CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters [MeDIP-Seq]
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PROVIDER: PRJNA1185257 | ENA |
REPOSITORIES: ENA
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Project description:Human and other vertebrate representative forms of CGGBP1 have been used in this study to assay global gene expression. HEK293T cells with endogenous CGGBP1 knocked down were used to over-express other vertebrate representative forms of CGGBP1 (Latimeria chalumnae (Lc), Anolis carolinensis (Ac), Gallus gallus (Gg)) followed by RNA extraction and one-coloured global gene expression analysis (Agilent). HEK293T cells with normal level of endogenous CGGBP1 were used to over-express Human CGGBP1 (Hs) or pcDNA3.1(+) empty vector (Ev). Overexpression of CGGBP1 forms resulted in the repression of specific gene sets at two different temperatures (37 degrees and 40 degrees Celsius). The proximal promoters of these repressed genes exhibit a marked difference in the occurrence of GC-rich transcription factor binding sites (TFBSs). Through additional studies on these samples we have separately assayed global cytosine methylation patterns (submitted separately to NCBI GEO) and reported that the GC content of these promoters is determined by a combination of motif occurrence as well as motif GC contents. Notably, the within these gene promoters human CGGBP1 was found to restrict cytosine methylation at certain GC-rich TFBSs. A high-throughput analysis of the GC compositional bias across these CGGBP1-regulated TFBSs, using orthologous sequences from over 100 species, revealed a strong link between CGGBP1-induced cytosine methylation restriction and GC retention at specific TFBSs. Further, orthology analysis showed that this regulatory mechanism of CGGBP1 is conserved in higher amniotes (birds and mammals) and exhibits lineage-specific variations in lower amniotes (reptiles).
2025-07-31 | GSE281705 | GEO
Project description:Human CGGBP1 has been attributed multiple function related to the regulation of gene expression, cytosine methylation (including non-CpG methylation), related epigenetic states of target gene promoter regions and somatic mutation rates. CGGBP1 has also been shown to be a prominent transcription repressor of protein coding genes as well as repetitive elements, mainly Alu-SINEs. There is a possibility that CGGBP1-regulated cytosine methylation affects base mutation rates (C-T transitions) thereby directing TFBS evolution in the human genome. Some recent data suggest that the DNA-binding activity of human CGGBP1 prevents TFBS from cytosine methylation and preserves their GC content. The DNA-binding domain of CGGBP1 is conserved more than its other segments which contain no identifiable domains. In this study we assay global cytosine methylation using MeDIP-seq on human cells (HEK293T) over-expressing only representative vertebrate species (Latimeria chalumnae (Lc), Anolis carolinenesis (Ac), Gallus gallus (Gg), Homo sapiens (Hs)) and perform comparative analyses. Our analyses encompass a parallel global expression profiling (using Agilent arrays, submitted separately to NCBI GEO) and a large-scale estimation of TFBS C-T transition mutation rates from orthologs of genes repressed by the various forms of CGGBP1 used in this study. We report that cytosine methylation restriction by CGGBP1 promotes GC retention in some GC-rich TFBSs.
2025-07-31 | GSE281704 | GEO
Project description:CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters [Array]
| PRJNA1185260 | ENA
Project description:By depleting CGGBP1 in normal human fibroblasts and by performing genome-wide sequencing (with and without bisulfite conversion) we show that upon CGGBP1 depletion cytosine methylation increases significantly at repeat regions. Using Pacbio sequencing of Alu and LINE-1 repeats amplified genome-wide from bisulfite converted DNA, we further establish the cytosine methylation-inhibitory functions of CGGBP1.
2015-08-26 | GSE60784 | GEO
Project description:To study if regulation of cytosine methylation and CTCF occupancy are interdependent and governed by the levels of CGGBP1, we specifically pulled-down methylated cytosines and found that some transcription factor binding sites including that of CTCF held out against the cytosine methylation changes. The cytosine methylation at CTCF-binding repeat-free motifs show a non-stochastic depdendence on CGGBP1 and occur at sites that mark cytosine methylation transition boundaries. We also show that allelic imbalance dictates stochastic methylation changes due to CGGBP1 depletion.
2020-07-20 | GSE145300 | GEO
Project description:Truncated forms of CGGBP1 with (N-term) or without (C-term) the DNA-binding domain (DBD) have been used to to assay global gene expression. HEK293T cells with endogenous CGGBP1 knocked down were used to over-express truncated forms of CGGBP1 followed by RNA extraction and one-coloured global gene expression analysis. The data suggests that while the C-term of CGGBP1 is the major repressor of transcription, just the N-term containing the DBD fails to achieve so. Proximal promoters of CGGBP1-repressed genes, although significantly GC-poor, contain GC-rich transcription factor binding motifs and exhibit base compositions indicative of low C-T transition rates due to targeted prevention of cytosine methylation. Our findings suggest that CGGBP1 protects transcription factor binding sites (TFBS) from cytosine methylation-associated loss and thereby regulates gene expression. By analysing orthologous promoter sequences, we show that protection from cytosine methylation is a function of CGGBP1 progressively acquired during vertebrate evolution.
