The Experts below are selected from a list of 13248 Experts worldwide ranked by ideXlab platform
Janos Zempleni - One of the best experts on this subject based on the ideXlab platform.
-
The Role of Histone H4 Biotinylation in the Structure of Nucleosomes
PloS one, 2011Co-Authors: Nina A. Filenko, Yousef I. Hassan, Janos Zempleni, Gloria E. O. Borgstahl, Carol Kolar, John T. West, S. Abbie Smith, Yuri L. LyubchenkoAbstract:Background Post-translational modifications of histones play important roles in regulating nucleosome structure and gene transcription. It has been shown that Biotinylation of histone H4 at lysine-12 in histone H4 (K12Bio-H4) is associated with repression of a number of genes. We hypothesized that Biotinylation modifies the physical structure of nucleosomes, and that biotin-induced conformational changes contribute to gene silencing associated with histone Biotinylation. Methodology/Principal Findings To test this hypothesis we used atomic force microscopy to directly analyze structures of nucleosomes formed with biotin-modified and non-modified H4. The analysis of the AFM images revealed a 13% increase in the length of DNA wrapped around the histone core in nucleosomes with biotinylated H4. This statistically significant (p
-
Novel histone Biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes
The Journal of nutritional biochemistry, 2010Co-Authors: Valerie Pestinger, Subhashinee S.k. Wijeratne, Rocio Rodriguez-melendez, Janos ZempleniAbstract:Covalent histone modifications play crucial roles in chromatin structure and genome stability. We previously reported Biotinylation of lysine (K) residues in histones H2A, H3 and H4 by holocarboxylase synthetase and demonstrated that K12-biotinylated histone H4 (H4K12bio) is enriched in repeat regions and participates in gene repression. The biological functions of Biotinylation marks other than H4K12bio are poorly understood. Here, novel Biotinylation site-specific antibodies against H3K9bio, H3K18bio and H4K8bio were used in chromatin immunoprecipitation studies to obtain first insights into possible biological functions of these marks. Chromatin immunoprecipitation assays were conducted in human primary fibroblasts and Jurkat lymphoblastoma cells, and revealed that H3K9bio, H3K18bio and H4K8bio are enriched in repeat regions such as pericentromeric alpha satellite repeats and long-terminal repeats while being depleted in transcriptionally active promoters in euchromatin. Transcriptional stimulation of the repressed interleukin-2 promoter triggered a rapid depletion of histone Biotinylation marks at this locus in Jurkat cells, which was paralleled by an increase in interleukin-2 mRNA. Importantly, the enrichment of H3K9bio, H3K18bio and H4K8bio at genomic loci depended on the concentration of biotin in culture media at nutritionally relevant levels, suggesting a novel mechanism of gene regulation by biotin.
-
Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate Biotinylation of K9 and K18.
The Journal of nutritional biochemistry, 2010Co-Authors: Baolong Bao, Yousef I. Hassan, Valerie Pestinger, Gloria E. O. Borgstahl, Carol Kolar, Janos ZempleniAbstract:Holocarboxylase synthetase (HCS) mediates the binding of biotin to lysine (K) residues in histones H2A, H3 and H4; HCS knockdown disturbs gene regulation and decreases stress resistance and lifespan in eukaryotes. We tested the hypothesis that HCS interacts physically with histone H3 for subsequent Biotinylation. Co-immunoprecipitation experiments were conducted and provided evidence that HCS co-localizes with histone H3 in human cells; physical interactions between HCS and H3 were confirmed using limited proteolysis assays. Yeast two-hybrid (Y2H) studies revealed that the N-terminal and C-terminal domains in HCS participate in H3 binding. Recombinant human HCS was produced and exhibited biological activity, as evidenced by Biotinylation of its known substrate, recombinant p67. Recombinant histone H3.2 and synthetic H3-based peptides were also good targets for Biotinylation by recombinant HCS (rHCS) in vitro, based on tracing histone-bound biotin with [(3)H]biotin, streptavidin and anti-biotin antibody. Biotinylation site-specific antibodies were generated and revealed that both K9 and K18 in H3 were biotinylated by HCS. Collectively, these studies provide conclusive evidence that HCS interacts directly with histone H3, causing Biotinylation of K9 and K18. We speculate that the targeting of HCS to distinct regions in human chromatin is mediated by DNA sequence, biotin, RNA, epigenetic marks or chromatin proteins.
