The Experts below are selected from a list of 2022 Experts worldwide ranked by ideXlab platform
Philippe Arnaud - One of the best experts on this subject based on the ideXlab platform.
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an annotated list of Bivalent Chromatin regions in human es cells a new tool for cancer epigenetic research
Oncotarget, 2017Co-Authors: Franck Court, Philippe ArnaudAbstract:// Franck Court 1, 2, 3 , Philippe Arnaud 1, 2, 3 1 CNRS-UMR 6293, Clermont-Ferrand, 63001, France 2 INSERM-U1103, Clermont-Ferrand, 63001, France 3 Universite Clermont Auvergne, GReD Laboratory, Clermont-Ferrand, 63000, France Correspondence to: Philippe Arnaud, email: philippe.arnaud@udamail.fr Franck Court, email: franck.court1@udamail.fr Keywords: cancer epigenetics, Bivalent Chromatin, DNA methylation, human stem cell Chromatin signature Received: September 13, 2016 Accepted: November 23, 2016 Published: December 01, 2016 ABSTRACT CpG islands (CGI) marked by Bivalent Chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be determined. To address this issue we developed a user-friendly approach to integrate the stem cell Chromatin signature in customized DNA methylation analyses. We used publicly available ChIP-sequencing datasets of several human embryonic stem cell (hESC) lines to determine the extent of Bivalent Chromatin genome-wide. We then created annotated lists of high-confidence Bivalent, H3K4me3-only and H3K27me3-only Chromatin regions. The main features of Bivalent regions included localization in CGI/promoters, depletion in retroelements and enrichment in specific histone modifications, including the poorly characterized H3K23me2 mark. Moreover, Bivalent promoters could be classified in three clusters based on PRC2 and PolII complexes occupancy. Genes with Bivalent promoters of the PRC2-defined cluster displayed the lowest expression upon differentiation. As proof-of-concept, we assessed the DNA methylation pattern of eight types of tumors and confirmed that aberrant cancer-associated DNA hypermethylation preferentially targets CGI characterized by Bivalent Chromatin in hESCs. We also found that such aberrant DNA hypermethylation affected particularly Bivalent CGI/promoters associated with genes that tend to remain repressed upon differentiation. Strikingly, Bivalent CGI were the most affected by aberrant DNA hypermethylation in both CpG Island Methylator Phenotype-positive (CIMP+) and CIMP-negative tumors, suggesting that, besides transcriptional silencing in the pre-tumorigenic cells, the Bivalent Chromatin signature in hESCs is a key determinant of the instructive program for aberrant DNA methylation.
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An annotated list of Bivalent Chromatin regions in human ES cells: a new tool for cancer epigenetic research
Oncotarget, 2017Co-Authors: Franck Court, Philippe ArnaudAbstract:CpG islands (CGI) marked by Bivalent Chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be determined. To address this issue we developed a user-friendly approach to integrate the stem cell Chromatin signature in customized DNA methylation analyses. We used publicly available ChIP-sequencing datasets of several human embryonic stem cell (hESC) lines to determine the extent of Bivalent Chromatin genome-wide. We then created annotated lists of high-confidence Bivalent, H3K4me3-only and H3K27me3-only Chromatin regions. The main features of Bivalent regions included localization in CGI/promoters, depletion in retroelements and enrichment in specific histone modifications, including the poorly characterized H3K23me2 mark. Moreover, Bivalent promoters could be classified in three clusters based on PRC2 and PolII complexes occupancy. Genes with Bivalent promoters of the PRC2-defined cluster displayed the lowest expression upon differentiation. As proof-of-concept, we assessed the DNA methylation pattern of eight types of tumors and confirmed that aberrant cancer-associated DNA hypermethylation preferentially targets CGI characterized by Bivalent Chromatin in hESCs. We also found that such aberrant DNA hypermethylation affected particularly Bivalent CGI/promoters associated with genes that tend to remain repressed upon differentiation. Strikingly, Bivalent CGI were the most affected by aberrant DNA hypermethylation in both CpG Island Methylator Phenotype-positive (CIMP+) and CIMP-negative tumors, suggesting that, besides transcriptional silencing in the pre-tumorigenic cells, the Bivalent Chromatin signature in hESCs is a key determinant of the instructive program for aberrant DNA methylation.
