scholarly journals Diverse roles of MeCP2 in the specification and maintenance of midbrain dopamine phenotype.

2021 ◽  
Author(s):  
Xi-Biao He ◽  
Fang Guo
Keyword(s):  
Dna Methylation ◽  
Tyrosine Hydroxylase ◽  
Dna Binding ◽  
Psychiatric Disorders ◽  
Binding Sites ◽  
Neuronal Phenotype ◽  
Midbrain Dopamine ◽  
And Function ◽  
Determining Factor

Midbrain dopamine (DA) neurons are associated with locomotor and psychiatric disorders. DA neuronal phenotype is specified in ancestral progenitors and maintained throughout differentiation. Here we demonstrate that premature MeCP2 expression prevents DA progenitors from acquiring DA phenotype through interfering NURR1 transactivation. By contrast, the maintenance of DA phenotype is not affected by MeCP2 overexpression in DA neurons. By analyzing the DNA methylation and MeCP2 binding to the promoter of DA phenotype gene tyrosine hydroxylase (Th) along differentiation, we show that Th expression is determined by TET1-mediated de-methylation of NURR1 binding sites within Th promoter. Premature MeCP2 dominates the DNA binding of these sites thereby blocking TET1 function in DA progenitors, whereas TET1 prevents excessive MeCP2 binding in DA neurons. Finally, we show that targeted de-methylation in DA progenitors protects phenotype specification from premature MeCP2 expression, whereas targeted methylation disturbs phenotype maintenance in MeCP2-overexpressed DA neurons. These findings demonstrate MeCP2 as a novel determining factor for DA neuronal phenotype and function.

scholarly journals Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles

PLoS Genetics ◽  
2020 ◽  
Vol 16 (11) ◽  
pp. e1009189
Author(s):  
Alejandro Martin-Trujillo ◽  
Nihir Patel ◽  
Felix Richter ◽  
Bharati Jadhav ◽  
Paras Garg ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Genetic Variation ◽  
Dna Binding ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Ctcf Binding ◽  
Factor Binding ◽  
Rare Genetic Variation

Although DNA methylation is the best characterized epigenetic mark, the mechanism by which it is targeted to specific regions in the genome remains unclear. Recent studies have revealed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Consistent with this finding, we have recently shown that disruption of CTCF-binding sites by rare single nucleotide variants (SNVs) can underlie cis-linked DNA methylation changes in patients with congenital anomalies. These data raise the hypothesis that rare genetic variation at transcription factor binding sites (TFBSs) might contribute to local DNA methylation patterning. In this work, by combining blood genome-wide DNA methylation profiles, whole genome sequencing-derived SNVs from 247 unrelated individuals along with 133 predicted TFBS motifs derived from ENCODE ChIP-Seq data, we observed an association between the disruption of binding sites for multiple TFs by rare SNVs and extreme DNA methylation values at both local and, to a lesser extent, distant CpGs. While the majority of these changes affected only single CpGs, 24% were associated with multiple outlier CpGs within ±1kb of the disrupted TFBS. Interestingly, disruption of functionally constrained sites within TF motifs lead to larger DNA methylation changes at nearby CpG sites. Altogether, these findings suggest that rare SNVs at TFBS negatively influence TF-DNA binding, which can lead to an altered local DNA methylation profile. Furthermore, subsequent integration of DNA methylation and RNA-Seq profiles from cardiac tissues enabled us to observe an association between rare SNV-directed DNA methylation and outlier expression of nearby genes. In conclusion, our findings not only provide insights into the effect of rare genetic variation at TFBS on shaping local DNA methylation and its consequences on genome regulation, but also provide a rationale to incorporate DNA methylation data to interpret the functional role of rare variants.

scholarly journals Functional Characterization of a Testis-Specific DNA Binding Activity at the H19/Igf2 Imprinting Control Region

2003 ◽  
Vol 23 (22) ◽  
pp. 8345-8351 ◽  
Author(s):  
Aaron B. Bowman ◽  
John M. Levorse ◽  
Robert S. Ingram ◽  
Shirley M. Tilghman
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Control Region ◽  
Binding Sites ◽  
Germ Line ◽  
Binding Activity ◽  
Wild Type ◽  
Dna Binding Activity ◽  
Epigenetic State ◽  
Imprinting Control Region

ABSTRACT The DNA methylation state of the H19/Igf2 imprinting control region (ICR) is differentially set during gametogenesis. To identify factors responsible for the paternally specific DNA methylation of the ICR, germ line and somatic extracts were screened for proteins that bind to the ICR in a germ line-specific manner. A specific DNA binding activity that was restricted to the male germ line and enriched in neonatal testis was identified. Its three binding sites within the ICR are very similar to the consensus sequence for nuclear receptor extended half sites. To determine if these binding sites are required for establishment of the paternal epigenetic state, a mouse strain in which the three sites were mutated was generated. The mutated ICR was able to establish a male-specific epigenetic state in sperm that was indistinguishable from that established by the wild-type ICR, indicating that these sequences are either redundant or have no function. An analysis of the methylated state of the mutant ICR in the soma revealed no differences from the wild-type ICR but did uncover in both mutant and wild-type chromosomes a significant relaxation in the stringency of the methylated state of the paternal allele and the unmethylated state of the maternal allele in neonatal and adult tissues.