-
Repression of Transposable Elements by Histone Biotinylation
The Journal of nutrition, 2009Co-Authors: Janos Zempleni, Yap Ching Chew, Baolong Bao, Valerie Pestinger, Subhashinee S.k. WijeratneAbstract:Transposable elements constitute >40% of the human genome; transposition of these elements increases genome instability and cancer risk. Epigenetic mechanisms are important for transcriptional repression of retrotransposons, thereby preventing transposition events. Binding of biotin to histones, mediated by holocarboxylase synthetase (HCS), is a novel histone mark that plays a role in gene regulation. Here, we review recent findings that Biotinylation of lysine-12 in histone H4 (H4K12bio) is an epigenetic mechanism to repress long terminal repeat (LTR) retrotransposons in human and mouse cell lines, primary cells from human adults, and in Drosophila melanogaster. Further, evidence is summarized that supports a causal relationship between the repression of LTR in H4K12bio-depleted cells and increased production of viral particles, increased frequency of retrotransposition events, and increased frequency of chromosomal abnormalities in mammals and Drosophila. Although HCS interacts physically with histones H3 and H4, the mechanism responsible for targeting HCS to retrotransposons to mediate histone Biotinylation is uncertain. We hypothesize that HCS binds specifically to genomic regions rich in methylated cytosines and catalyzes increased Biotinylation of histone H4 at lysine-12. Further, we hypothesize that this Biotinylation promotes the subsequent dimethylation of lysine-9 in histone H3, resulting in an overall synergistic effect of 3 diet-dependent covalent modifications of histones in the repression of LTR.
-
A novel, enigmatic histone modification: Biotinylation of histones by holocarboxylase synthetase
Nutrition Reviews, 2008Co-Authors: Yousef I. Hassan, Janos ZempleniAbstract:Holocarboxylase synthetase catalyzes the covalent binding of biotin to histones in humans and other eukaryotes. Eleven Biotinylation sites have been identified in histones H2A, H3, and H4. K12-biotinylated histone H4 is enriched in heterochromatin, repeat regions, and plays a role in gene repression. About 30% of the histone H4 molecules are biotinylated at K12 in histone H4 in human fibroblast telomeres. The abundance of biotinylated histones at distinct genomic loci depends on biotin availability. Decreased histone Biotinylation decreases life span and stress resistance in Drosophila. Low enrichment of biotinylated histones at transposable elements impairs repression of these elements.
Anne-claude Gingras - One of the best experts on this subject based on the ideXlab platform.
-
a versatile lentiviral delivery toolkit for proximity dependent Biotinylation in diverse cell types
Molecular & Cellular Proteomics, 2018Co-Authors: Payman Samavarchitehrani, Hala Abdouni, Reuben Samson, Anne-claude GingrasAbstract:Proximity-dependent Biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein eNAbles the covalent Biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that eNAble the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent Biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.
-
A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types *
Molecular & cellular proteomics : MCP, 2018Co-Authors: Payman Samavarchi-tehrani, Hala Abdouni, Reuben Samson, Anne-claude GingrasAbstract:Proximity-dependent Biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein eNAbles the covalent Biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that eNAble the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent Biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.
Shao Q. Yao - One of the best experts on this subject based on the ideXlab platform.
-
Improving the intein-mediated, site-specific protein Biotinylation strategies both in vitro and in vivo.
Bioorganic & medicinal chemistry letters, 2004Co-Authors: Lay Pheng Tan, Rina Y. P. Lue, Grace Y. J. Chen, Shao Q. YaoAbstract:One of the critical issues in the generation of a protein microarray lies in the choice of immobilization strategies, which ensure proteins are adhered to the glass surface while properly retaining their native biological activities. We previously developed intein-mediated strategies for protein Biotinylation and site-specific protein microarray generation. Herein, we report new findings of these strategies, which improve the Biotinylation efficiency of proteins by up to 10-folds.
-
Versatile protein Biotinylation strategies for potential high-throughput proteomics
Journal of the American Chemical Society, 2004Co-Authors: Rina Y. P. Lue, Grace Y. J. Chen, Qing Zhu, Shao Q. YaoAbstract:We present intein-mediated approaches for efficient Biotinylation of proteins site-specifically. The reactive C-terminal thioester generated from intein-assisted protein splicing (either in vitro or in live cells) served as an attractive and exclusive site for attaching cysteine-containing biotin. Using these novel Biotinylation strategies, we were able to efficiently biotinylate many proteins from different biological sources in a potentially high-throughput, high-content fashion. Some of these proteins were subsequently immobilized, in a very simple manner, onto different avidin-functionalized solid surfaces for applications such as protein microarray and surface plasmon resonance (SPR) spectroscopy, highlighting the numerous advantages of using biotin over other tags (e.g., GST, His-tag, etc.) as the method of choice in protein purification/immobilization. In addition, our intein-mediated strategies provided critical advantages over other protein Biotinylation strategies in a number of ways. For the fi...
