scholarly journals Conserved Structure and Evolution of DPF Domain of PHF10—The Specific Subunit of PBAF Chromatin Remodeling Complex

2021 ◽  
Vol 22 (20) ◽  
pp. 11134
Author(s):  
Anton O. Chugunov ◽  
Nadezhda A. Potapova ◽  
Natalia S. Klimenko ◽  
Victor V. Tatarskiy ◽  
Sofia G. Georgieva ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Histone Modifications ◽  
Transcription Activation ◽  
Sequence Structure ◽  
Histone Tails ◽  
Phd Finger ◽  
Chromatin Remodeling Complex ◽  
Regulation Functions ◽  
Distinct Features ◽  
Structure And Functions

Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.

scholarly journals SWI/SNF remains localized to chromatin in the presence of SCHLAP1

2018 ◽  
Author(s):  
Jesse R. Raab ◽  
Keriayn N. Smith ◽  
Camarie C. Spear ◽  
Carl J. Manner ◽  
J. Mauro Calabrese ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Chromatin Remodeling ◽  
Histone Modifications ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Metastatic Prostate Cancer ◽  
The Core ◽  
Prostate Cells ◽  
Chromatin Remodeling Complex ◽  
Non Coding Rnas

AbstractSCHLAP1 is a long-noncoding RNA that is prognostic for progression to metastatic prostate cancer and promotes an invasive phenotype. SCHLAP1 is reported to function by depleting the core SWI/SNF subunit, SMARCB1, from the genome. SWI/SNF is a large, multi-subunit, chromatin remodeling complex that can be combinatorially assembled to yield hundreds to thousands of distinct complexes. Here, we investigated the hypothesis that SCHLAP1 affects only specific forms of SWI/SNF and that the remaining SWI/SNF complexes were important for the increased invasion in SCHLAP1 expressing prostate cells. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1 expression. We find that SCHLAP1 induces changes to chromatin openness but is not sufficient to drive changes in histone modifications. Additionally, we show that SWI/SNF binds many coding and non-coding RNAs. Together these results suggest that SCHLAP1 has roles independent of canonical SWI/SNF and that SWI/SNF broadly interacts with RNA.

scholarly journals The DPF Domain As a Unique Structural Unit Participating in Transcriptional Activation, Cell Differentiation, and Malignant Transformation

Acta Naturae ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 57-65
Author(s):  
N. V. Soshnikova ◽  
A. A. Sheynov ◽  
Eu. V. Tatarskiy ◽  
S. G. Georgieva
Keyword(s):  
Malignant Transformation ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Mammalian Cells ◽  
Protein Complexes ◽  
Active Chromatin ◽  
Phd Finger ◽  
Chromatin Remodeling Complex ◽  
Single Structure ◽  
Chromatin Proteins

The DPF (double PHD finger) domain consists of two PHD fingers organized in tandem. The two PHD-finger domains within a DPF form a single structure that interacts with the modification of the N-terminal histone fragment in a way different from that for single PHD fingers. Several histone modifications interacting with the DPF domain have already been identified. They include acetylation of H3K14 and H3K9, as well as crotonylation of H3K14. These modifications are found predominantly in transcriptionally active chromatin. Proteins containing DPF belong to two classes of protein complexes, which are the transcriptional coactivators involved in the regulation of the chromatin structure. These are the histone acetyltransferase complex belonging to the MYST family and the SWI/SNF chromatin-remodeling complex. The DPF domain is responsible for the specificity of the interactions between these complexes and chromatin. Proteins containing DPF play a crucial role in the activation of the transcription of a number of genes expressed during the development of an organism. These genes are important in the differentiation and malignant transformation of mammalian cells.

scholarly journals Molecular Basis of Histone Tail Recognition by Human TIP5 PHD Finger and Bromodomain of the Chromatin Remodeling Complex NoRC

