Limits...
Loss of the insulator protein CTCF during nematode evolution.

Heger P, Marin B, Schierenberg E - BMC Mol. Biol. (2009)

Bottom Line: We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes.Here, all or some of these components are missing.Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly adopted their function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Zoological Institute, University of Cologne, Kerpener Strasse 15, 50937 Köln, Germany. peter.heger@uni-koeln.de

ABSTRACT

Background: The zinc finger (ZF) protein CTCF (CCCTC-binding factor) is highly conserved in Drosophila and vertebrates where it has been shown to mediate chromatin insulation at a genomewide level. A mode of genetic regulation that involves insulators and insulator binding proteins to establish independent transcriptional units is currently not known in nematodes including Caenorhabditis elegans. We therefore searched in nematodes for orthologs of proteins that are involved in chromatin insulation.

Results: While orthologs for other insulator proteins were absent in all 35 analysed nematode species, we find orthologs of CTCF in a subset of nematodes. As an example for these we cloned the Trichinella spiralis CTCF-like gene and revealed a genomic structure very similar to the Drosophila counterpart. To investigate the pattern of CTCF occurrence in nematodes, we performed phylogenetic analysis with the ZF protein sets of completely sequenced nematodes. We show that three ZF proteins from three basal nematodes cluster together with known CTCF proteins whereas no zinc finger protein of C. elegans and other derived nematodes does so.

Conclusion: Our findings show that CTCF and possibly chromatin insulation are present in basal nematodes. We suggest that the insulator protein CTCF has been secondarily lost in derived nematodes like C. elegans. We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes. Here, all or some of these components are missing. Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly adopted their function.

Show MeSH

Related in: MedlinePlus

Conserved genomic organisation of invertebrate CTCFs. A, B, C: Genomic CTCF loci of vertebrates, Drosophila [19] and Trichinella, drawn to scale. Transcription start (arrow), transcription end (polyA), translation start (ATG) and stop (TAA, TAG, TGA), exons (box), introns (line), protein coding region (shaded), and zinc finger region (light green) are indicated. To illustrate the structure of vertebrate CTCFs, human CTCF is depicted (accession number NT_010498). D: Domain organisation of tsCTCF. Ⓟ: Predicted Tyrosine phosphorylation site, polyQ: poly-Glutamine tract, S-rich: Serine-rich region, N-rich: Asparagine-rich region, RCC1: RCC1 chromatin binding motif, ZF: Zinc finger region. Predicted N-glycosylation, N-myristoylation and most phosphorylation sites are not shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2749850&req=5

Figure 1: Conserved genomic organisation of invertebrate CTCFs. A, B, C: Genomic CTCF loci of vertebrates, Drosophila [19] and Trichinella, drawn to scale. Transcription start (arrow), transcription end (polyA), translation start (ATG) and stop (TAA, TAG, TGA), exons (box), introns (line), protein coding region (shaded), and zinc finger region (light green) are indicated. To illustrate the structure of vertebrate CTCFs, human CTCF is depicted (accession number NT_010498). D: Domain organisation of tsCTCF. Ⓟ: Predicted Tyrosine phosphorylation site, polyQ: poly-Glutamine tract, S-rich: Serine-rich region, N-rich: Asparagine-rich region, RCC1: RCC1 chromatin binding motif, ZF: Zinc finger region. Predicted N-glycosylation, N-myristoylation and most phosphorylation sites are not shown.

Mentions: To confirm our computational identification of putative CTCF orthologs in basal nematodes, we cloned the mRNA of the T. spiralis CTCF ortholog (tsCTCF). Comparison with the unpublished T. spiralis genome sequence assembly (accession number ABIR01000000) revealed that tsCTCF lies on a 6.5 kb genomic locus. The primary transcript contains four exons, with the first and last being untranslated, and three introns, with a large second intron (1.7 kb). The resulting 4.6 kb mRNA has a 414 bp 5'UTR and a 1328 bp 3'UTR, both harboring a small intron of about 100 bp. The deduced protein coding region (948 AA) is a fusion of two exons, a small first one and a large second exon carrying the entire ZF region (Figure 1B).


