Mutational analysis ofH3F3A, a chromatin remodeling gene in common solid tumors

Bromodomains (BRDs) are small protein interaction modules of about 110 amino acids that selectively recognize acetylated lysine in histones and other proteins. These domains have been identified in a variety of multi-domain proteins involved in transcriptional regulation or chromatin remodeling in eukaryotic cells. BRD inhibition is considered an attractive therapeutic approach in epigenetic disorders, particularly in oncology. Here, we present a Φ value analysis to investigate the folding pathway of the second domain of BRD2 (BRD2(2)). Using an extensive mutational analysis based on 25 site-directed mutants, we provide structural information on both the intermediate and late transition state of BRD2(2). The data reveal that the C-terminal region represents part of the initial folding nucleus, while the N-terminal region of the domain consolidates its structure only later in the folding process. Furthermore, only a small number of native-like interactions have been identified, suggesting the presence of a non-compact, partially folded state with scarce native-like characteristics. Taken together, these results indicate that, in BRD2(2), a hierarchical mechanism of protein folding can be described with non-native interactions that play a significant role in folding.

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Binding of Acf1 to DNA Involves a WAC Motif and Is Important for ACF-Mediated Chromatin Assembly

Molecular and Cellular Biology ◽

10.1128/mcb.22.18.6344-6353.2002 ◽

2002 ◽

Vol 22 (18) ◽

pp. 6344-6353 ◽

Cited By ~ 46

Author(s):

Dmitry V. Fyodorov ◽

James T. Kadonaga

Keyword(s):

Dna Binding ◽

Chromatin Remodeling ◽

Atp Hydrolysis ◽

Mutational Analysis ◽

Large Subunit ◽

Deposition Process ◽

Chromatin Assembly ◽

Sequence Motifs ◽

Binding Region ◽

Conserved Sequence

ABSTRACT ACF is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilizes the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. We performed a systematic mutational analysis of Acf1 to elucidate the functions of specific subregions of the protein. These studies revealed DNA- and ISWI-binding regions that are important for the chromatin assembly and ATPase activities of ACF. The DNA-binding region of Acf1 includes a WAC motif, which is necessary for the efficient binding of ACF complex to DNA. The interaction of Acf1 with ISWI requires a DDT domain, which has been found in a variety of transcription and chromatin-remodeling factors. Chromatin assembly by ACF is also impaired upon mutation of an acidic region in Acf1, which may interact with histones during the deposition process. Lastly, we observed modest chromatin assembly defects on mutation of other conserved sequence motifs. Thus, Acf1 facilitates chromatin assembly via an N-terminal DNA-binding region with a WAC motif, a central ISWI-binding segment with a DDT domain, and a C-terminal region with an acidic stretch, a WAKZ motif, PHD fingers, and bromodomain.

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Crucial Roles for Interactions between MLL3/4 and INI1 in Nuclear Receptor Transactivation

Molecular Endocrinology ◽

10.1210/me.2008-0455 ◽

2009 ◽

Vol 23 (5) ◽

pp. 610-619 ◽

Cited By ~ 36

Author(s):

Seunghee Lee ◽

Dae-Hwan Kim ◽

Young Hwa Goo ◽

Young Chul Lee ◽

Soo-Kyung Lee ◽

...

Keyword(s):

Nuclear Receptor ◽

Chromatin Remodeling ◽

Target Genes ◽

Mutational Analysis ◽

Specific Protein ◽

Transcriptional Coactivator ◽

Set Domain ◽

Protein Protein Interaction ◽

Terminal Set ◽

Chromatin Remodeling Complex

Abstract Nuclear receptor (NR) transactivation involves multiple coactivators, and the molecular basis for how these are functionally integrated needs to be determined to fully understand the NR action. Activating signal cointegrator-2 (ASC-2), a transcriptional coactivator of many NRs and transcription factors, forms a steady-state complex, ASCOM (for ASC-2 complex), which contains histone H3-lysine-4 (H3K4) methyltransferase MLL3 or its paralog MLL4. Here, we show that ASCOM requires a functional cross talk with the ATPase-dependent chromatin remodeling complex Swi/Snf for efficient NR transactivation. Our results reveal that ASCOM and Swi/Snf are tightly colocalized in the nucleus and that ASCOM and Swi/Snf promote each other’s binding to NR target genes. We further show that the C-terminal SET domain of MLL3 and MLL4 directly interacts with INI1, an integral subunit of Swi/Snf. Our mutational analysis demonstrates that this interaction underlies the mutual facilitation of ASCOM and Swi/Snf recruitment to NR target genes. Importantly, this study uncovers a specific protein-protein interaction as a novel venue to couple two distinct enzymatic coactivator complexes during NR transactivation.

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Hypoxia and the phenomenon of immune exclusion

Journal of Translational Medicine ◽

10.1186/s12967-020-02667-4 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Violena Pietrobon ◽

Francesco M. Marincola

Keyword(s):

Solid Tumors ◽

Chromatin Remodeling ◽

In Vivo Imaging ◽

Ex Vivo ◽

Cell Distribution ◽

Common Phenomenon ◽

Current State ◽

Promising Strategy ◽

Immune Exclusion

AbstractOver the last few years, cancer immunotherapy experienced tremendous developments and it is nowadays considered a promising strategy against many types of cancer. However, the exclusion of lymphocytes from the tumor nest is a common phenomenon that limits the efficiency of immunotherapy in solid tumors. Despite several mechanisms proposed during the years to explain the immune excluded phenotype, at present, there is no integrated understanding about the role played by different models of immune exclusion in human cancers. Hypoxia is a hallmark of most solid tumors and, being a multifaceted and complex condition, shapes in a unique way the tumor microenvironment, affecting gene transcription and chromatin remodeling. In this review, we speculate about an upstream role for hypoxia as a common biological determinant of immune exclusion in solid tumors. We also discuss the current state of ex vivo and in vivo imaging of hypoxic determinants in relation to T cell distribution that could mechanisms of immune exclusion and discover functional-morphological tumor features that could support clinical monitoring.

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Recent Studies on a Murine Leukemia Virus Grown in Tissue Culture

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100060544 ◽

1967 ◽

Vol 25 ◽

pp. 106-107

Author(s):

L. Z. de Tkaczevski ◽

E. de Harven ◽

C. Friend

Keyword(s):

Tissue Culture ◽

Solid Tumors ◽

Murine Leukemia Virus ◽

Leukemia Virus ◽

Supernatant Fluid ◽

Virus Particles ◽

Friend Leukemia ◽

Type C ◽

Leukemia Viruses ◽

Murine Leukemia

Despite extensive studies, the correlation between the morphology and pathogenicity of murine leukemia viruses (MLV) has not yet been clarified. The virus particles found in the plasma of leukemic mice belong to 2 distinct groups, 1 or 2% of them being enveloped A particles and the vast majority being of type C. It is generally believed that these 2 types of particles represent different phases in the development of the same virus. Particles of type A have been thought to be an earlier form of type C particles. One of the tissue culture lines established from Friend leukemia solid tumors has provided the material for the present study. The supernatant fluid of the line designated C-1A contains an almost pure population of A particles as illustrated in Figure 1. The ratio is, therefore, the reverse of what is unvariably observed in the plasma of leukemic mice where C particles predominate.

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