Structure ◽  
2015 ◽  
Vol 23 (1) ◽  
pp. 80-92 ◽  
Author(s):  
Cynthia Tallant ◽  
Erica Valentini ◽  
Oleg Fedorov ◽  
Lois Overvoorde ◽  
Fleur M. Ferguson ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Molecular Basis ◽  
Histone Tail ◽  
Phd Finger ◽  
Chromatin Remodeling Complex

scholarly journals Actin-Related Protein 4 Interacts with PIE1 and Regulates Gene Expression in Arabidopsis

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 520
Author(s):  
Wenfeng Nie ◽  
Jinyu Wang
Keyword(s):  
Gene Expression ◽  
Plant Growth ◽  
Chromatin Remodeling ◽  
Leaf Size ◽  
Early Flowering ◽  
Physical Interaction ◽  
Loss Of Function ◽  
Single Nucleotide Change ◽  
Chromatin Remodeling Complex ◽  
Related Proteins

As essential structural components of ATP-dependent chromatin-remodeling complex, the nucleolus-localized actin-related proteins (ARPs) play critical roles in many biological processes. Among them, ARP4 is identified as an integral subunit of chromatin remodeling complex SWR1, which is conserved in yeast, humans and plants. It was shown that RNAi mediated knock-down of Arabidopsis thaliana ARP4 (AtARP4) could affect plant development, specifically, leading to early flowering. However, so far, little is known about how ARP4 functions in the SWR1 complex in plant. Here, we identified a loss-of-function mutant of AtARP4 with a single nucleotide change from glycine to arginine, which had significantly smaller leaf size. The results from the split luciferase complementation imaging (LCI) and yeast two hybrid (Y2H) assays confirmed its physical interaction with the scaffold and catalytic subunit of SWR1 complex, photoperiod-independent early flowering 1 (PIE1). Furthermore, mutation of AtARP4 caused altered transcription response of hundreds of genes, in which the number of up-regulated differentially expressed genes (DEGs) was much larger than those down-regulated. Although most DEGs in atarp4 are related to plant defense and response to hormones such as salicylic acid, overall, it has less overlapping with other swr1 mutants and the hta9 hta11 double-mutant. In conclusion, our results reveal that AtARP4 is important for plant growth and such an effect is likely attributed to its repression on gene expression, typically at defense-related loci, thus providing some evidence for the coordination of plant growth and defense, while the regulatory patterns and mechanisms are distinctive from other SWR1 complex components.

scholarly journals Interplay of BAF and MLL4 promotes cell type-specific enhancer activation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Young-Kwon Park ◽  
Ji-Eun Lee ◽  
Zhijiang Yan ◽  
Kaitlin McKernan ◽  
Tommy O’Haren ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Chromatin Remodeling ◽  
Direct Evidence ◽  
Cell Type ◽  
Chromatin Regulators ◽  
Chromatin Remodeling Complex ◽  
Histone H3k4 ◽  
Cell Type Specific ◽  
Pioneer Transcription Factor ◽  
Factor C

AbstractCell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF chromatin remodeling complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other’s binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic pioneer transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers.

scholarly journals The mammalian INO80 chromatin remodeling complex is required for replication stress recovery

2014 ◽  
Vol 42 (14) ◽  
pp. 9074-9086 ◽  
Author(s):  
Ivelina Vassileva ◽  
Iskra Yanakieva ◽  
Michaela Peycheva ◽  
Anastas Gospodinov ◽  
Boyka Anachkova
Keyword(s):  
Chromatin Remodeling ◽  
Replication Stress ◽  
Stress Recovery ◽  
Chromatin Remodeling Complex

scholarly journals Rvb1p/Rvb2p Recruit Arp5p and Assemble a Functional Ino80 Chromatin Remodeling Complex

2004 ◽  
Vol 16 (3) ◽  
pp. 465-477 ◽  
Author(s):  
Zophonı́as O. Jónsson ◽  
Sudhakar Jha ◽  
James A. Wohlschlegel ◽  
Anindya Dutta
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Remodeling Complex
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