Influence of sequence length and charged residues on Swc5 binding with histone <scp>H2A‐H2B</scp>

Chu, Wen-Ting; Wang, Jin

doi:10.1002/prot.26035

Cited by 5 publications

(4 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some previous studies have demonstrated that H2A.Z was shown to interact with components of complexes involved in a multitude of biological processes, such as DNA damage repair [ 26 ], gene activation [ 27 ], gene repression [ 28 ], various transcription factors [ 29 – 31 ], and chromatin remodeling [ 32 ]; however, the underlying mechanism of action remains unclear in ICC. Using the STRING database, we identified potential molecules that interact with H2A.Z (Fig.…”

Section: Resultsmentioning

confidence: 99%

The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

Wang

Xiong

et al. 2022

BMC Cancer

View full text Add to dashboard Cite

Background Intrahepatic cholangiocarcinoma (ICC), originating from the bile ducts, is the second most common primary liver malignancy, and its incidence has recently increased. H2A.Z, a highly conserved H2A variant, is emerging as a key regulatory molecule in cancer. However, its underlying mechanism of action in ICC cells remains unclear. Methods Here, we examined the expression of H2A.Z and SFRP1 in normal intrahepatic cholangiocytes, ICC cell lines, ICC tissue microarrays, and fresh specimens. The correlations between H2A.Z or SFRP1 expression and clinical features were analysed. The overall survival rate was analysed based on H2A.Z and SFRP1 expression. Immunoprecipitation was used to analyse the recruitment of KDM1A, and ChIP sequencing and BSP were used to analyse the enrichment of methylation-related molecules such as H3K4me1 and H3K4me2 in the SFRP1 promoter and reveal the underlying mechanisms. Knockdown and rescue experiments were used to determine the potential mechanism by which H2A.Z and SFRP1 promote tumorigenesis in vitro. Results We showed that upregulation of H2A.Z expression is linked to downregulation of SFRP1 expression in ICC tissues and poor overall survival in patients with ICC. H2A.Z interacted with KDM1A in the nucleus to bind to the -151 ~ -136 bp region upstream of the SFRP1 promoter to increase its demethylation in ICC cells. Functionally, H2A.Z silencing inhibited the proliferation and invasion of ICC cells, and these effects were mitigated by SFRP1 silencing in ICC cells. Conclusions Our findings reveal that H2A.Z inhibits SFRP1 expression through chromatin modification in the context of ICC by forming a complex with KDM1A in the nucleus.

show abstract

Section: Resultsmentioning

confidence: 99%

The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

Wang

Xiong

et al. 2022

BMC Cancer

View full text Add to dashboard Cite

show abstract

“…In addition, experimental data show that the more negatively charged cMybTAD (a longer chain with −3.3 charges) has kinetic rate constants that are higher and more dependent upon salt concentration than those of cMyb25 [328,329]. Other simulation studies of IDPs have also suggested the important role of electrostatic interactions during binding [325,330,331].…”

Section: Flexible Binding Of Puma To Mcl-1 and Cmyb/mll Tomentioning

confidence: 99%

Physics of biomolecular recognition and conformational dynamics

Chu¹,

Yan²,

Chu³

et al. 2021

Rep. Prog. Phys.

Self Cite

View full text Add to dashboard Cite

Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to aﬃnity, speciﬁcity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic speciﬁcity based on the underlying energy landscape theory provides a practical way to quantify the speciﬁcity. Optimization of aﬃnity and speciﬁcity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying ﬂexible binding or binding-folding mechanisms. In this review, we ﬁrst introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) speciﬁcity quantiﬁcation of molecular recognition; (2) evolution and design in molecular recognition; (3) ﬂexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.

show abstract

“…Although the CFDP1 gene is highly conserved, there is limited knowledge about its function, both at the cellular and organismal levels. The yeast Swc5 gene is essential for the optimal function of the chromatin remodeler SWR, which has histone exchange activity in an ATP-dependent manner [12][13][14][15]. Studies in Drosophila melanogaster have shown that the loss of the BCNT gene Yeti causes lethality before pupation and that it mechanistically provides a chaperone-like activity that is required in higher-order chromatin organization by its interaction with histone variant H2A.V and chromatin remodeling machinery [16].…”

Section: Introductionmentioning

confidence: 99%

Cfdp1 Is Essential for Cardiac Development and Function

Giardoglou

Deloukas

Dedoussis

et al. 2023

Cells

View full text Add to dashboard Cite

Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide. A combination of environmental and genetic effectors modulates the risk of developing them. Thus, it is vital to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in Coronary Artery Disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family, and to date, its function and mechanism of action in Cardiovascular Development are still unclear. We utilized zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology, and ease of experimental manipulations. We showed that cfdp1 was expressed during development, and we tested two morpholinos and generated a cfdp1 mutant line. The cfdp1−/− embryos developed arrhythmic hearts and exhibited defective cardiac performance, which led to a lethal phenotype. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process. The cfdp1 zebrafish mutant line provides a valuable tool for unveiling the novel mechanism of regulating cardiac physiology and function. cfdp1 is essential for cardiac development, a previously unreported phenotype most likely due to early lethality in mice. The detected phenotype of bradycardia and arrhythmias is an observation with potential clinical relevance for humans carrying heterozygous CFDP1 mutations and their risk of developing CAD.

show abstract

Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B

Cited by 5 publications

References 36 publications

The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

Physics of biomolecular recognition and conformational dynamics

Cfdp1 Is Essential for Cardiac Development and Function

Contact Info

Product

Resources

About