Chienchia Wang - One of the best experts on this subject based on the ideXlab platform.
-
modulating the structure and function of an aminoacyl trna synthetase cofactor by Biotinylation
Journal of Biological Chemistry, 2016Co-Authors: Chihyao Chang, Chiapei Chang, Shruti Chakraborty, Shaowin Wang, Yikuan Tseng, Chienchia WangAbstract:Abstract Arc1p is a yeast-specific tRNA-binding protein that forms a ternary complex with glutamyl-tRNA synthetase (GluRSc) and methionyl-tRNA synthetase (MetRS) in the cytoplasm to regulate their catalytic activities and subcellular distributions. Despite Arc1p not being involved in any known biotin-dependent reaction, it is a natural target of biotin modification. Results presented herein show that biotin modification had no obvious effect on Arc1p's growth-supporting activity, subcellular distribution, tRNA binding, or interactions with GluRSc and MetRS. Nevertheless, Biotinylation of Arc1p was temperature dependent; raising the growth temperature from 30oC to 37oC drastically reduced its Biotinylation level. As a result, Arc1p purified from a yeast culture that had been grown overnight at 37oC was essentially biotin free. Non-biotinylated Arc1p was more heat stable, more flexible in structure, and more effective than its biotinylated counterpart in promoting glutamylation activity of the otherwise inactive GluRSc at 37oC in vitro. Our study suggests that the structure and function of Arc1p can be modulated via Biotinylation in response to temperature changes.
-
modulating the structure and function of an aminoacyl trna synthetase cofactor by Biotinylation
Journal of Biological Chemistry, 2016Co-Authors: Chihyao Chang, Chiapei Chang, Shruti Chakraborty, Shaowin Wang, Yikuan Tseng, Chienchia WangAbstract:Arc1p is a yeast-specific tRNA-binding protein that forms a ternary complex with glutamyl-tRNA synthetase (GluRSc) and methionyl-tRNA synthetase (MetRS) in the cytoplasm to regulate their catalytic activities and subcellular distributions. Despite Arc1p not being involved in any known biotin-dependent reaction, it is a natural target of biotin modification. Results presented herein show that biotin modification had no obvious effect on the growth-supporting activity, subcellular distribution, tRNA binding, or interactions of Arc1p with GluRSc and MetRS. Nevertheless, Biotinylation of Arc1p was temperature dependent; raising the growth temperature from 30 to 37 °C drastically reduced its Biotinylation level. As a result, Arc1p purified from a yeast culture that had been grown overnight at 37 °C was essentially biotin free. Non-biotinylated Arc1p was more heat stable, more flexible in structure, and more effective than its biotinylated counterpart in promoting glutamylation activity of the otherwise inactive GluRSc at 37 °C in vitro. Our study suggests that the structure and function of Arc1p can be modulated via Biotinylation in response to temperature changes.
Reuben Samson - One of the best experts on this subject based on the ideXlab platform.
-
a versatile lentiviral delivery toolkit for proximity dependent Biotinylation in diverse cell types
Molecular & Cellular Proteomics, 2018Co-Authors: Payman Samavarchitehrani, Hala Abdouni, Reuben Samson, Anne-claude GingrasAbstract:Proximity-dependent Biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein eNAbles the covalent Biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that eNAble the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent Biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.
-
A Versatile Lentiviral Delivery Toolkit for Proximity-dependent Biotinylation in Diverse Cell Types *
Molecular & cellular proteomics : MCP, 2018Co-Authors: Payman Samavarchi-tehrani, Hala Abdouni, Reuben Samson, Anne-claude GingrasAbstract:Proximity-dependent Biotinylation strategies have emerged as powerful tools to characterize the subcellular context of proteins in living cells. The popular BioID approach employs an abortive E. coli biotin ligase mutant (R118G; denoted as BirA*), which when fused to a bait protein eNAbles the covalent Biotinylation of endogenous proximal polypeptides. This approach has been mainly applied to the study of protein proximity in immortalized mammalian cell lines. To expand the application space of BioID, here we describe a set of lentiviral vectors that eNAble the inducible expression of BirA*-tagged bait fusion proteins for performing proximity-dependent Biotinylation in diverse experimental systems. We benchmark this highly adaptable toolkit across immortalized and primary cell systems, demonstrating the ease, versatility and robustness of the system. We also provide guidelines to perform BioID using these reagents.