Loss of the insulator protein CTCF during nematode evolution.

Heger P, Marin B, Schierenberg E - BMC Mol. Biol. (2009)

Conserved genomic organisation of invertebrate CTCFs. A, B, C: Genomic CTCF loci of vertebrates, Drosophila [19] and Trichinella, drawn to scale. Transcription start (arrow), transcription end (polyA), translation start (ATG) and stop (TAA, TAG, TGA), exons (box), introns (line), protein coding region (shaded), and zinc finger region (light green) are indicated. To illustrate the structure of vertebrate CTCFs, human CTCF is depicted (accession number NT_010498). D: Domain organisation of tsCTCF. Ⓟ: Predicted Tyrosine phosphorylation site, polyQ: poly-Glutamine tract, S-rich: Serine-rich region, N-rich: Asparagine-rich region, RCC1: RCC1 chromatin binding motif, ZF: Zinc finger region. Predicted N-glycosylation, N-myristoylation and most phosphorylation sites are not shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2749850&req=5

Figure 1: Conserved genomic organisation of invertebrate CTCFs. A, B, C: Genomic CTCF loci of vertebrates, Drosophila [19] and Trichinella, drawn to scale. Transcription start (arrow), transcription end (polyA), translation start (ATG) and stop (TAA, TAG, TGA), exons (box), introns (line), protein coding region (shaded), and zinc finger region (light green) are indicated. To illustrate the structure of vertebrate CTCFs, human CTCF is depicted (accession number NT_010498). D: Domain organisation of tsCTCF. Ⓟ: Predicted Tyrosine phosphorylation site, polyQ: poly-Glutamine tract, S-rich: Serine-rich region, N-rich: Asparagine-rich region, RCC1: RCC1 chromatin binding motif, ZF: Zinc finger region. Predicted N-glycosylation, N-myristoylation and most phosphorylation sites are not shown.
Mentions: To confirm our computational identification of putative CTCF orthologs in basal nematodes, we cloned the mRNA of the T. spiralis CTCF ortholog (tsCTCF). Comparison with the unpublished T. spiralis genome sequence assembly (accession number ABIR01000000) revealed that tsCTCF lies on a 6.5 kb genomic locus. The primary transcript contains four exons, with the first and last being untranslated, and three introns, with a large second intron (1.7 kb). The resulting 4.6 kb mRNA has a 414 bp 5'UTR and a 1328 bp 3'UTR, both harboring a small intron of about 100 bp. The deduced protein coding region (948 AA) is a fusion of two exons, a small first one and a large second exon carrying the entire ZF region (Figure 1B).

Bottom Line: We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes.Here, all or some of these components are missing.Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly adopted their function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Zoological Institute, University of Cologne, Kerpener Strasse 15, 50937 Köln, Germany. peter.heger@uni-koeln.de

ABSTRACT

Background: The zinc finger (ZF) protein CTCF (CCCTC-binding factor) is highly conserved in Drosophila and vertebrates where it has been shown to mediate chromatin insulation at a genomewide level. A mode of genetic regulation that involves insulators and insulator binding proteins to establish independent transcriptional units is currently not known in nematodes including Caenorhabditis elegans. We therefore searched in nematodes for orthologs of proteins that are involved in chromatin insulation.

Results: While orthologs for other insulator proteins were absent in all 35 analysed nematode species, we find orthologs of CTCF in a subset of nematodes. As an example for these we cloned the Trichinella spiralis CTCF-like gene and revealed a genomic structure very similar to the Drosophila counterpart. To investigate the pattern of CTCF occurrence in nematodes, we performed phylogenetic analysis with the ZF protein sets of completely sequenced nematodes. We show that three ZF proteins from three basal nematodes cluster together with known CTCF proteins whereas no zinc finger protein of C. elegans and other derived nematodes does so.

Conclusion: Our findings show that CTCF and possibly chromatin insulation are present in basal nematodes. We suggest that the insulator protein CTCF has been secondarily lost in derived nematodes like C. elegans. We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes. Here, all or some of these components are missing. Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly adopted their function.

Show MeSH
Related in: MedlinePlus