Limits...
Functional diversity of CTCFs is encoded in their binding motifs.

Fang R, Wang C, Skogerbo G, Zhang Z - BMC Genomics (2015)

Bottom Line: Supported by transcriptomic, epigenomic and chromatin-interactomic data, we show that the functional diversity of the CTCF binding motifs is strongly associated with their GC content, CpG dinucleotide coverage and relative DNA methylation level at the 12th position of the motifs.Finally, we present evidences for a hypothetical model in which chromatin interactions between promoters and distal regulatory regions are likely mediated by CTCFs binding to sequences with high CpG.These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. r3fang@eng.ucsd.edu.

ABSTRACT

Background: The CCCTC-binding factor (CTCF) has diverse regulatory functions. However, the definitive characteristics of the CTCF binding motif required for its functional diversity still remains elusive.

Results: Here, we describe a new motif discovery workflow by which we have identified three CTCF binding motif variations with highly divergent functionalities. Supported by transcriptomic, epigenomic and chromatin-interactomic data, we show that the functional diversity of the CTCF binding motifs is strongly associated with their GC content, CpG dinucleotide coverage and relative DNA methylation level at the 12th position of the motifs. Further analysis suggested that the co-localization of cohesin, the key factor in cohesion of sister chromatids, is negatively correlated with the CpG coverage and the relative DNA methylation level at the 12th position. Finally, we present evidences for a hypothetical model in which chromatin interactions between promoters and distal regulatory regions are likely mediated by CTCFs binding to sequences with high CpG.

Conclusion: These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.

No MeSH data available.


CpG coverage and methylation status at the 12th position of the CTCF motifs. a CpG coverage (%) distribution within regions [−50 bp, +50 bp] of the center of CTCF-A and CTCF-C binding sites in GM12878 (see Additional file 10: Figure S5 for K562 and HeLaS3). See Additional file 11: Figure S6 for the corresponding DNA methylation distribution. b Depletion of cohesin (represented by overlapping binding peaks of SMC3 and Rad21) at CTCF binding sites. The black and gray bars represent cohesin coverage at all CTCF binding regions and at CTCF binding sites that are methylated (methylation level >20 %) at the 12th position, respectively. c Correlation (Pearson’s correlation coefficients) between the ChIP-seq read counts for cohesin (Rad21) and the DNA methylation level at the 12th position of the CTCF binding sites across the three cell lines. The stars (*) indicate the statistical significance in each test (***, p-value < 1E-5, **, p-value < 1E-2, * p-value < 5E-2)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4552278&req=5

Fig5: CpG coverage and methylation status at the 12th position of the CTCF motifs. a CpG coverage (%) distribution within regions [−50 bp, +50 bp] of the center of CTCF-A and CTCF-C binding sites in GM12878 (see Additional file 10: Figure S5 for K562 and HeLaS3). See Additional file 11: Figure S6 for the corresponding DNA methylation distribution. b Depletion of cohesin (represented by overlapping binding peaks of SMC3 and Rad21) at CTCF binding sites. The black and gray bars represent cohesin coverage at all CTCF binding regions and at CTCF binding sites that are methylated (methylation level >20 %) at the 12th position, respectively. c Correlation (Pearson’s correlation coefficients) between the ChIP-seq read counts for cohesin (Rad21) and the DNA methylation level at the 12th position of the CTCF binding sites across the three cell lines. The stars (*) indicate the statistical significance in each test (***, p-value < 1E-5, **, p-value < 1E-2, * p-value < 5E-2)

Mentions: CTCF-A sequence regions have a relatively high overall CpG content and high DNA methylation levels at the 12th position. Since the overall GC content varies among the CTCF-A, −B and -C sequences, it was not surprising to find that of all CpG dinucleotides detected in the three examined cell lines (13,714, 18,105 and 15,241 in GM12878, K562 and HeLaS3, respectively), CTCF-A sequences had much higher overall CpG levels than CTCF- B and -C sequences (Wilcoxon test p-value < 5e-12, < 5e-13 and < 5e-10 for GM12878, K562 and HeLaS3, respectively). In agreement with Wang et al. [9], we also observed ultrahigh enrichment of CpG dinucleotides at the 12th position of CTCF recognition sequences particularly in the CTCF-A subgroup (5-fold over that in CTCF-C, p-value < 1e-14; Fig. 5a and Additional file 10: Figure S5). Given the high CpG level at the 12th position of the CTCF-A sequences, we would also expect a correspondingly high DNA methylation level. Indeed, the DNA methylation level at the 12th position of CTCF-A binding sites was relatively high compared to other CpG sites (Additional file 11: Figure S6).Fig. 5


Functional diversity of CTCFs is encoded in their binding motifs.

