The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Robert A Mcknight - One of the best experts on this subject based on the ideXlab platform.
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epigenetics intrauterine growth retardation iugr modifies the Histone Code along the rat hepatic igf 1 gene
The FASEB Journal, 2009Co-Authors: Christopher W Callaway, Robert H Lane, Robert A McknightAbstract:Intrauterine growth restriction (IUGR) decreases serum insulin growth factor-1 (IGF-1) levels. IGF-1 is an epigenetically regulated gene that has two promoters, alternative exon 5 splicing, and multiple termination sites. The regulation of gene expression involves the whole gene, as evidenced by the aforementioned IGF-1 paradigm. We hypothesized that IUGR in the rat would affect hepatic IGF-1 expression and alter the epigenetic characteristics of the IGF-1 gene along its length. IUGR was induced through a bilateral uterine artery ligation of the pregnant rat, a well-characterized model of IUGR. Pups from anesthesia and sham-operated dams were used as controls. Real-time RT-PCR and ELISA was used to measure expression at day of life (DOL) 0 and 21. Bisulfite sequencing and chromatin immunoprecipitation (ChIP) quantified IGF-1 epigenetic characteristics. A nontranscribed intergenic control was used for ChIP studies. IUGR decreased hepatic and serum IGF-1. Concurrently, IUGR modified epigenetic characteristics, particularly the Histone Code, along the length of the hepatic IGF-1 gene. Many changes persisted postnatally, and the postnatal effect of IUGR on the Histone Code was gender-specific. We conclude that IUGR modifies epigenetic characteristics of the rat hepatic IGF-1 gene along the length of the whole gene.—Fu, Q., Yu, X., Callaway, C. W., Lane, R. H., McKnight, R. A. Epigenetics: intrauterine growth retardation (IUGR) modifies the Histone Code along the rat hepatic IGF-1 gene.
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epigenetics intrauterine growth retardation iugr modifies the Histone Code along the rat hepatic igf 1 gene
The FASEB Journal, 2009Co-Authors: Christopher W Callaway, Robert H Lane, Robert A McknightAbstract:Intrauterine growth restriction (IUGR) decreases serum insulin growth factor-1 (IGF-1) levels. IGF-1 is an epigenetically regulated gene that has two promoters, alternative exon 5 splicing, and multiple termination sites. The regulation of gene expression involves the whole gene, as evidenced by the aforementioned IGF-1 paradigm. We hypothesized that IUGR in the rat would affect hepatic IGF-1 expression and alter the epigenetic characteristics of the IGF-1 gene along its length. IUGR was induced through a bilateral uterine artery ligation of the pregnant rat, a well-characterized model of IUGR. Pups from anesthesia and sham-operated dams were used as controls. Real-time RT-PCR and ELISA was used to measure expression at day of life (DOL) 0 and 21. Bisulfite sequencing and chromatin immunoprecipitation (ChIP) quantified IGF-1 epigenetic characteristics. A nontranscribed intergenic control was used for ChIP studies. IUGR decreased hepatic and serum IGF-1. Concurrently, IUGR modified epigenetic characteristics, particularly the Histone Code, along the length of the hepatic IGF-1 gene. Many changes persisted postnatally, and the postnatal effect of IUGR on the Histone Code was gender-specific. We conclude that IUGR modifies epigenetic characteristics of the rat hepatic IGF-1 gene along the length of the whole gene.
Judd C Rice - One of the best experts on this subject based on the ideXlab platform.
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the pr set7 binding domain of riz1 is required for the h4k20me1 h3k9me1 trans tail Histone Code and riz1 tumor suppressor function
Nucleic Acids Research, 2014Co-Authors: Lauren M Congdon, Jennifer K Sims, Creighton T Tuzon, Judd C RiceAbstract:PR-Set7/Set8/KMT5a is the sole Histone H4 lysine 20 monomethyltransferase (H4K20me1) in metazoans and is essential for proper cell division and genomic stability. We unexpectedly discovered that normal cellular levels of monomethylated Histone H3 lysine 9 (H3K9me1) were also dependent on PR-Set7, but independent of its catalytic activity. This observation suggested that PR-Set7 interacts with an H3K9 monomethyltransferase to establish the previously reported H4K20me1-H3K9me1 trans-tail 'Histone Code'. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. The PR-Set7 binding domain was required for Riz1 nuclear localization and maintenance of the H4K20me1-H3K9me1 trans-tail 'Histone Code'. Although Riz1 can function as a repressor, Riz1/H3K9me1 was dispensable for the repression of genes regulated by PR-Set7/H4K20me1. Frameshift mutations resulting in a truncated Riz1 incapable of binding PR-Set7 occur frequently in various aggressive cancers. In these cancer cells, expression of wild-type Riz1 restored tumor suppression by decreasing proliferation and increasing apoptosis. These phenotypes were not observed in cells expressing either the Riz1 PR/SET domain or PR-Set7 binding domain indicating that Riz1 methyltransferase activity and PR-Set7 binding domain are both essential for Riz1 tumor suppressor function.
