scholarly journals miR-1279, miR-548j, miR-548m, and miR-548d-5p Binding Sites in CDSs of Paralogous and OrthologousPTPN12,MSH6, andZEB1Genes

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Anatoliy T. Ivashchenko ◽  
Assel S. Issabekova ◽  
Olga A. Berillo
Keyword(s):  
Gene Family ◽  
Mismatch Repair ◽  
Zinc Finger ◽  
Binding Sites ◽  
Animal Species ◽  
Tyrosine Phosphatase ◽  
Nucleotide Sequences ◽  
Orthologous Genes ◽  
Zinc Finger Gene ◽  
Dna Mismatch

OnlyPTPN12, MSH6, andZEB1have significant miR-1279 binding sites among paralogous genes of human tyrosine phosphatase family, DNA mismatch repair family, and zinc finger family, respectively. All miRNA binding sites are located within CDSs of studied mRNAs. Nucleotide sequences of hsa-miR-1279 binding sites with mRNAs of humanPTPN12, MSH6, andZEB1genes encode TKEQYE, EGSSDE, and GEKPYE oligopeptides, respectively. The conservation of miRNA binding sites encoding oligopeptides has been revealed. MRNAs of many paralogs of zinc finger gene family have from 1 to 12 binding sites coding the same GEKPYE hexapeptide. MRNAs ofPTPN12, MSH6, andZEB1orthologous genes from different animal species have binding sites for hsa-miR-1279 which consist of homologous oligonucleotides encoding similar human oligopeptides TKEQYE, EGSSDE, and GEKPYE. MiR-548j, miR-548m, and miR-548d-5p have homologous binding sites in the mRNA ofPTPN12orthologous genes which encode PRTRSC, TEATDI, and STASAT oligopeptides, respectively. All regions of miRNA are important for binding with the mRNA.

Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization

2014 ◽  
Vol 289 (5) ◽  
pp. 855-872 ◽  
Author(s):  
Shengrui Liu ◽  
Muhammad Rehman Gul Khan ◽  
Yongping Li ◽  
Jinzhi Zhang ◽  
Chungen Hu
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Comprehensive Analysis ◽  
Zinc Finger Gene ◽  
Genome Wide

scholarly journals The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e48242 ◽  
Author(s):  
Jianyan Huang ◽  
Xiaobo Zhao ◽  
Xiaoyu Weng ◽  
Lei Wang ◽  
Weibo Xie
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Expression Profiling ◽  
Zinc Finger Gene

Phylogenic analysis revealed an expanded C2H2-homeobox subfamily and expression profiles of C2H2 zinc finger gene family in Verticillium dahliae

Gene ◽  
2015 ◽  
Vol 562 (2) ◽  
pp. 169-179 ◽  
Author(s):  
Dianguang Xiong ◽  
Yonglin Wang ◽  
Chenglin Deng ◽  
Ruowen Hu ◽  
Chengming Tian
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Verticillium Dahliae ◽  
Expression Profiles ◽  
Zinc Finger Gene ◽  
C2h2 Zinc Finger ◽  
Phylogenic Analysis

scholarly journals The properties of Msh2–Msh6 ATP binding mutants suggest a signal amplification mechanism in DNA mismatch repair

2018 ◽  
Vol 293 (47) ◽  
pp. 18055-18070 ◽  
Author(s):  
William J. Graham ◽  
Christopher D. Putnam ◽  
Richard D. Kolodner
Keyword(s):  
Mismatch Repair ◽  
Binding Sites ◽  
Signal Amplification ◽  
Dna Mismatch Repair ◽  
Nucleotide Binding ◽  
Atp Binding ◽  
Dna Mismatch ◽  
Nucleotide Binding Sites ◽  
Sliding Clamp ◽  
Atp Concentration

DNA mismatch repair (MMR) corrects mispaired DNA bases and small insertion/deletion loops generated by DNA replication errors. After binding a mispair, the eukaryotic mispair recognition complex Msh2–Msh6 binds ATP in both of its nucleotide-binding sites, which induces a conformational change resulting in the formation of an Msh2–Msh6 sliding clamp that releases from the mispair and slides freely along the DNA. However, the roles that Msh2–Msh6 sliding clamps play in MMR remain poorly understood. Here, using Saccharomyces cerevisiae, we created Msh2 and Msh6 Walker A nucleotide–binding site mutants that have defects in ATP binding in one or both nucleotide-binding sites of the Msh2–Msh6 heterodimer. We found that these mutations cause a complete MMR defect in vivo. The mutant Msh2–Msh6 complexes exhibited normal mispair recognition and were proficient at recruiting the MMR endonuclease Mlh1–Pms1 to mispaired DNA. At physiological (2.5 mm) ATP concentration, the mutant complexes displayed modest partial defects in supporting MMR in reconstituted Mlh1–Pms1-independent and Mlh1–Pms1-dependent MMR reactions in vitro and in activation of the Mlh1–Pms1 endonuclease and showed a more severe defect at low (0.1 mm) ATP concentration. In contrast, five of the mutants were completely defective and one was mostly defective for sliding clamp formation at high and low ATP concentrations. These findings suggest that mispair-dependent sliding clamp formation triggers binding of additional Msh2–Msh6 complexes and that further recruitment of additional downstream MMR proteins is required for signal amplification of mispair binding during MMR.

scholarly journals Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhicheng Jiao ◽  
Liping Wang ◽  
Huan Du ◽  
Ying Wang ◽  
Weixu Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Medicago Truncatula ◽  
Zinc Finger Gene ◽  
C2h2 Zinc Finger ◽  
Genome Wide ◽  
Genome Wide Study

Genome-wide analysis of the CCCH zinc finger gene family in Medicago truncatula

2013 ◽  
Vol 32 (10) ◽  
pp. 1543-1555 ◽  
Author(s):  
Cuiqin Zhang ◽  
Hongmei Zhang ◽  
Yang Zhao ◽  
Haiyang Jiang ◽  
Suwen Zhu ◽  
...  
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Medicago Truncatula ◽  
Zinc Finger Gene ◽  
Genome Wide Analysis ◽  
Ccch Zinc Finger ◽  
Genome Wide

Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis

2007 ◽  
Vol 65 (4) ◽  
pp. 467-485 ◽  
Author(s):  
Pinky Agarwal ◽  
Rita Arora ◽  
Swatismita Ray ◽  
Ashok K. Singh ◽  
Vijay P. Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Expression Analysis ◽  
Zinc Finger Gene ◽  
C2h2 Zinc Finger ◽  
Genome Wide
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