2024-11-17 | GSE269654 | GEO
Project description:Truncated forms of CGGBP1 with (N-term) or without (C-term) the DNA-binding domain (DBD) have been used to to assay global cytosine methylation. HEK293T cells with endogenous CGGBP1 knocked down were used to over-express truncated forms of CGGBP1 followed by MeDIP-Seq analysis. Genome-wide analyses of cytosine methylation and binding of CGGBP1 DBD show that CGGBP1 restricts cytosine methylation in a manner that depends on its DBD and its DNA-binding. Our findings suggest that CGGBP1 protects transcription factor binding sites (TFBS) from cytosine methylation-associated loss. A superimposition of our results and evolution of CGGBP1 suggests that mitigation of cytosine methylation is majorly achieved by its N-terminal DBD. Our results position CGGBP1 DNA-binding as a major evolutionarily acquired mechanism through which it keeps cytosine methylation under check and regulates TFBS retention.
2024-11-17 | GSE269791 | GEO
Project description:Alu SINEs are the most numerous frequently occurring transcription units in our genome and possess sequence competence for transcription by RNA Pol III. However, through poorly understood mechanisms, the Alu RNA levels are maintained at very low levels in normal somatic cells with obvious benefits of low rates of Alu retrotransposition and energy-economical deployment of RNA Pol III to the tRNA genes which share promoter structure and polymerase requirements with Alu SINEs. Using comparative ChIP sequencing, we unveil that a repeat binding protein, CGGBP1, binds to the transcriptional regulatory regions of Alu SINEs thereby impeding Alu transcription by inhibiting RNA Pol III recruitment. We show that this Alu-silencing depends on growth factor stimulation of cells and subsequent tyrosine phosphorylation of CGGBP1. Importantly, CGGBP1 ensures a sequence-specific discriminative inhibition of RNA Pol III activity at Alu promoters, while sparing the structurally similar tRNA promoters. Our data suggest that CGGBP1 contributes to growth-related transcription by preventing the hijacking of RNA Pol III by Alu SINEs. This study was used to find out the effect of CGGBP1 on serum-induced changes in gene expression and effect of serum on gene expression regulation by CGGBP1. Gene expression profiling of normal human fibroblasts under 4 different experimental perturbations: serum starvation or serum stimulation and CGGBP1 depletion or normal CGGBP1 levels.
2015-12-21 | E-GEOD-54058 | biostudies-arrayexpress
Project description:CGGBP1-dependent CTCF-binding sites identified in Patel et. al. 2019 [PMID 31547883] serve as barrier elements consistent with asymmetrical levels of H3K9me3 in the flanks and asymmetrical RNA levels at these sites in the genome. In this study we have characterised the function of such CGGBP1-depenedent CTCF binding sites which are usually repeat rich in nature. By cloning one such CTCF-binding site in an episomal system, we have studied the barrier activity of this CGGBP1-dependent CTCF-binding sites in the prsesnce and absence of CGGBP1 in HEK293T cells through various molecular assays and RNA-sequencing. Our results show that these sites act as barrier for the ectopic transcription as the depletion of CGGBP1 lead to starnd-specific bidirectional transcription as a result of loss of barrier activity concomitant with the loss of CTCF-binding. Further, analysing the RNA-seq revealed that weakly transcribed sites are flanked by the CTCF-binding at transcription start and end sites in the presence of CGGBP1. However, CGGBP1 depletion leads to loss of barrier activity maintained by CGGBP1 with dispersed CTCF binding and a loss of transcription restriction. Such CGGBP1-dependent CTCF-binding sites prevents ectopic transcription.
2022-01-06 | GSE171990 | GEO
Project description:To study the role of CGGBP1 in regulation of CTCF occupancy, we performed CTCF ChIP-seq in HEK293T cells with three different levels of CGGBP1: (i) endogenous levels of CGGBP1 (ii) CGGBP1 knockdown, and (iii) CGGBP1 overexpression. Here, we show that CTCF binds to repeats as well as canonical CTCF-motifs and CGGBP1 determines the CTCF occupancy preference for repeats over canonical CTCF-motif. By combining CTCF ChIP-seq with histone modifications ChIP-seq (for H3K4me3, H3K9me3 and H3K27me3) under conditions of normal or CGGBP1 knockdown, we demonstrate that CTCF binding sites regulated by CGGBP1 correspond to chromatin barrier elements with profound effects on H3K9me3 distribution. In conclusion, these finding shows that CGGBP1 is a regulator of CTCF occupancy and serve as a regulator of barrier functions of CTCF-binding sites.
2019-09-23 | GSE129548 | GEO