Effect of the linkers between the zinc fingers in zinc finger protein 809 on gene silencing and nuclear localization

Yu, I.; Utsunomiya, Yuko; Onodera, Masafumi

doi:10.1016/j.bbrc.2016.02.040

Cited by 4 publications

(5 citation statements)

References 22 publications

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“…Zinc finger proteins refer to a class of proteins which contain stable Zn 2+ and can self-fold to form a "finger"like structure (23). They are the largest family of transcriptional regulatory factors in mammals, and are involved in embryonic development, cell differentiation, cell transformation, and cell cycle (24)(25)(26). Studies have discovered most zinc finger proteins are closely related to the occurrence and development of malignant tumors (27).…”

Section: Discussionmentioning

confidence: 99%

Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma

Bao¹,

Wang²,

Fan³

2021

J Gastrointest Oncol

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Section: Discussionmentioning

confidence: 99%

Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma

Bao¹,

Wang²,

Fan³

2021

J Gastrointest Oncol

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“…Functional dependencies of experimentally introduced zinc finger linker mutations have been studied with ZFP809 by immunostaining methods, which provided evidence of mutation-related protein location alteration, that is, protein staining by immunofluorescence-labeled antibodies switched from the nucleus to the nucleolus. 53 This latter study points to the importance of specific antibodies as tools for structure/ function correlation investigations.…”

Section: ■ Discussionmentioning

confidence: 93%

“…This H to Y amino acid exchange has been found enriched by somatic mutations in several carcinomas and hits a crucial amino acid residue, which is important for both zinc coordination within a zinc finger domain and participation in the interdomain linker sequence. Functional dependencies of experimentally introduced zinc finger linker mutations have been studied with ZFP809 by immunostaining methods, which provided evidence of mutation-related protein location alteration, that is, protein staining by immunofluorescence-labeled antibodies switched from the nucleus to the nucleolus . This latter study points to the importance of specific antibodies as tools for structure/function correlation investigations.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C₂H₂ Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis

Scherf

Koy

Röwer

et al. 2023

J. Am. Soc. Mass Spectrom.

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Weak-force Order (ITEM-TWO) analysis in combination with molecular modeling, the phosphorylation-dependent molecular recognition motif of the anti-HpTGEKP antibody has been investigated with binary and ternary component mixtures consisting of antibody and (phospho-) peptides. Amino acid sequences have been selected to match either the antibody's recognition motif or the cancer-related zinc finger protein mutations and phosphorylations of the respective amino acid residues. Upon electrospraying of all the components of the mixtures, that is, hexapeptides, antibody, and intact immune complexes, the produced ions were subjected to mass spectrometric mass filtering. The antibody ions as well as the immune complex ions traversed into the mass spectrometer's collision chamber, whereas paths of unbound peptide ions were blocked prior to entering the collision cell. After dissociation of the multiply charged immune complexes in the gas phase, the complex-released peptide ions were recorded after having traversed the second mass filter. Complex-released peptides were unambiguously identified by their masses using mass analysis with isotope resolution. From the results of our studies with seven (phospho-) peptides with distinct amino acid sequences, which resembled either the antibody's binding motif or mutations, we conclude the following: (i) A negatively charged phospho group, located near the peptide's N-terminus is mandatory for antibody binding when placed on the peptide surface at a precise distance to the C-terminally located positively charged ε-amino group of a lysinyl residue. (ii) A bulky amino acid residue, such as the tyrosinyl residue at the N-terminal position of the (phospho-) threoninyl residue, abolishes antibody binding. (iii) Two closely spaced phospho groups negatively interfere with the surface polarity pattern and abolish antibody binding as well. (iv) Non-phosphorylated peptides are not binding partners of the anti-HpTGEKP antibody.

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“…During these processes, the target specificity of KRAB-Zfps was dynamically screened and specialized, and the “peace” of the genome would be reset until the emergence of the functionally matched defenders. Some evidence has been provided to support the key regulatory roles of the linkers as DNA recognition determinants during the evolutionary selection of KRAB-Zfps [ 40 , 41 ]. Therefore, more thorough investigations are necessary to further uncover the correlations between the sequence variations of linkers and the DNA binding capability of their adjacent ZnFs.…”

Section: Discussionmentioning

confidence: 99%

Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

Zhang

et al. 2022

Mobile DNA

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Background Krüppel Associated Box-containing Zinc Finger Proteins (KRAB-ZFPs), representing the largest superfamily of transcription factors in mammals, are predicted to primarily target and repress transposable elements (TEs). It is challenging to dissect the distinct functions of these transcription regulators due to their sequence similarity and diversity, and also the complicated repetitiveness of their targeting TE sequences. Results Mouse KRAB-Zfps are mainly organized into clusters genomewide. In this study, we revealed that the intra-cluster members had a close evolutionary relationship, and a similar preference for zinc finger (ZnF) usage. KRAB-Zfps were expressed in a cell type- or tissue type specific manner and they tended to be actively transcribed together with other cluster members. Further sequence analyses pointed out the linker sequences in between ZnFs were conserved, and meanwhile had distinct cluster specificity. Based on these unique characteristics of KRAB-Zfp clusters, sgRNAs were designed to edit cluster-specific linkers to abolish the functions of the targeted cluster(s). Using mouse embryonic stem cells (mESC) as a model, we screened and obtained a series of sgRNAs targeting various highly expressed KRAB-Zfp clusters. The effectiveness of sgRNAs were verified in a reporter assay exclusively developed for multi-target sgRNAs and further confirmed by PCR-based analyses. Using mESC cell lines inducibly expressing Cas9 and these sgRNAs, we found that editing different KRAB-Zfp clusters resulted in the transcriptional changes of distinct categories of TEs. Conclusions Collectively, the intrinsic sequence correlations of intra-cluster KRAB-Zfp members discovered in this study suggest that the conserved cluster specific linkers played crucial roles in diversifying the tandem ZnF array and the related target specificity of KRAB-Zfps during clusters’ evolution. On this basis, an effective CRISPR-Cas9 based approach against the linker sequences is developed and verified for rapidly editing KRAB-Zfp clusters to identify the regulatory correlation between the cluster members and their potential TE targets.

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Effect of the linkers between the zinc fingers in zinc finger protein 809 on gene silencing and nuclear localization

Cited by 4 publications

References 22 publications

Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma

Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma

Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C₂H₂ Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis

Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

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Effect of the linkers between the zinc fingers in zinc finger protein 809 on gene silencing and nuclear localization

Cited by 4 publications

References 22 publications

Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma

Hsa_circ_NOTCH3 regulates ZNF146 through sponge adsorption of miR-875-5p to promote tumorigenesis of hepatocellular carcinoma

Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C2H2 Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis

Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

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Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C₂H₂ Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis