progress for the structure of the ENT domain of the human EMSY protein (Chavali et al, 2005; PDB code 1uz3) solved using ACORN. This is typical of that found for the many structures investigated so far.…”

Section: Maps Dynamic Density Modification (Ddm) and CC Smentioning

confidence: 98%

“…Table 1 lists some of these using various types of starting phases. We have revisited the solution of the human chromatin regulator (Chavali et al, 2005; PDB code 1uz3) using the data deposited by the authors. This largely helical structure belongs to space group P2 1 with 204 residues (1550 atoms) in two chains.…”

Section: Successful Applicationsmentioning

confidence: 99%

ACORN: a review

Yao

Dodson

Wilson

et al. 2006

Acta Crystallogr D Biol Crystallogr

View full text Add to dashboard Cite

The ACORN system was originally developed as a means of ab initio solution of protein structures when atomic resolution data were available. The first step is to obtain a starting set of phases, which must be at least slightly better than random. These may be calculated from a fragment of the structure, which can be anything from a single metal atom to a complete molecular-replacement model. A number of standard procedures are available in ACORN to orientate and position such a fragment. The fragment provides initial phases that give the first of a series of maps that are iteratively refined by a dynamic density-modification (DDM) process. Another FFTbased procedure is Sayre-equation refinement (SER), which modifies phases better to satisfy the Sayre equation. With good-quality atomic resolution data, the final outcome of applying DDM and SER is a map similar in appearance to that found from a refined structure, which is readily interpreted by automated procedures. Further development of ACORN now enables structures to be solved with less than atomic resolution data. A critical part of this development is the artificial extension of the data from the observed limit to 1 Å resolution. These extended reflections are allocated unit normalized structure amplitudes and then treated in a similar way to observed reflections except that they are downweighted in the calculation of maps. ACORN maps, especially at low resolution, tend to show C atoms less well, in particular C atoms which fall within the first diffraction minimum of their three neighbours. Two new density-modification procedures (DDM1 and DDM2) and a density-enhancement procedure (ENH) have been devised to counter this problem. It is demonstrated that high-quality maps showing individual atoms can be produced with the new ACORN. ACORN has also been demonstrated to be very effective in refining phase sets derived from physical processes such as those using anomalous scattering or isomorphous derivative data. Future work will be directed towards applying ACORN to resolutions down to 2 Å .

show abstract

“…Early studies described EMSY acting as a transcription factor via its interaction with chromatin-associated proteins BS69 and HP1-β, proposing a role for EMSY in the suppression of target genes [5, 16, 17]. Phosphorylation by AKT1, a protein kinase activated by phosphoinositide-3-kinase (PI3K), has recently been suggested to be important in EMSY's role as a transcription factor [18].…”

Section: Introductionmentioning

confidence: 99%

The EMSY threonine 207 phospho-site is required for EMSY-driven suppression of DNA damage repair

et al. 2017

View full text Add to dashboard Cite

BRCA1 and BRCA2 are essential for the repair of double-strand DNA breaks, and alterations in these genes are a hallmark of breast and ovarian carcinomas. Other functionally related genes may also play important roles in carcinogenesis. Amplification of EMSY, a putative BRCAness gene, has been suggested to impair DNA damage repair by suppressing BRCA2 function. We employed direct repeat GFP (DR-GFP) and RAD51 foci formation assays to show that EMSY overexpression impairs the repair of damaged DNA, suggesting that EMSY belongs to the family of BRCAness proteins. We also identified a novel phospho-site at threonine 207 (T207) and demonstrated its role in EMSY-driven suppression of DNA damage repair. In vitro kinase assays established that protein kinase A (PKA) directly phosphorylates the T207 phospho-site. Immunoprecipitation experiments suggest that EMSY-driven suppression of DNA damage repair is a BRCA2-independent process. The data also suggest that EMSY amplification is a BRCAness feature, and may help to expand the population of patients who could benefit from targeted therapies that are also effective in BRCA1/2-mutant cancers.

show abstract

Crystal Structure of the ENT Domain of Human EMSY

Cited by 23 publications

References 24 publications

The basic helix–loop–helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor

The basic helix–loop–helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor

ACORN: a review

The EMSY threonine 207 phospho-site is required for EMSY-driven suppression of DNA damage repair

Contact Info

Product

Resources

About