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ring1b and suv39h1 delineate distinct Chromatin states at Bivalent genes during early mouse lineage commitment
Development, 2010Co-Authors: Olivia Alder, Philippe Arnaud, Fabrice Lavial, Anne Helness, Emily Brookes, Sandra Pinho, Anil Chandrashekran, Ana Pombo, Laura P Oneill, Veronique AzuaraAbstract:Pluripotent cells develop within the inner cell mass of blastocysts, a mosaic of cells surrounded by an extra-embryonic layer, the trophectoderm. We show that a set of somatic lineage regulators (including Hox, Gata and Sox factors) that carry Bivalent Chromatin enriched in H3K27me3 and H3K4me2 are selectively targeted by Suv39h1-mediated H3K9me3 and de novo DNA methylation in extra-embryonic versus embryonic (pluripotent) lineages, as assessed both in blastocyst-derived stem cells and in vivo. This stably repressed state is linked with a loss of gene priming for transcription through the exclusion of PRC1 (Ring1B) and RNA polymerase II complexes at Bivalent, lineage-inappropriate genes upon trophoblast lineage commitment. Collectively, our results suggest a mutually exclusive role for Ring1B and Suv39h1 in regulating distinct Chromatin states at key developmental genes and propose a novel mechanism by which lineage specification can be reinforced during early development.
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reciprocal imprinting of human grb10 in placental trophoblast and brain evolutionary conservation of reversed allelic expression
Human Molecular Genetics, 2009Co-Authors: David Monk, Robert Feil, Philippe Arnaud, Jennifer M Frost, Frank Hills, Philip Stanier, Gudrun E MooreAbstract:Genomic imprinting may have evolved not only to regulate fetal growth and development, but also behaviour. The mouse Grb10 gene provides a remarkable model to explore this idea because it shows paternal expression in brain, whereas in the placenta and most other embryonic tissues, expression is from the maternal allele. To assess the biological relevance of this reciprocal pattern of imprinting, we explored its conservation in humans. As in mice, we find the human GRB10 gene to be paternally expressed in brain. Maternal allele-specific expression is conserved only in the placental villous trophoblasts, an essential part of the placenta involved in nutrient transfer. All other fetal tissues tested showed equal expression from both alleles. These data suggest that the maternal GRB10 expression in placenta is evolutionarily important, presumably in the control of fetal growth. As in the mouse, the maternal transcripts originate from several kilobases upstream of the imprinting control region (ICR) of the domain, from a promoter region at which we find no allelic Chromatin differences. The brain-specific paternal expression from the ICR shows mechanistic similarities with the mouse as well. This conserved CpG island is DNA-methylated on the maternal allele and is marked on the paternal allele by developmentally regulated Bivalent Chromatin, with the presence of both H3 lysine-4 and H3 lysine-27 methylation. The strong conservation of the opposite allelic expression in placenta versus brain supports the hypothesis that GRB10 imprinting evolved to mediate diverse roles in mammalian growth and behaviour.
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A mono-allelic Bivalent Chromatin domain controls tissue-specific imprinting at Grb10.
EMBO Journal, 2008Co-Authors: Lionel Sanz, Stormy Chamberlain, Jean-charles Sabourin, Amandine Henckel, Terry Magnuson, Jean-philippe Hugnot, Robert Feil, Philippe ArnaudAbstract:Genomic imprinting is a developmental mechanism that mediates parent-of-origin-specific expression in a subset of genes. How the tissue specificity of imprinted gene expression is controlled remains poorly understood. As a model to address this question, we studied Grb10, a gene that displays brain-specific expression from the paternal chromosome. Here, we show in the mouse that the paternal promoter region is marked by allelic Bivalent Chromatin enriched in both H3K4me2 and H3K27me3, from early embryonic stages onwards. This is maintained in all somatic tissues, but brain. The Bivalent domain is resolved upon neural commitment, during the developmental window in which paternal expression is activated. Our data indicate that Bivalent Chromatin, in combination with neuronal factors, controls the paternal expression of Grb10 in brain. This finding highlights a novel mechanism to control tissue-specific imprinting.
