MutM: Single C2C2 Zinc Finger-DNA Interaction

2007 ◽  
pp. 31-34
Author(s):  
Ryoji Masui ◽  
Noriko Nakagawa ◽  
Seiki Kuramitsu
Keyword(s):  
Zinc Finger ◽  
Dna Interaction

scholarly journals Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants

2021 ◽  
Vol 22 (2) ◽  
pp. 512
Author(s):  
Kateryna Fal ◽  
Denisa Tomkova ◽  
Gilles Vachon ◽  
Marie-Edith Chabouté ◽  
Alexandre Berr ◽  
...  
Keyword(s):  
Cell Fate ◽  
Dna Sequence ◽  
Zinc Finger ◽  
Chromatin Structure ◽  
New Technologies ◽  
Dna Interaction ◽  
The Other ◽  
Proof Of Concept ◽  
Epigenetic Marks ◽  
Molecular Events

An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of “second generation”, chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.

scholarly journals Analysis of DNA Binding by a Eubacterial Zinc Finger Transcription Factor

2009 ◽  
Vol 191 (14) ◽  
pp. 4513-4521 ◽  
Author(s):  
Victor J. McAlister ◽  
Gail E. Christie
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Specific Binding ◽  
Dna Interaction ◽  
Late Gene ◽  
Major Groove ◽  
Late Gene Expression ◽  
Zinc Finger Transcription Factor

ABSTRACT The Serratia marcescens NucC protein is structurally and functionally homologous to the P2 Ogr family of eubacterial zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. These activators exhibit site-specific binding to a conserved DNA sequence, TGT-N3-R-N4-Y-N3-aCA, that is located upstream of NucC-dependent S. marcescens promoters and the late promoters of P2-related phages. In this report we describe the interactions of NucC with the P2 FETUD late operon promoter P F . NucC is shown to bind P F as a tetramer and to make 12 symmetrical contacts to the DNA phosphodiester backbone. The backbone contacts are centered on the TGT-N3-R-N4-Y-N3-aCA motif. Major groove base contacts can be seen at most positions within the ∼24-bp binding site. Minor groove contacts map to adjacent positions in the downstream half of the binding site, which corresponds to the area in which the DNA also appears to be bent by NucC binding. NucC binding provides a new example of protein-DNA interaction that is strikingly different from the DNA binding demonstrated for eukaryotic zinc-finger transcription factors.

Murine Modeling of Human Severe Congenital Neutropenia and Non-Immune Chronic Idopathic Neutropenia.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 93-93 ◽  
Author(s):  
Adrian P. Zarebski ◽  
Wojciech Pawlak ◽  
Avinash M. Baktula ◽  
Sudeep Basu ◽  
John Trent ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Bone Marrow Cells ◽  
Fungal Infections ◽  
Dna Interaction ◽  
Molecular Defect ◽  
Severe Congenital Neutropenia ◽  
Congenital Neutropenia ◽  
Gene Encoding ◽  
Mild Phenotype

Abstract Severe Congenital Neutropenia (SCN) is a rare hematological disease manifested by a complete block in the maturation of neutrophils. The lack of neutrophils leads to recurrent bacterial and fungal infections. Most SCN patients have mutations in Ela2, the gene encoding neutrophil elastase; however, introduction of SCN-patient mutations into murine Ela2 or disruption of murine Ela2 does not recapitulate neutropenia in mice. Thus, there are no mouse models of SCN. Gfi1 is a transcriptional repressor leukemia oncoprotein involved in HSC maintenance as well as proper lymphoid and myeloid development. Mice lacking Gfi1 have profound neutropenia. We recently described four patients in which Ela2 was intact but mutant for Gfi1. The heterozygous single aminoacid substitutions were found in zinc finger 5 (N382S) and zinc finger 6 (K403R) correlating to either SCN or Non-immune Chronic Idiopathic Neutropenia of Adults (NICINA) respectively. Given that Gfi1 null mice lack neutrophils, and that people with Gfi1 mutations display SCN or NICINA, we asked whether the human mutations when introduced into murine Gfi1 are sufficient to model neutropenia in mice. To this end, we constructed murine Gfi1 cDNAs containing the SCN and NICINA patient mutations, retrovirally overexpressed them in murine Lin- bone marrow cells, then analyzed them by in vitro differentiation assays. Strikingly, cells overexpressing Gfi1-N382S produced no granulocytic colonies (similar to the profound phenotype of SCN). Whereas, the expression of Gfi1-K403R mutation resulted in a moderate reduction in granulocytic colonies (corresponding to the mild phenotype of NICINA). We have constructed a virtual model of Gfi1 zinc finger/DNA interaction to explore the molecular defect engendered by the N382S mutation. At the meeting, we will discuss the molecular basis of the profound phenotype engendered by Gfi1-N382S expression. These data demonstrate for the first time that human neutropenia can be modeled in murine cultures through the introduction of mutations in Gfi1 found in SCN and NICINA patients.

scholarly journals Alteration of zif268 zinc-finger motifs gives rise to non-native zinc-co-ordination sites but preserves wild-type DNA recognition

