scholarly journals Igf2/H19 Imprinting Control Region (ICR): An Insulator or a Position-Dependent Silencer?

2001 ◽  
Vol 1 ◽  
pp. 218-224 ◽  
Author(s):  
Subhasis Banerjee ◽  
Alan Smallwood ◽  
Scott Lamond ◽  
Stuart Campbell ◽  
Geeta Nargund
Keyword(s):  
Control Region ◽  
Transcriptional Repression ◽  
Histone Deacetylases ◽  
Specific Binding ◽  
Regulatory Sequences ◽  
Allele Specific ◽  
H19 Gene ◽  
Chromatin Boundary ◽  
Imprinting Control Region ◽  
Mechanistic Basis

The imprinting control region (ICR) located far upstream of the H19 gene, in conjunction with enhancers, modulates the transcription of Igf2 and H19 genes in an allele-specific manner. On paternal inheritance, the methylated ICR silences the H19 gene and indirectly facilitates transcription from the distant Igf2 promoter, whereas on the maternal chromosome the unmethylated ICR, together with enhancers, activates transcription of the H19 gene and thereby contributes to the repression of Igf2. This repression of maternal Igf2 has recently been postulated to be due to a chromatin boundary or insulator function of the unmethylated ICR. Central to the insulator model is the site-specific binding of a ubiquitous nuclear factor CTCF which exhibits remarkable flexibility in functioning as transcriptional activator or silencer. We suggest that the ICR positioned close to the enhancers in an episomal context might function as a transcriptional silencer by virtue of interaction of CTCF with its modifiers such as SIN3A and histone deacetylases. Furthermore, a localised folded chromatin structure resulting from juxtaposition of two disparate regulatory sequences (enhancer ICR) could be the mechanistic basis of ICR-mediated position-dependent (ICR-promoter) transcriptional repression in transgenic Drosophila.

scholarly journals Which genetic variants in DNase I sensitive regions are functional?

2014 ◽  
Author(s):  
Gregory A Moyerbrailean ◽  
Chris T Harvey ◽  
Cynthia A Kalita ◽  
Xiaoquan Wen ◽  
Francesca Luca ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Complex Traits ◽  
Computational Models ◽  
Specific Binding ◽  
Dnase I ◽  
Regulatory Sequences ◽  
Dnase I Footprinting ◽  
Show Evidence ◽  
Allele Specific ◽  
The Impact

Ongoing large experimental characterization is crucial to determine all regulatory sequences, yet we do not know which genetic variants in those regions are non-silent. Here, we present a novel analysis integrating sequence and DNase I footprinting data for 653 samples to predict the impact of a sequence change on transcription factor binding for a panel of 1,372 motifs. Most genetic variants in footprints (5,810,227) do not show evidence of allele-specific binding (ASB). In contrast, functional genetic variants predicted by our computational models are highly enriched for ASB (3,217 SNPs at 20% FDR). Comparing silent to functional non-coding genetic variants, the latter are 1.22-fold enriched for GWAS traits, have lower allele frequencies, and affect footprints more distal to promoters or active in fewer tissues. Finally, integration of the annotations into 18 GWAS meta-studies improves identification of likely causal SNPs and transcription factors relevant for complex traits.

scholarly journals Allele-Specific Binding of CTCF to the Multipartite Imprinting Control Region KvDMR1

2007 ◽  
Vol 27 (7) ◽  
pp. 2636-2647 ◽  
Author(s):  
Galina V. Fitzpatrick ◽  
Elena M. Pugacheva ◽  
Jong-Yeon Shin ◽  
Ziedulla Abdullaev ◽  
Youwen Yang ◽  
...  
Keyword(s):  
Control Region ◽  
Binding Sites ◽  
Noncoding Rna ◽  
Specific Binding ◽  
Ctcf Binding ◽  
Luciferase Reporter ◽  
Imprinting Control Region ◽  
Enhancer Blocking ◽  
Functional Components

ABSTRACT Paternal deletion of the imprinting control region (ICR) KvDMR1 results in loss of expression of the Kcnq1ot1 noncoding RNA and derepression of flanking paternally silenced genes. Truncation of Kcnq1ot1 also results in the loss of imprinted expression of these genes in most cases, demonstrating a role for the RNA or its transcription in gene silencing. However, enhancer-blocking studies indicate that KvDMR1 also contains chromatin insulator or silencer activity. In this report we demonstrate by electrophoretic mobility shift assays and chromatin immunoprecipitation the existence of two CTCF binding sites within KvDMR1 that are occupied in vivo only on the unmethylated paternally derived allele. Methylation interference and mutagenesis allowed the precise mapping of protein-DNA contact sites for CTCF within KvDMR1. Using a luciferase reporter assay, we mapped the putative transcriptional promoter for Kcnq1ot1 upstream and to a site functionally separable from enhancer-blocking activity and CTCF binding sites. Luciferase reporter assays also suggest the presence of an additional cis-acting element in KvDMR1 upstream of the putative promoter that can function as an enhancer. These results suggest that the KvDMR1 ICR consists of multiple, independent cis-acting modules. Dissection of KvDMR1 into its functional components should help elucidate the mechanism of its function in vivo.

scholarly journals High throughput characterization of genetic effects on DNA:protein binding and gene transcription