Tamar Schlick - One of the best experts on this subject based on the ideXlab platform.
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Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes.
Biophysical journal, 2019Co-Authors: Christopher G. Myers, Donald E. Olins, Ada L. Olins, Tamar SchlickAbstract:Interactions of Chromatin with Bivalent immunoglobin nucleosome-binding antibodies and their monovalent (papain-derived) antigen-binding fragment analogs are useful probes for examining Chromatin conformational states. To help interpret antibody-Chromatin interactions and explore how antibodies might compete for interactions with Chromatin components, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale Chromatin model. We analyze interactions and fiber structures for the antibody-Chromatin complexes in open and condensed Chromatin, with and without H1 linker histone (LH). Despite minimal and transient interactions at physiological salt, we capture significant differences in antibody-Chromatin complex configurations in open fibers, with more intense interactions between the Bivalent antibody and Chromatin compared to monovalent antigen-binding fragments. For these open Chromatin fiber morphologies, antibody binding to histone tails is increased and compaction is greater for Bivalent compared to monovalent and antibody-free systems. Differences between monovalent and Bivalent binding result from antibody competition with internal Chromatin fiber components (nucleosome core and linker DNA) for histone tail (H3, H4, H2A, H2B) interactions. This antibody competition for tail contacts reduces tail-core and tail-linker interactions and increases tail-antibody interactions. Such internal structural changes in open fibers resemble mechanisms of LH condensation, driven by charge screening and entropy changes. For condensed fibers at physiological salt, the three systems are much more similar overall, but some subtle tail interaction differences can be noted. Adding LH results in less-dramatic changes for all systems, except that the Bivalent complex at physiological salt shows cooperative effects between LH and the antibodies in condensing Chromatin fibers. Such dynamic interactions that depend on the internal structure and complex-stabilizing interactions within the Chromatin fiber have implications for gene regulation and other Chromatin complexes such as with LH, remodeling proteins, and small molecular chaperones that bind and modulate Chromatin structure.
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Mesoscale Modeling of a Nucleosome-Binding Antibody (PL2-6): Mono- vs. Bivalent Chromatin Complexes
2019Co-Authors: Christopher G. Myers, Donald E. Olins, Ada L. Olins, Tamar SchlickAbstract:ABSTRACT Visualizing Chromatin adjacent to the nuclear envelope (denoted “epiChromatin”) by in vitro immunostaining with a Bivalent nucleosome-binding antibody (termed monoclonal antibody PL2-6) has suggested a distinct and conserved Chromatin structure. Moreover, different staining patterns for Chromatin complexed with the monovalent “Fab” fragment of PL2-6, compared to the Bivalent form, point to distinct binding interactions. To help interpret antibody/Chromatin interactions and these differential binding modes, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale Chromatin model and analyze interactions and fiber structures for the antibody/Chromatin complexes in open and condensed Chromatin, with and without linker histone H1 (LH). Despite minimal and transient interactions at physiological salt, we capture differential binding for monomer and dimer antibody forms to open fibers, with much more intense interactions in the Bivalent antibody/Chromatin complex. For these open “zigzag” fiber morphologies, differences result from antibody competition for peptide tail contacts with internal Chromatin fiber components (nucleosome core and linker DNA). Antibody competition results in dramatic conformational and energetic differences among monovalent, Bivalent, and free Chromatin systems in the parental linker DNA / tail interactions. These differences in binding modes and changes in internal fiber structure, driven by conformational entropy gains, help interpret the differential staining patterns for the monovalent versus Bivalent antibody/Chromatin complexes. More generally, such dynamic interactions which depend on the complex internal structure and self-interactions of the Chromatin fiber have broader implications to other systems that bind to Chromatin, such as linker histones and remodeling proteins. STATEMENT OF SIGNIFICANCE Using mesoscale modeling, we help interpret differential binding modes for antibody/Chromatin interactions to elucidate the structural details of “epiChromatin” (Chromatin adjacent to the nuclear envelope), which had been visualized to produce different staining patterns for monovalent and Bivalent forms of the PL2-6 antibody. To our knowledge, this is the first application of such a coarse-grained computational antibody model to probe Chromatin structure and mechanisms of antibody/Chromatin binding. Our work emphasizes how antibody units compete with native internal Chromatin fiber units (histone tails, nucleosome core, and linker DNA) for fiber-stabilizing interactions and thereby drive differential antibody binding for open zigzag Chromatin fibers. Such competition, which dynamically alters internal Chromatin structure upon binding, could be relevant to other Chromatin binding mechanisms such as those involving linker histones or Chromatin remodeling proteins.