1998 ◽  
Vol 333 (1) ◽  
pp. 85-90 ◽  
Author(s):  
Andrew GREEN ◽  
Bibudhendra SARKAR
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Fingers ◽  
Dna Recognition ◽  
Dna Interaction ◽  
Wild Type ◽  
Zinc Finger Motifs ◽  
Eukaryotic Gene ◽  
First Time ◽  
The Relationship

Zinc fingers are among the major structural motifs found in proteins that are involved in eukaryotic gene regulation. Many of these zinc-finger domains are involved in DNA binding. This study investigated whether the zinc-co-ordinating (Cys)2(His)2 motif found in the three zinc fingers of zif268 could be replaced by a (Cys)4 motif while still preserving DNA recognition. (Cys)2(His)2-to-(Cys)4 mutations were generated in each of the three zinc fingers of zif268 individually, as well as in fingers 1 and 3, and fingers 2 and 3 together. Whereas finger 1 and finger 3 tolerate the switch, such an alteration in finger 2 renders the polypeptide incapable of DNA recognition. The protein–DNA interaction was examined in greater detail by using a methylation-interference assay. The mutant polypeptides containing the (Cys)4 motif in fingers 1 or 3 recognize DNA in a manner identical to the wild-type protein, suggesting that the (Cys)4 motif appears to give rise to a properly folded finger. Additional results indicate that a zif268 variant containing a (Cys)2(His)(Ala) arrangement in finger 1 is also capable of DNA recognition in a manner identical to the wild-type polypeptide. This appears to be the first time that such alterations, in the context of an intact DNA-binding domain, have still allowed for specific DNA recognition. Taken together, the work presented here enhances our understanding of the relationship between metal ligation and DNA-binding by zinc fingers.

scholarly journals The Plant Zinc Finger Protein ZPT2–2 Has a Unique Mode of DNA Interaction

2001 ◽  
Vol 276 (38) ◽  
pp. 35802-35807 ◽  
Author(s):  
Ken-ichi Yoshioka ◽  
Setsuko Fukushima ◽  
Toshimasa Yamazaki ◽  
Michiteru Yoshida ◽  
Hiroshi Takatsuji
Keyword(s):  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Dna Interaction ◽  
Finger Protein ◽  
Unique Mode

Analysis and Prediction of DNA-Recognition by Zinc Finger Proteins

2011 ◽  
pp. 303-317
Author(s):  
Anita Sarkar ◽  
Sonu Kumar ◽  
Ankita Punetha ◽  
Abhinav Grover ◽  
Durai Sundar
Keyword(s):  
Zinc Finger ◽  
Computational Methods ◽  
Zinc Finger Protein ◽  
Zinc Fingers ◽  
Dna Interaction ◽  
Zinc Finger Proteins ◽  
Specific Target ◽  
Molecular Therapeutics ◽  
Custom Design ◽  
Target Dna

Zinc fingers are the most abundant class of DNA-binding proteins encoded in the eukaryotic genomes. Custom-designed zinc finger proteins attached to various DNA-modifying domains can be used to achieve highly specific genome modification, which has tremendous applications in molecular therapeutics. Analysis of sequence and structure of the zinc finger proteins provides clues for understanding protein-DNA interactions and aid in custom-design of zinc finger proteins with tailor-made specificity. Computational methods for prediction of recognition helices for C2H2 zinc fingers that bind to specific target DNA sites could provide valuable insights for researchers interested in designing specific zinc finger proteins for biological and biomedical applications. In this chapter, we describe the zinc finger protein-DNA interaction patterns, challenges in engineering the recognition-specificity of zinc finger proteins, the computational methods of prediction of proteins that recognize specific target DNA sequence and their applications in molecular therapeutics.

Analysis and Prediction of DNA-Recognition by Zinc Finger Proteins

2013 ◽  
pp. 330-344
Author(s):  
Anita Sarkar ◽  
Sonu Kumar ◽  
Ankita Punetha ◽  
Abhinav Grover ◽  
Durai Sundar
Keyword(s):  
Zinc Finger ◽  
Computational Methods ◽  
Zinc Finger Protein ◽  
Zinc Fingers ◽  
Dna Interaction ◽  
Zinc Finger Proteins ◽  
Specific Target ◽  
Molecular Therapeutics ◽  
Custom Design ◽  
Target Dna

Zinc fingers are the most abundant class of DNA-binding proteins encoded in the eukaryotic genomes. Custom-designed zinc finger proteins attached to various DNA-modifying domains can be used to achieve highly specific genome modification, which has tremendous applications in molecular therapeutics. Analysis of sequence and structure of the zinc finger proteins provides clues for understanding protein-DNA interactions and aid in custom-design of zinc finger proteins with tailor-made specificity. Computational methods for prediction of recognition helices for C2H2 zinc fingers that bind to specific target DNA sites could provide valuable insights for researchers interested in designing specific zinc finger proteins for biological and biomedical applications. In this chapter, we describe the zinc finger protein-DNA interaction patterns, challenges in engineering the recognition-specificity of zinc finger proteins, the computational methods of prediction of proteins that recognize specific target DNA sequence and their applications in molecular therapeutics.

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

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