2018 ◽  
Author(s):  
Cynthia A. Kalita ◽  
Christopher D. Brown ◽  
Andrew Freiman ◽  
Jenna Isherwood ◽  
Xiaoquan Wen ◽  
...  
Keyword(s):  
High Throughput ◽  
Complex Traits ◽  
Disease Risk ◽  
Specific Binding ◽  
P Value ◽  
Regulatory Sequences ◽  
Specific Expression ◽  
Pcr Duplicates ◽  
Allele Specific ◽  
Altered Gene

Many variants associated with complex traits are in non-coding regions, and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, BiT-STARR-seq (Biallelic Targeted STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2,720 SNPs with significant ASE (FDR 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high throughput allele specific binding assay for NFKB-p50. We identified 2,951 SNPs with allele-specific binding (ASB) (FDR 10%); 173 of these SNPs also had ASE (OR=1.97, p-value=0.0006). Of variants associated with complex traits, 1,531 resulted in ASE and 1,662 showed ASB. For example, we characterized that the Crohn’s disease risk variant for rs3810936 increases NFKB binding and results in altered gene expression.

scholarly journals Direct p53 Transcriptional Repression: In Vivo Analysis of CCAAT-Containing G2/M Promoters

2005 ◽  
Vol 25 (9) ◽  
pp. 3737-3751 ◽  
Author(s):  
Carol Imbriano ◽  
Aymone Gurtner ◽  
Fabienne Cocchiarella ◽  
Silvia Di Agostino ◽  
Valentina Basile ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Damage ◽  
Transcriptional Repression ◽  
Histone Deacetylases ◽  
Specific Binding ◽  
Cell Cycle Control ◽  
Tetramerization Domain ◽  
Before And After

ABSTRACT In response to DNA damage, p53 activates G1/S blocking and apoptotic genes through sequence-specific binding. p53 also represses genes with no target site, such as those for Cdc2 and cyclin B, key regulators of the G2/M transition. Like most G2/M promoters, they rely on multiple CCAAT boxes activated by NF-Y, whose binding to DNA is temporally regulated during the cell cycle. NF-Y associates with p53 in vitro and in vivo through the αC helix of NF-YC (a subunit of NF-Y) and a region close to the tetramerization domain of p53. Chromatin immunoprecipitation experiments indicated that p53 is associated with cyclin B2, CDC25C, and Cdc2 promoters in vivo before and after DNA damage, requiring DNA-bound NF-Y. Following DNA damage, p53 is rapidly acetylated at K320 and K373 to K382, histones are deacetylated, and the release of PCAF and p300 correlates with the recruitment of histone deacetylases (HDACs)—HDAC1 before HDAC4 and HDAC5—and promoter repression. HDAC recruitment requires intact NF-Y binding sites. In transfection assays, PCAF represses cyclin B2, and a nonacetylated p53 mutant shows a complete loss of repression potential, despite its abilities to bind NF-Y and to be recruited on G2/M promoters. These data (i) detail a strategy of direct p53 repression through associations with multiple NF-Y trimers that is independent of sequence-specific binding of p53 and that requires C-terminal acetylation, (ii) suggest that p53 is a DNA damage sentinel of the G2/M transition, and (iii) delineate a new role for PCAF in cell cycle control.

scholarly journals Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hitomi Matsuzaki ◽  
Yu Miyajima ◽  
Akiyoshi Fukamizu ◽  
Keiji Tanimoto
Keyword(s):  
Gene Expression ◽  
Critical Role ◽  
Maternal Allele ◽  
Detailed Mechanism ◽  
Parental Allele ◽  
Insulator Activity ◽  
Allele Specific ◽  
H19 Gene ◽  
Imprinting Control Region ◽  
Endogenous Locus

AbstractThe mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.

scholarly journals The mRNA Expression and Methylation Status in Imprinting Control Region of H19 Gene Between Cattle-Yak and Their Parents

2012 ◽  
Vol 11 (10) ◽  
pp. 1691-1699 ◽  
Author(s):  
Ming-gui LI ◽  
Zhen-shan LIU ◽  
Zeng-xiang PAN ◽  
Hua LUO ◽  
Zhuang XIE ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Control Region ◽  
Methylation Status ◽  
H19 Gene ◽  
Imprinting Control Region

scholarly journals Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies

2021 ◽  
Vol 7 (2) ◽  
pp. eabd4413
Author(s):  
Jung-Hoon Lee ◽  
Daniel Bollschweiler ◽  
Tillman Schäfer ◽  
Robert Huber
Keyword(s):  
Transcriptional Repression ◽  
Histone Deacetylases ◽  
Active Sites ◽  
Chromatin Modification ◽  
Structural Basis ◽  
Amino Terminal ◽  
Cryo Electron Microscopy ◽  
Multiple Contacts ◽  
Lysine Residues ◽  
Nucleosome Binding

The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo–electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda12-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.

scholarly journals Transcriptional repression by wild-type p53 utilizes histone deacetylases, mediated by interaction with mSin3a

1999 ◽  
Vol 13 (19) ◽  
pp. 2490-2501 ◽  
Author(s):  
M. Murphy ◽  
J. Ahn ◽  
K. K. Walker ◽  
W. H. Hoffman ◽  
R. M. Evans ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Histone Deacetylases ◽  
Wild Type ◽  
Wild Type P53
Sign in / Sign up

Export Citation Format

Share Document