Christopher G. Myers - One of the best experts on this subject based on the ideXlab platform.
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Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes.
Biophysical journal, 2019Co-Authors: Christopher G. Myers, Donald E. Olins, Ada L. Olins, Tamar SchlickAbstract:Interactions of Chromatin with Bivalent immunoglobin nucleosome-binding antibodies and their monovalent (papain-derived) antigen-binding fragment analogs are useful probes for examining Chromatin conformational states. To help interpret antibody-Chromatin interactions and explore how antibodies might compete for interactions with Chromatin components, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale Chromatin model. We analyze interactions and fiber structures for the antibody-Chromatin complexes in open and condensed Chromatin, with and without H1 linker histone (LH). Despite minimal and transient interactions at physiological salt, we capture significant differences in antibody-Chromatin complex configurations in open fibers, with more intense interactions between the Bivalent antibody and Chromatin compared to monovalent antigen-binding fragments. For these open Chromatin fiber morphologies, antibody binding to histone tails is increased and compaction is greater for Bivalent compared to monovalent and antibody-free systems. Differences between monovalent and Bivalent binding result from antibody competition with internal Chromatin fiber components (nucleosome core and linker DNA) for histone tail (H3, H4, H2A, H2B) interactions. This antibody competition for tail contacts reduces tail-core and tail-linker interactions and increases tail-antibody interactions. Such internal structural changes in open fibers resemble mechanisms of LH condensation, driven by charge screening and entropy changes. For condensed fibers at physiological salt, the three systems are much more similar overall, but some subtle tail interaction differences can be noted. Adding LH results in less-dramatic changes for all systems, except that the Bivalent complex at physiological salt shows cooperative effects between LH and the antibodies in condensing Chromatin fibers. Such dynamic interactions that depend on the internal structure and complex-stabilizing interactions within the Chromatin fiber have implications for gene regulation and other Chromatin complexes such as with LH, remodeling proteins, and small molecular chaperones that bind and modulate Chromatin structure.
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Mesoscale Modeling of a Nucleosome-Binding Antibody (PL2-6): Mono- vs. Bivalent Chromatin Complexes
2019Co-Authors: Christopher G. Myers, Donald E. Olins, Ada L. Olins, Tamar SchlickAbstract:ABSTRACT Visualizing Chromatin adjacent to the nuclear envelope (denoted “epiChromatin”) by in vitro immunostaining with a Bivalent nucleosome-binding antibody (termed monoclonal antibody PL2-6) has suggested a distinct and conserved Chromatin structure. Moreover, different staining patterns for Chromatin complexed with the monovalent “Fab” fragment of PL2-6, compared to the Bivalent form, point to distinct binding interactions. To help interpret antibody/Chromatin interactions and these differential binding modes, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale Chromatin model and analyze interactions and fiber structures for the antibody/Chromatin complexes in open and condensed Chromatin, with and without linker histone H1 (LH). Despite minimal and transient interactions at physiological salt, we capture differential binding for monomer and dimer antibody forms to open fibers, with much more intense interactions in the Bivalent antibody/Chromatin complex. For these open “zigzag” fiber morphologies, differences result from antibody competition for peptide tail contacts with internal Chromatin fiber components (nucleosome core and linker DNA). Antibody competition results in dramatic conformational and energetic differences among monovalent, Bivalent, and free Chromatin systems in the parental linker DNA / tail interactions. These differences in binding modes and changes in internal fiber structure, driven by conformational entropy gains, help interpret the differential staining patterns for the monovalent versus Bivalent antibody/Chromatin complexes. More generally, such dynamic interactions which depend on the complex internal structure and self-interactions of the Chromatin fiber have broader implications to other systems that bind to Chromatin, such as linker histones and remodeling proteins. STATEMENT OF SIGNIFICANCE Using mesoscale modeling, we help interpret differential binding modes for antibody/Chromatin interactions to elucidate the structural details of “epiChromatin” (Chromatin adjacent to the nuclear envelope), which had been visualized to produce different staining patterns for monovalent and Bivalent forms of the PL2-6 antibody. To our knowledge, this is the first application of such a coarse-grained computational antibody model to probe Chromatin structure and mechanisms of antibody/Chromatin binding. Our work emphasizes how antibody units compete with native internal Chromatin fiber units (histone tails, nucleosome core, and linker DNA) for fiber-stabilizing interactions and thereby drive differential antibody binding for open zigzag Chromatin fibers. Such competition, which dynamically alters internal Chromatin structure upon binding, could be relevant to other Chromatin binding mechanisms such as those involving linker histones or Chromatin remodeling proteins.
