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
Conserved zinc finger region of tsCTCF. Multiple sequence alignment of the ZF domains of T. spiralis, human, and D. melanogaster CTCF. Similar and identical residues (grey), zinc coordinating residues (red, blue), and identical residues for DNA recognition (yellow) are indicated. ZF11 is missing in T. spiralis and is less conserved between D. melanogaster and man than ZF1 – 10.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Conserved zinc finger region of tsCTCF. Multiple sequence alignment of the ZF domains of T. spiralis, human, and D. melanogaster CTCF. Similar and identical residues (grey), zinc coordinating residues (red, blue), and identical residues for DNA recognition (yellow) are indicated. ZF11 is missing in T. spiralis and is less conserved between D. melanogaster and man than ZF1 – 10.

Mentions: The central region of the protein contains ten C2H2 ZFs conserved in all reported CTCF sequences [19,32]. Within vertebrates, the eleventh ZF is of the C2HC-type. In Drosophila however, ZF11 is a C2H2-type finger and displays only weak conservation of the critical DNA binding residues as well as a small insertion (Figure 2). In tsCTCF, ZF11 is missing entirely, and neither 3'Race PCR nor the genomic sequence at this locus gave indications for its presence. These observations suggest that conservation of ZF11 is not a strict requirement for functional CTCF proteins.


Loss of the insulator protein CTCF during nematode evolution.

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

Conserved zinc finger region of tsCTCF. Multiple sequence alignment of the ZF domains of T. spiralis, human, and D. melanogaster CTCF. Similar and identical residues (grey), zinc coordinating residues (red, blue), and identical residues for DNA recognition (yellow) are indicated. ZF11 is missing in T. spiralis and is less conserved between D. melanogaster and man than ZF1 – 10.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Conserved zinc finger region of tsCTCF. Multiple sequence alignment of the ZF domains of T. spiralis, human, and D. melanogaster CTCF. Similar and identical residues (grey), zinc coordinating residues (red, blue), and identical residues for DNA recognition (yellow) are indicated. ZF11 is missing in T. spiralis and is less conserved between D. melanogaster and man than ZF1 – 10.
Mentions: The central region of the protein contains ten C2H2 ZFs conserved in all reported CTCF sequences [19,32]. Within vertebrates, the eleventh ZF is of the C2HC-type. In Drosophila however, ZF11 is a C2H2-type finger and displays only weak conservation of the critical DNA binding residues as well as a small insertion (Figure 2). In tsCTCF, ZF11 is missing entirely, and neither 3'Race PCR nor the genomic sequence at this locus gave indications for its presence. These observations suggest that conservation of ZF11 is not a strict requirement for functional CTCF proteins.

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