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pr set7 establishes a repressive trans tail Histone Code that regulates differentiation
Molecular and Cellular Biology, 2008Co-Authors: Jennifer K Sims, Judd C RiceAbstract:Posttranslational modifications of the DNA-associated Histone proteins play fundamental roles in eukaryotic transcriptional regulation. We previously discovered a novel trans-tail Histone Code involving monomethylated Histone H4 lysine 20 (H4K20) and H3 lysine 9 (H3K9); however, the mechanisms that establish this Code and its function in transcription were unknown. In this report, we demonstrate that H3K9 monomethylation is dependent upon the PR-Set7 H4K20 monomethyltransferase but independent of its catalytic function, indicating that PR-Set7 recruits an H3K9 monomethyltransferase to establish the trans-tail Histone Code. We determined that this Histone Code is involved in a transcriptional regulatory pathway in vivo whereby monomethylated H4K20 binds the L3MBTL1 repressor protein to repress specific genes, including RUNX1, a critical regulator of hematopoietic differentiation. The selective loss of monomethylated H4K20 at the RUNX1 promoter resulted in the displacement of L3MBTL1 and a concomitant increase in RUNX1 transcription. Importantly, the lack of monomethylated H4K20 in the human K562 multipotent cell line was specifically associated with spontaneous megakaryocytic differentiation, in part, by activating RUNX1. Our findings demonstrate that this newly described repression pathway is required for regulating proper megakaryopoiesis and suggests that it is likely to function similarly in other multipotent cell types to regulate specific differentiation pathways.
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a trans tail Histone Code defined by monomethylated h4 lys 20 and h3 lys 9 demarcates distinct regions of silent chromatin
Journal of Biological Chemistry, 2006Co-Authors: Jennifer K Sims, Sabrina I Houston, Tanya Magazinnik, Judd C RiceAbstract:The specific post-translational modifications of the Histone proteins are associated with specific DNA-templated processes, such as transcriptional activation or repression. To investigate the biological role(s) of Histone H4 lysine 20 (H4 Lys-20) methylation, we created a novel panel of antibodies that specifically detected mono-, di-, or trimethylated H4 Lys-20. We report that the different methylated forms of H4 Lys-20 are compartmentalized within visually distinct, transcriptionally silent regions in the mammalian nucleus. Interestingly, direct comparison of methylated H4 Lys-20 with the different methylated states of Histone H3 lysine 9 (H3 Lys-9) revealed significant overlap and exclusion between the specific groups of methyl modifications. Trimethylated H4 Lys-20 and H3 Lys-9 were both selectively enriched within pericentric heterochromatin. Similarly, monomethylated H4 Lys-20 and H3 Lys-9 partitioned together and the dimethylated forms partitioned together within the chromosome arms; however, the mono- and dimethylated modifications were virtually exclusive. These findings strongly suggest that the combinatorial presence or absence of the different methylated states of H4 Lys-20 and H3 Lys-9 define particular types of silent chromatin. Consistent with this, detailed analysis of monomethylated H4 Lys-20 and H3 Lys-9 revealed that both were preferentially and selectively enriched within the same nucleosome particle in vivo. Collectively, these findings define a novel trans-tail Histone Code involving monomethylated H4 Lys-20 and H3 Lys-9 that act cooperatively to mark distinct regions of silent chromatin within the mammalian epigenome.
Christopher W Callaway - One of the best experts on this subject based on the ideXlab platform.