Janine M Lasalle - One of the best experts on this subject based on the ideXlab platform.
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genome wide dna methylation profiles of neurodevelopmental disorder genes in mouse placenta and fetal brain following prenatal exposure to polychlorinated biphenyls
bioRxiv, 2021Co-Authors: Ben Laufer, Kari Neier, Anthony Valenzuela, Dag H Yasui, Rebecca J Schmidt, Pamela J Lein, Janine M LasalleAbstract:Background: Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDD), including autism spectrum disorders (ASD). Objective: We examined the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylome of fetal mouse brain and placenta to determine if there was a shared subset of differentially methylated regions (DMRs). Methods: A PCB mixture formulated to model the 12 most abundant congeners detected in the serum of pregnant women from a prospective high-risk ASD cohort was administered to female mice prior to and during pregnancy. Whole-genome bisulfite sequencing (WGBS) was performed to assess genome-wide DNA methylation profiles of placenta and brain on gestational day 18. Results: We found thousands of significant (empirical p 2.4, q < 0.003) enriched for Bivalent Chromatin marks. The placenta and brain PCB DMRs overlapped significantly (Z-score = 4.5, p = 0.0001) by genomic coordinate and mapped to a shared subset of genes significantly (q < 0.05) enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in multiple NDD/ASD models. The placenta and brain DMRs also significantly (q < 0.05) overlapped by genomic coordinate with brain samples from humans with Rett syndrome and Dup15q syndrome. Discussion: These results demonstrate that placenta can be used as a surrogate for embryonic brain DNA methylation changes over genes relevant to NDD/ASD in a mouse model of prenatal PCB exposure.
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stable dnmt3l overexpression in sh sy5y neurons recreates a facet of the genome wide down syndrome dna methylation signature
Epigenetics & Chromatin, 2021Co-Authors: Benjamin I Laufer, Antonio J Gomez, Julia M Jianu, Janine M LasalleAbstract:Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of Bivalent Chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heteroChromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of Bivalent Chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS.
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stable dnmt3l overexpression in sh sy5y neurons recreates a facet of the genome wide down syndrome dna methylation signature
bioRxiv, 2020Co-Authors: Benjamin I Laufer, Antonio J Gomez, Julia M Jianu, Janine M LasalleAbstract:Abstract Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing at three different developmental phases (undifferentiated, differentiating, and differentiated). DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Merging the DMRs into a consensus profile where the cell lines clustered by genotype and then phase demonstrated that different regions of common genes are affected. The hypermethylated DMRs from all pairwise comparisons were enriched for regions of Bivalent Chromatin marked by H3K4me3 as well as differentially methylated CpGs from previous DS studies of diverse tissues. In contrast, the hypomethylated DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heteroChromatin marked by H3K9me3 during embryonic development. Taken together, we propose a mechanism whereby regions of Bivalent Chromatin that lose H3K4me3 during development are targeted by excess DNMT3L and become hypermethylated, while excess DNMT3L also evicts DNMT3A from heteroChromatin, resulting in hypomethylation. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the DS DNA methylation signature.
Ada L. Olins - One of the best experts on this subject based on the ideXlab platform.
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Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes.
