Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

Schwalie, Petra; Ward, Michelle C.; Cain, Carolyn E.; Faure, Aline; Gilad, Yoav; Odom, Duncan T.; Flicek, Paul

doi:10.1186/gb-2013-14-12-r148

Cited by 77 publications

(82 citation statements)

References 97 publications

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“…To determine whether it actually was an active TFBS, we looked for overlapping regions with the ubiquitous TF CTCF, and with active transcription marks H3Kme3 and Pol II. As previously reported in more detail in [40] , YY1 co-bound with CTCF in a great extent in the human genome, and they show a significant genome-wide interaction across species, which suggests a heavy association through evolution. YY1-CTCF co-bound regions are also frequently related to Pol II and H3Kme3 histone marks, as well as to CpG islands at active transcription sites [40] .…”

Section: Discussionsupporting

confidence: 72%

A CpG-SNP Located within the ARPC3 Gene Promoter Is Associated with Hypertriglyceridemia in Severely Obese Patients

J¹,

Guénard²,

Tchernof

et al. 2016

Ann Nutr Metab

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Aims: To test the potential association of cytosine-phosphate-guanine dinucleotides (CpG)-single-nucleotide polymorphisms (SNPs) located within actin-related protein 2/3 complex subunit 3 (ARPC3), a gene recently linked to adipogenesis and lipid accumulation, with metabolic syndrome (MetS) features in severely obese patients. Methods: Prioritized SNPs within the ARPC3 locus were genotyped and tested for associations with MetS features in a cohort of 1,749 obese patients with and without MetS. Association testing with CpG methylation levels was performed in a methylation sub-cohort of 16 obese men. Results: A significant association was found between the CpG-SNP rs3759384 (C>T) and plasma triglyceride (TG) levels (false discovery rate-corrected p = 3.5 × 10^-2), with 0.6% of the phenotypic variance explained by the CpG-SNP, and with TT homozygotes showing the highest plasma TG levels (1.89 mmol/l). The carriers of the rs3759384 T allele also showed a significant decrease in methylation levels of the ARPC3 promoter-associated CpG site cg10738648 in both visceral adipose tissue and blood. ARPC3 expression levels showed a strong correlation with plasma TG levels (r = 0.70; p = 0.02). Conclusions: The increased plasma TG levels found in homozygous rs3759384 T allele carriers argue for a relevant role of this CpG-SNP in lipid management among obese individuals, which may be driven by an epigenetic-mediated mechanism.

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Section: Discussionsupporting

confidence: 72%

A CpG-SNP Located within the ARPC3 Gene Promoter Is Associated with Hypertriglyceridemia in Severely Obese Patients

J¹,

Guénard²,

Tchernof

et al. 2016

Ann Nutr Metab

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“…In agreement with this idea, Ruan and colleagues reported evidence that CTCF-mediated looping interactions might function to coordinate nearby interactions involving RNA Pol II . Furthermore, a recent genomics analysis showed that up to 30% of YY1 sites bind at locations directly adjacent to CTCF and might work together to cooperatively influence occupancy (Schwalie et al 2013). Thus we posit that architectural proteins such as YY1 might cooperatively build upon a constitutive CTCF architectural "seed" scaffold to connect nearby developmentally regulated genes and enhancers.…”

Section: Wwwgenomeorgmentioning

confidence: 99%

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

et al. 2017

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CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. Unexpectedly, we observe a sharp decrease in CTCF occupancy during the transition from naï ve/primed pluripotency to multipotent primary neural progenitor cells (NPCs). Many pluripotency gene-enhancer interactions are anchored by CTCF, and its occupancy is lost in parallel with loop decommissioning during differentiation. Conversely, CTCF binding sites in NPCs are largely preexisting in pluripotent stem cells. Only a small number of CTCF sites arise de novo in NPCs. We identify another zinc finger protein, Yin Yang 1 (YY1), at the base of looping interactions between NPC-specific genes and enhancers. Putative NPC-specific enhancers exhibit strong YY1 signal when engaged in 3D contacts and negligible YY1 signal when not in loops. Moreover, siRNA knockdown of Yy1 specifically disrupts interactions between key NPC enhancers and their target genes. YY1-mediated interactions between NPC regulatory elements are often nested within constitutive loops anchored by CTCF. Together, our results support a model in which YY1 acts as an architectural protein to connect developmentally regulated looping interactions; the location of YY1-mediated interactions may be demarcated in development by a preexisting topological framework created by constitutive CTCF-mediated interactions.

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“…4A; Supplemental Methods SM1.11). In addition, we used a previously published data set to identify CTCF genome-wide binding in immortalized lymphoblast cells from four primate species (Schwalie et al 2013). We found between ∼24,000 and 48,000 CTCF binding sites across the four Muridae species and between ∼21,000 and 57,000 across the four Hominidae species (Supplemental Fig.…”

Section: Retrotransposition Of Sine B2_mm1 Elements Drove a Species-smentioning

confidence: 99%

“…The paired-end libraries were sequenced at 100 bp on the HiSeq2000 platform. In addition, the data set from Schwalie et al (2013) was used to identify the CTCF binding sites in primates. Sequencing reads were aligned to the appropriate reference genome using Bowtie 2 version 2.2.6 (Langmead and Salzberg 2012).…”

Section: Ctcf Binding Site Analysismentioning

confidence: 99%

“…At present, primates are one of the mammalian clades (if not the only one) with enough sequenced genomes (The Chimpanzee Sequencing and Analysis Consortium 2005; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007; Locke et al 2011;Scally et al 2012;Carbone et al 2014;Gordon et al 2016) to facilitate high-resolution studies of genome evolution within a single mammalian lineage (Marques-Bonet et al 2009;Gazave et al 2011;Schwalie et al 2013;Navarro and Galante 2015). It remains uncertain whether the evolutionary dynamics observed in the primates are common across other mammalian clades.…”

mentioning

confidence: 99%

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Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

et al. 2018

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Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four-and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

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Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

Cited by 77 publications

References 97 publications

A CpG-SNP Located within the <b><i>ARPC3</i></b> Gene Promoter Is Associated with Hypertriglyceridemia in Severely Obese Patients

A CpG-SNP Located within the <b><i>ARPC3</i></b> Gene Promoter Is Associated with Hypertriglyceridemia in Severely Obese Patients

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

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