Fang R, Wang C, Skogerbo G, Zhang Z - BMC Genomics (2015)

CpG coverage and methylation status at the 12th position of the CTCF motifs. a CpG coverage (%) distribution within regions [−50 bp, +50 bp] of the center of CTCF-A and CTCF-C binding sites in GM12878 (see Additional file 10: Figure S5 for K562 and HeLaS3). See Additional file 11: Figure S6 for the corresponding DNA methylation distribution. b Depletion of cohesin (represented by overlapping binding peaks of SMC3 and Rad21) at CTCF binding sites. The black and gray bars represent cohesin coverage at all CTCF binding regions and at CTCF binding sites that are methylated (methylation level >20 %) at the 12th position, respectively. c Correlation (Pearson’s correlation coefficients) between the ChIP-seq read counts for cohesin (Rad21) and the DNA methylation level at the 12th position of the CTCF binding sites across the three cell lines. The stars (*) indicate the statistical significance in each test (***, p-value < 1E-5, **, p-value < 1E-2, * p-value < 5E-2)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4552278&req=5

Fig5: CpG coverage and methylation status at the 12th position of the CTCF motifs. a CpG coverage (%) distribution within regions [−50 bp, +50 bp] of the center of CTCF-A and CTCF-C binding sites in GM12878 (see Additional file 10: Figure S5 for K562 and HeLaS3). See Additional file 11: Figure S6 for the corresponding DNA methylation distribution. b Depletion of cohesin (represented by overlapping binding peaks of SMC3 and Rad21) at CTCF binding sites. The black and gray bars represent cohesin coverage at all CTCF binding regions and at CTCF binding sites that are methylated (methylation level >20 %) at the 12th position, respectively. c Correlation (Pearson’s correlation coefficients) between the ChIP-seq read counts for cohesin (Rad21) and the DNA methylation level at the 12th position of the CTCF binding sites across the three cell lines. The stars (*) indicate the statistical significance in each test (***, p-value < 1E-5, **, p-value < 1E-2, * p-value < 5E-2)
Mentions: CTCF-A sequence regions have a relatively high overall CpG content and high DNA methylation levels at the 12th position. Since the overall GC content varies among the CTCF-A, −B and -C sequences, it was not surprising to find that of all CpG dinucleotides detected in the three examined cell lines (13,714, 18,105 and 15,241 in GM12878, K562 and HeLaS3, respectively), CTCF-A sequences had much higher overall CpG levels than CTCF- B and -C sequences (Wilcoxon test p-value < 5e-12, < 5e-13 and < 5e-10 for GM12878, K562 and HeLaS3, respectively). In agreement with Wang et al. [9], we also observed ultrahigh enrichment of CpG dinucleotides at the 12th position of CTCF recognition sequences particularly in the CTCF-A subgroup (5-fold over that in CTCF-C, p-value < 1e-14; Fig. 5a and Additional file 10: Figure S5). Given the high CpG level at the 12th position of the CTCF-A sequences, we would also expect a correspondingly high DNA methylation level. Indeed, the DNA methylation level at the 12th position of CTCF-A binding sites was relatively high compared to other CpG sites (Additional file 11: Figure S6).Fig. 5

Bottom Line: Supported by transcriptomic, epigenomic and chromatin-interactomic data, we show that the functional diversity of the CTCF binding motifs is strongly associated with their GC content, CpG dinucleotide coverage and relative DNA methylation level at the 12th position of the motifs.Finally, we present evidences for a hypothetical model in which chromatin interactions between promoters and distal regulatory regions are likely mediated by CTCFs binding to sequences with high CpG.These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. r3fang@eng.ucsd.edu.

ABSTRACT

Background: The CCCTC-binding factor (CTCF) has diverse regulatory functions. However, the definitive characteristics of the CTCF binding motif required for its functional diversity still remains elusive.

Results: Here, we describe a new motif discovery workflow by which we have identified three CTCF binding motif variations with highly divergent functionalities. Supported by transcriptomic, epigenomic and chromatin-interactomic data, we show that the functional diversity of the CTCF binding motifs is strongly associated with their GC content, CpG dinucleotide coverage and relative DNA methylation level at the 12th position of the motifs. Further analysis suggested that the co-localization of cohesin, the key factor in cohesion of sister chromatids, is negatively correlated with the CpG coverage and the relative DNA methylation level at the 12th position. Finally, we present evidences for a hypothetical model in which chromatin interactions between promoters and distal regulatory regions are likely mediated by CTCFs binding to sequences with high CpG.

Conclusion: These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.

No MeSH data available.