Cargando…

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of...

Descripción completa

Detalles Bibliográficos
Autores principales: Amândio, Ana Rita, Beccari, Leonardo, Lopez-Delisle, Lucille, Mascrez, Bénédicte, Zakany, Jozsef, Gitto, Sandra, Duboule, Denis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559674/
https://www.ncbi.nlm.nih.gov/pubmed/34711654
http://dx.doi.org/10.1101/gad.348934.121
_version_ 1784592806808911872
author Amândio, Ana Rita
Beccari, Leonardo
Lopez-Delisle, Lucille
Mascrez, Bénédicte
Zakany, Jozsef
Gitto, Sandra
Duboule, Denis
author_facet Amândio, Ana Rita
Beccari, Leonardo
Lopez-Delisle, Lucille
Mascrez, Bénédicte
Zakany, Jozsef
Gitto, Sandra
Duboule, Denis
author_sort Amândio, Ana Rita
collection PubMed
description Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the misregulation of Hoxd genes in specific structures. Altogether, while most enhancer–promoter interactions can occur in the absence of this series of CTCF sites, the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer–promoter interactions, and some doing both, whereas they all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites among paralogous Hox clusters or between various vertebrates.
format Online
Article
Text
id pubmed-8559674
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Cold Spring Harbor Laboratory Press
record_format MEDLINE/PubMed
spelling pubmed-85596742021-11-10 Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster Amândio, Ana Rita Beccari, Leonardo Lopez-Delisle, Lucille Mascrez, Bénédicte Zakany, Jozsef Gitto, Sandra Duboule, Denis Genes Dev Research Paper Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the misregulation of Hoxd genes in specific structures. Altogether, while most enhancer–promoter interactions can occur in the absence of this series of CTCF sites, the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer–promoter interactions, and some doing both, whereas they all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites among paralogous Hox clusters or between various vertebrates. Cold Spring Harbor Laboratory Press 2021-11-01 /pmc/articles/PMC8559674/ /pubmed/34711654 http://dx.doi.org/10.1101/gad.348934.121 Text en © 2021 Amândio et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/This article, published in Genes & Development, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) .
spellingShingle Research Paper
Amândio, Ana Rita
Beccari, Leonardo
Lopez-Delisle, Lucille
Mascrez, Bénédicte
Zakany, Jozsef
Gitto, Sandra
Duboule, Denis
Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
title Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
title_full Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
title_fullStr Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
title_full_unstemmed Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
title_short Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
title_sort sequential in cis mutagenesis in vivo reveals various functions for ctcf sites at the mouse hoxd cluster
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559674/
https://www.ncbi.nlm.nih.gov/pubmed/34711654
http://dx.doi.org/10.1101/gad.348934.121
work_keys_str_mv AT amandioanarita sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster
AT beccarileonardo sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster
AT lopezdelislelucille sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster
AT mascrezbenedicte sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster
AT zakanyjozsef sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster
AT gittosandra sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster
AT dubouledenis sequentialincismutagenesisinvivorevealsvariousfunctionsforctcfsitesatthemousehoxdcluster