scholarly journals Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation

2018 ◽  
Vol 115 (37) ◽  
pp. E8793-E8802 ◽  
Author(s):  
Xueqin Li ◽  
C. Jake Harris ◽  
Zhenhui Zhong ◽  
Wei Chen ◽  
Rui Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Dna Sequences ◽  
Conformational Transition ◽  
H3k9 Methylation ◽  
Set Domain ◽  
And Function ◽  
Methylation Patterns

DNA methylation functions in gene silencing and the maintenance of genome integrity. In plants, non-CG DNA methylation is linked through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases) bind to DNA methylation marks and catalyze H3K9 methylation. Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains methylation patterns in the genome. We reveal that SUVH6 has a distinct 5-methyl-dC (5mC) base-flipping mechanism involving a thumb loop element. Autoinhibition of H3 substrate entry is regulated by a SET domain loop, and a conformational transition in the post-SET domain upon cofactor binding may control catalysis. In vitro DNA binding and in vivo ChIP-seq data reveal that the different SUVH family H3K9 MTases have distinct DNA binding preferences, targeting H3K9 methylation to sites with different methylated DNA sequences, explaining the context biased non-CG DNA methylation in plants.

scholarly journals A Functional Map of Genomic HIF1α-DNA Complexes in The Eye Lens Revealed Through Multiomics Analysis

2021 ◽  
Author(s):  
Joshua Disatham ◽  
Lisa Brennan ◽  
Daniel Chauss ◽  
Jason Kantorow ◽  
Behdad Afzali ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Structure And Function ◽  
Eye Lens ◽  
Dna Complexes ◽  
Functional Map ◽  
Lens Formation ◽  
And Function ◽  
Development Structure ◽  
Dna Binding Complexes

Abstract Background: During eye lens development the fetal vasculature regresses leaving the lens without a direct oxygen source. Both embryonically and throughout adult life, the lens contains a decreasing oxygen gradient from the surface to the core that parallels the natural differentiation of immature surface epithelial cells into mature core transparent fiber cells. These properties of the lens suggest a potential role for hypoxia in the regulation of genes required for mature lens structure and function. Since HIF1α is a master regulator of the hypoxic response, these lens properties also implicate HIF1α as a potential requirement for lens formation and homeostasis. Here, we employed a multiomics approach combining CUT&RUN, RNAseq and ATACseq analysis to establish the genomic complement of lens HIF1α binding sites, genes activated or repressed by HIF1α and the chromatin states of HIF1α-regulated genes.Results: CUT&RUN analysis revealed 8,375 HIF1α-DNA binding complexes in the chick lens genome. 1,190 HIF1α-DNA binding complexes were significantly clustered within chromatin accessible regions (χ2 test p < 1x10-55) identified by ATACseq. Formation of the identified HIF1α-DNA complexes paralleled the activation or repression of 526 genes, 116 of which contained HIF1α binding sites within 10kB of the transcription start sites. Some of the identified HIF1α genes have previously established lens functions while others have novel functions never before examined in the lens. GO and pathway analysis of these genes implicate HIF1α in the control of a wide-variety of cellular pathways potentially critical for lens formation, structure and function including glycolysis, cell cycle regulation, chromatin remodeling, Notch and Wnt signaling, differentiation, development, and transparency. Conclusions: These data establish the first functional map of genomic HIF1α-DNA complexes in the eye lens. They identify HIF1α as an important regulator of a wide-variety of genes previously shown to be critical for lens formation and function and they reveal a requirement for HIF1α in the regulation of a wide-variety of genes not yet examined for lens function. They support a requirement for HIF1α in lens development, structure and function and they provide a basis for understanding the potential roles and requirements for HIF1α in the development, structure and function of more complex tissues.

scholarly journals B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse

2021 ◽  
Author(s):  
Tomoko Ichiyanagi ◽  
Hirokazu Katoh ◽  
Yoshinobu Mori ◽  
Keigo Hirafuku ◽  
Beverly Ann Boyboy ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone Modifications ◽  
Binding Sites ◽  
Short Interspersed Elements ◽  
Sequencing Method ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Mammalian Genomes ◽  
Mouse Species ◽  
And Function ◽  
Genomic Regions

Abstract More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of SINE B1 and B2 families within Mus musculus. Using a novel RNA sequencing method designated as melRNA-seq, we detected the expression of SINEs in male germ cells at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs originated from both young and old subfamilies. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses in liver revealed that polymorphic B2 insertions served as a boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Moreover, genomic B2 copies were enriched at the boundary of various histone modifications, and chromatin insulator protein, CCCTC-binding factor, a well-known chromatin boundary protein, bound to &gt;100 polymorphic and &gt;10,000 non-polymorphic B2 insertions. These results suggest that the currently active B2 copies are mobile boundary elements that can modulate chromatin modifications and gene expression, and are likely involved in epigenomic and phenotypic diversification of the mouse species.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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