Loss of the insulator protein CTCF during nematode evolution

Heger, Peter; Marin, Birger; Schierenberg, Einhard

doi:10.1186/1471-2199-10-84

Cited by 88 publications

(89 citation statements)

References 92 publications

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“…S6). In agreement with this view, such an enrichment was not detectable in the genomes of the platyhelminth Schmidtea mediterranea and the nematode Caenorhabditis elegans that lack CTCF (22). Another nematode, Trichinella spiralis, behaved similarly despite the presence of CTCF (22), illustrating that CTCF may have lost its genome-wide function in this lineage.…”

supporting

confidence: 55%

“…S2). Absence of CTCF from this phylum is possibly due to a secondary loss, a phenomenon also reported for some nematodes (22).…”

mentioning

confidence: 94%

“…Sequence alignment of CTCF candidates was performed as described elsewhere (22). The sequence dataset for phylogenetic analysis consisted of 170 sequences.…”

Section: Methodsmentioning

confidence: 99%

“…1, inferred from the absence in 51,000 ESTs; 2, SI Appendix, Fig. S10; 3, presence of CTCF in basal nematodes and absence in C. elegans and other derived nematodes (22). References for the state of Hox gene clustering are in SI Appendix, Table S3.…”

Section: Conservation Of Ctcf Sites In Vertebrate and Drosophila Hox mentioning

confidence: 99%

“…The presence of CTCF in vertebrates (11,(18)(19)(20), flies (10,21), and some nematodes (22) suggests that all protostomes and deuterostomes might possess this 11-ZF protein. To investigate this possibility, we searched in public databases for CTCF candidates and determined their orthology to CTCF in a phylogenetic analysis.…”

mentioning

confidence: 99%

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The chromatin insulator CTCF and the emergence of metazoan diversity

Heger

Marin²,

Bartkuhn

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

176

173

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The great majority of metazoans belong to bilaterian phyla. They diversified during a short interval in Earth's history known as the Cambrian explosion, ∼540 million years ago. However, the genetic basis of these events is poorly understood. Here we argue that the vertebrate genome organizer CTCF (CCCTC-binding factor) played an important role for the evolution of bilaterian animals. We provide evidence that the CTCF protein and a genome-wide abundance of CTCF-specific binding motifs are unique to bilaterian phyla, but absent in other eukaryotes. We demonstrate that CTCF-binding sites within vertebrate and Drosophila Hox gene clusters have been maintained for several hundred million years, suggesting an ancient origin of the previously known interaction between Hox gene regulation and CTCF. In addition, a close correlation between the presence of CTCF and Hox gene clusters throughout the animal kingdom suggests conservation of the Hox-CTCF link across the Bilateria. On the basis of these findings, we propose the existence of a Hox-CTCF kernel as principal organizer of bilaterian body plans. Such a kernel could explain (i) the formation of Hox clusters in Bilateria, (ii) the diversity of bilaterian body plans, and (iii) the uniqueness and time of onset of the Cambrian explosion.

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supporting

confidence: 55%

“…S2). Absence of CTCF from this phylum is possibly due to a secondary loss, a phenomenon also reported for some nematodes (22).…”

mentioning

confidence: 94%

“…Sequence alignment of CTCF candidates was performed as described elsewhere (22). The sequence dataset for phylogenetic analysis consisted of 170 sequences.…”

Section: Methodsmentioning

confidence: 99%

Section: Conservation Of Ctcf Sites In Vertebrate and Drosophila Hox mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

The chromatin insulator CTCF and the emergence of metazoan diversity

Heger

Marin²,

Bartkuhn

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

176

173

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Broad Chromatin Domains: An Important Facet of Genome Regulation

2017

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Chromatin composition differs across the genome, with distinct compositions characterizing regions associated with different properties and functions. Whereas many histone modifications show local enrichment over genes or regulatory elements, marking can also span large genomic intervals defining broad chromatin domains. Here we highlight structural and functional features of chromatin domains marked by histone modifications, with a particular emphasis on the potential roles of H3K27 methylation domains in the organization and regulation of genome activity in metazoans.

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C2H2 proteins: Evolutionary aspects of domain architecture and diversification

Bonchuk,

Georgiev

2024

BioEssays

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The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2‐type zinc finger domains that specifically bind to DNA. Few well‐studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.

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Loss of the insulator protein CTCF during nematode evolution

Cited by 88 publications

References 92 publications

The chromatin insulator CTCF and the emergence of metazoan diversity

The chromatin insulator CTCF and the emergence of metazoan diversity

Broad Chromatin Domains: An Important Facet of Genome Regulation

C2H2 proteins: Evolutionary aspects of domain architecture and diversification

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