Biophysical journal, 2019Co-Authors: Christopher G. Myers, Donald E. Olins, Ada L. Olins, Tamar SchlickAbstract:Interactions of Chromatin with Bivalent immunoglobin nucleosome-binding antibodies and their monovalent (papain-derived) antigen-binding fragment analogs are useful probes for examining Chromatin conformational states. To help interpret antibody-Chromatin interactions and explore how antibodies might compete for interactions with Chromatin components, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale Chromatin model. We analyze interactions and fiber structures for the antibody-Chromatin complexes in open and condensed Chromatin, with and without H1 linker histone (LH). Despite minimal and transient interactions at physiological salt, we capture significant differences in antibody-Chromatin complex configurations in open fibers, with more intense interactions between the Bivalent antibody and Chromatin compared to monovalent antigen-binding fragments. For these open Chromatin fiber morphologies, antibody binding to histone tails is increased and compaction is greater for Bivalent compared to monovalent and antibody-free systems. Differences between monovalent and Bivalent binding result from antibody competition with internal Chromatin fiber components (nucleosome core and linker DNA) for histone tail (H3, H4, H2A, H2B) interactions. This antibody competition for tail contacts reduces tail-core and tail-linker interactions and increases tail-antibody interactions. Such internal structural changes in open fibers resemble mechanisms of LH condensation, driven by charge screening and entropy changes. For condensed fibers at physiological salt, the three systems are much more similar overall, but some subtle tail interaction differences can be noted. Adding LH results in less-dramatic changes for all systems, except that the Bivalent complex at physiological salt shows cooperative effects between LH and the antibodies in condensing Chromatin fibers. Such dynamic interactions that depend on the internal structure and complex-stabilizing interactions within the Chromatin fiber have implications for gene regulation and other Chromatin complexes such as with LH, remodeling proteins, and small molecular chaperones that bind and modulate Chromatin structure.
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Mesoscale Modeling of a Nucleosome-Binding Antibody (PL2-6): Mono- vs. Bivalent Chromatin Complexes
2019Co-Authors: Christopher G. Myers, Donald E. Olins, Ada L. Olins, Tamar SchlickAbstract:ABSTRACT Visualizing Chromatin adjacent to the nuclear envelope (denoted “epiChromatin”) by in vitro immunostaining with a Bivalent nucleosome-binding antibody (termed monoclonal antibody PL2-6) has suggested a distinct and conserved Chromatin structure. Moreover, different staining patterns for Chromatin complexed with the monovalent “Fab” fragment of PL2-6, compared to the Bivalent form, point to distinct binding interactions. To help interpret antibody/Chromatin interactions and these differential binding modes, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale Chromatin model and analyze interactions and fiber structures for the antibody/Chromatin complexes in open and condensed Chromatin, with and without linker histone H1 (LH). Despite minimal and transient interactions at physiological salt, we capture differential binding for monomer and dimer antibody forms to open fibers, with much more intense interactions in the Bivalent antibody/Chromatin complex. For these open “zigzag” fiber morphologies, differences result from antibody competition for peptide tail contacts with internal Chromatin fiber components (nucleosome core and linker DNA). Antibody competition results in dramatic conformational and energetic differences among monovalent, Bivalent, and free Chromatin systems in the parental linker DNA / tail interactions. These differences in binding modes and changes in internal fiber structure, driven by conformational entropy gains, help interpret the differential staining patterns for the monovalent versus Bivalent antibody/Chromatin complexes. More generally, such dynamic interactions which depend on the complex internal structure and self-interactions of the Chromatin fiber have broader implications to other systems that bind to Chromatin, such as linker histones and remodeling proteins. STATEMENT OF SIGNIFICANCE Using mesoscale modeling, we help interpret differential binding modes for antibody/Chromatin interactions to elucidate the structural details of “epiChromatin” (Chromatin adjacent to the nuclear envelope), which had been visualized to produce different staining patterns for monovalent and Bivalent forms of the PL2-6 antibody. To our knowledge, this is the first application of such a coarse-grained computational antibody model to probe Chromatin structure and mechanisms of antibody/Chromatin binding. Our work emphasizes how antibody units compete with native internal Chromatin fiber units (histone tails, nucleosome core, and linker DNA) for fiber-stabilizing interactions and thereby drive differential antibody binding for open zigzag Chromatin fibers. Such competition, which dynamically alters internal Chromatin structure upon binding, could be relevant to other Chromatin binding mechanisms such as those involving linker histones or Chromatin remodeling proteins.