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epigenetics intrauterine growth retardation iugr modifies the Histone Code along the rat hepatic igf 1 gene
The FASEB Journal, 2009Co-Authors: Christopher W Callaway, Robert H Lane, Robert A McknightAbstract:Intrauterine growth restriction (IUGR) decreases serum insulin growth factor-1 (IGF-1) levels. IGF-1 is an epigenetically regulated gene that has two promoters, alternative exon 5 splicing, and multiple termination sites. The regulation of gene expression involves the whole gene, as evidenced by the aforementioned IGF-1 paradigm. We hypothesized that IUGR in the rat would affect hepatic IGF-1 expression and alter the epigenetic characteristics of the IGF-1 gene along its length. IUGR was induced through a bilateral uterine artery ligation of the pregnant rat, a well-characterized model of IUGR. Pups from anesthesia and sham-operated dams were used as controls. Real-time RT-PCR and ELISA was used to measure expression at day of life (DOL) 0 and 21. Bisulfite sequencing and chromatin immunoprecipitation (ChIP) quantified IGF-1 epigenetic characteristics. A nontranscribed intergenic control was used for ChIP studies. IUGR decreased hepatic and serum IGF-1. Concurrently, IUGR modified epigenetic characteristics, particularly the Histone Code, along the length of the hepatic IGF-1 gene. Many changes persisted postnatally, and the postnatal effect of IUGR on the Histone Code was gender-specific. We conclude that IUGR modifies epigenetic characteristics of the rat hepatic IGF-1 gene along the length of the whole gene.—Fu, Q., Yu, X., Callaway, C. W., Lane, R. H., McKnight, R. A. Epigenetics: intrauterine growth retardation (IUGR) modifies the Histone Code along the rat hepatic IGF-1 gene.
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epigenetics intrauterine growth retardation iugr modifies the Histone Code along the rat hepatic igf 1 gene
The FASEB Journal, 2009Co-Authors: Christopher W Callaway, Robert H Lane, Robert A McknightAbstract:Intrauterine growth restriction (IUGR) decreases serum insulin growth factor-1 (IGF-1) levels. IGF-1 is an epigenetically regulated gene that has two promoters, alternative exon 5 splicing, and multiple termination sites. The regulation of gene expression involves the whole gene, as evidenced by the aforementioned IGF-1 paradigm. We hypothesized that IUGR in the rat would affect hepatic IGF-1 expression and alter the epigenetic characteristics of the IGF-1 gene along its length. IUGR was induced through a bilateral uterine artery ligation of the pregnant rat, a well-characterized model of IUGR. Pups from anesthesia and sham-operated dams were used as controls. Real-time RT-PCR and ELISA was used to measure expression at day of life (DOL) 0 and 21. Bisulfite sequencing and chromatin immunoprecipitation (ChIP) quantified IGF-1 epigenetic characteristics. A nontranscribed intergenic control was used for ChIP studies. IUGR decreased hepatic and serum IGF-1. Concurrently, IUGR modified epigenetic characteristics, particularly the Histone Code, along the length of the hepatic IGF-1 gene. Many changes persisted postnatally, and the postnatal effect of IUGR on the Histone Code was gender-specific. We conclude that IUGR modifies epigenetic characteristics of the rat hepatic IGF-1 gene along the length of the whole gene.
Benjamin A. Garcia - One of the best experts on this subject based on the ideXlab platform.
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recent achievements in characterizing the Histone Code and approaches to integrating epigenomics and systems biology
Methods in Enzymology, 2017Co-Authors: Kevin A Janssen, Simone Sidoli, Benjamin A. GarciaAbstract:Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), Histone proteins, and other nuclear proteins. Due to the highly complex nature of the Histone Code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial Histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing Histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of Histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for Histone analysis at its state of the art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating Histone MS results with genomics and proteomics datasets.
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properly reading the Histone Code by ms based proteomics
Proteomics, 2015Co-Authors: Simone Sidoli, Benjamin A. GarciaAbstract:Histone proteins are essential elements for DNA packaging. Their PTMs contribute in modeling chromatin structure and recruiting enzymes involved in gene regulation, DNA repair, and chromosome condensation. This fundamental aspect, together with the fact that Histone PTMs can be epigenetically inherited through cell generations, enlightens their importance in chromatin biology, and the consequent necessity of having biochemical techniques for their characterization. Nanoflow LC coupled to MS (nanoLC-MS) is the strategy of choice for protein PTM accurate quantification. However, Histones require adjustments to the digestion protocol such as lysine derivatization to obtain suitable peptides for the analysis. nanoLC-MS has numerous advantages, spanning from high confidence identification to possibility of high throughput analyses, but the peculiarity of the Histone preparation protocol requires continuous monitoring with the most modern available technologies to question its reliability. The work of Meert et al. (Proteomics 2015, 15, 2966-2971) establishes which protocols lead to either incomplete derivatization or derivatization of undesired amino acid residues using a combination of high resolution MS and bioinformatics tools for the alignment and the characterization of nanoLC-MS runs. As well, they identify a number of side reactions that could be potentially misinterpreted as biological PTMs.
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breaking the Histone Code with quantitative mass spectrometry
Expert Review of Proteomics, 2011Co-Authors: Lauramae P Britton, Michelle Gonzalescope, Barry M Zee, Benjamin A. GarciaAbstract:Histone post-translational modifications (PTMs) comprise one of the most intricate nuclear signaling networks that govern gene expression in a long-term and dynamic fashion. These PTMs are considered to be ‘epigenetic’ or heritable from one cell generation to the next and help establish genomic expression patterns. While much of the analyses of Histones have historically been performed using site-specific antibodies, these methods are replete with technical obstacles (i.e., cross-reactivity and epitope occlusion). Mass spectrometry-based proteomics has begun to play a significant role in the interrogation of Histone PTMs, revealing many new aspects of these modifications that cannot be easily determined with standard biological approaches. Here, we review the accomplishments of mass spectrometry in the Histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists.
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The significance, development and progress of high-throughput combinatorial Histone Code analysis
Cellular and Molecular Life Sciences, 2010Co-Authors: Nicolas L. Young, Peter A. Dimaggio, Benjamin A. GarciaAbstract:The physiological state of eukaryotic DNA is chromatin. Nucleosomes, which consist of DNA in complex with Histones, are the fundamental unit of chromatin. The post-translational modifications (PTMs) of Histones play a critical role in the control of gene transcription, epigenetics and other DNA-templated processes. It has been known for several years that these PTMs function in concert to allow for the storage and transduction of highly specific signals through combinations of modifications. This Code, the combinatorial Histone Code, functions much like a bar Code or combination lock providing the potential for massive information content. The capacity to directly measure these combinatorial Histone Codes has mostly been laborious and challenging, thus limiting efforts often to one or two samples. Recently, progress has been made in determining such information quickly, quantitatively and sensitively. Here we review both the historical and recent progress toward routine and rapid combinatorial Histone Code analysis.
Joao Antonio Pegas Henriques - One of the best experts on this subject based on the ideXlab platform.
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what Histone Code for dna repair
Mutation Research-reviews in Mutation Research, 2008Co-Authors: Alexandre E Escargueil, Daniele G Soares, Mirian Salvador, Annette K Larsen, Joao Antonio Pegas HenriquesAbstract:Chromatin structure plays a key role in most processes involving DNA metabolism. Chromatin modifications implicated in transcriptional regulation are relatively well characterized and are thought to be the result of a Code on the Histone proteins (Histone Code). This Code, involving phosphorylation, ubiquitylation, sumoylation, acetylation and methylation, is believed to regulate chromatin accessibility either by disrupting chromatin contacts or by recruiting non-Histone proteins to chromatin. Recent evidences suggest that such mechanisms are also involved in DNA damage detection and DNA repair. One of the most well-characterized modifications is caused by the formation of DNA double strand breaks (DSBs), resulting in phosphorylation of Histone H2AX (the so-called γ-H2AX) on the chromatin surrounding the DNA lesion. It is generally believed that Histone H2AX phosphorylation is required for the concentration and stabilization of DNA repair proteins to the damaged chromatin. The phosphorylation of this Histone seems to play a role in both non-homologous end-joining (NHEJ) and homologous recombination (HR) repair pathways. However, the choice of the repair pathway might depend on or induce additional post-translational modifications affecting other Histone proteins necessary to the completion of the entire DNA repair process. Interestingly, even in the absence of DSBs, Histone modifications occur. Indeed, following UV-exposure, Histone acetylation takes place and is believed to facilitate the nucleotide excision repair (NER) process by promoting chromatin accessibility to the repair factors. This review focuses on recent data characterizing the function of Histone modification in various repair processes and discusses if the combination of such modifications can be the trademark of a specific DNA repair pathway.