MESOMELIC DYSPLASIAS ASSOCIATED WITH THE<i>HOXD</i>LOCUS ARE CAUSED BY REGULATORY REALLOCATIONS

Bolt, Christopher Chase; Lopez-Delisle, Lucille; Mascrez, Bénédicte; Duboule, Denis

doi:10.1101/2021.02.01.429171

Cited by 6 publications

(17 citation statements)

References 69 publications

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“…We next asked whether these changes in expression were due to reallocations in interactions between the genes and their regulatory landscapes. We performed Capture Hi-C in micro-dissected proximal forelimb cells of the Del(CBS1), Del(CBS1-3) and Del(CBS1-5) alleles and compared them with control samples (Bolt et al, 2021). In the Del(CBS1) allele, we observed a minor loss of interaction with the CS38-40 T-DOM sub-TAD boundary and a gain of ectopic interactions with T-DOMa, as seen on the subtraction maps (Fig.…”

Section: Effects Of Cbs Disruptions Upon Hoxd Gene Regulation In Developing Proximal Limb Budsmentioning

confidence: 83%

“…All four mammalian Hox clusters are partitioned in between two TADs, with a boundary systematically isolating the most posterior group 13 Hox gene from the others. Group 13 Hox genes are coding for proteins that participate to the morphogenesis of terminal structures and hence embryo development must be protected from the action of such proteins, which can abrogate axial extension (Young et al, 2009) or affect proper morphogenesis (Bolt et al, 2021;Darbellay et al, 2019) through their dominant negative function over other HOX proteins. This isolation is achieved through the positioning of Hox13 genes into a different TAD, thus making them unresponsive to the numerous enhancer sequences acting upon other Hox genes during development.…”

Section: Cbss In the Making Of The Tad Boundary At The Hoxd Clustermentioning

confidence: 99%

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

Lhopitallier

Beccari

Lopez-Delisle

et al. 2021

Preprint

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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 mis-regulation of Hoxd genes in specific structures. Altogether, while most enhancer-promoter interactions can occur in the absence of this series of CTCF sites, it seems that 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 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 amongst paralogous Hox clusters or between various vertebrates.

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Section: Effects Of Cbs Disruptions Upon Hoxd Gene Regulation In Developing Proximal Limb Budsmentioning

confidence: 83%

Section: Cbss In the Making Of The Tad Boundary At The Hoxd Clustermentioning

confidence: 99%

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

Lhopitallier

Beccari

Lopez-Delisle

et al. 2021

Preprint

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“…Sheth et al [2014]; Beccari et al [2016]; Kherdjemil et al [2016] showed that Hoxd13 represses the transcription of Hoxa11 in the embryonic distal limb leading to two distinct domains of expression. We use the scRNA-seq from Bolt et al [2021] which has been generated from embryonic forelimbs. A clustering analysis revealed 17 clusters.…”

Section: Estimating the Distribution Of Expression Values Of Amentioning

confidence: 99%

“…A clustering analysis revealed 17 clusters. Using Hoxd13 as a marker, 4 clusters (3,4,5,9) were attributed to the distal part of the limb [see Bolt et al, 2021]. Unexpectedly, Hoxa11 was not totally absent from these clusters.…”

Section: Estimating the Distribution Of Expression Values Of Amentioning

confidence: 99%

baredSC: Bayesian Approach to Retrieve Expression Distribution of Single-Cell

Lopez-Delisle¹,

Delisle

2021

Preprint

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The number of studies using single-cell RNA sequencing (scRNA-seq) is constantly growing. This powerful technique provides a sampling of the whole transcriptome of a cell. However, the commonly used droplet-based method often produces very sparse samples. Sparsity can be a major hurdle when studying the distribution of the expression of a specific gene or the correlation between the expressions of two genes. We show that the main technical noise associated with these scRNA-seq experiments is due to the sampling (i.e. Poisson noise). We developed a new tool named baredSC, for Bayesian Approach to Retrieve Expression Distribution of Single-Cell, which infers the intrinsic expression distribution in noisy single-cell data using a Gaussian mixture model (GMM). baredSC can be used to obtain the distribution in one dimension for individual genes and in two dimensions for pairs of genes, in particular to estimate the correlation in the two genes' expressions. We apply baredSC to simulated scRNA-seq data and show that the algorithm is able to uncover the expression distribution used to simulate the data, even in multi-modal cases with very sparse data. We also apply baredSC to two real biological data sets. First, we use it to measure the anti-correlation between Hoxd13 and Hoxa11, two genes with known genetic interaction in embryonic limb. Then, we study the expression of Pitx1 in embryonic hindlimb, for which a trimodal distribution has been identified through flow cytometry. While other methods to analyze scRNA-seq are too sensitive to sampling noise, baredSC reveals this trimodal distribution.

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“…While genomic rearrangements altering the structure of TADs were reported to impact proper gene regulation during development leading to genetic syndromes (e.g. (Bolt et al, 2021; Lupiáñez et al, 2015), in most cases, these rearrangements also affected enhancer-promoter spatial relationships, which makes a causal assessment difficult.…”

Section: Introductionmentioning

confidence: 99%

Developmental and Evolutionary Comparative Analysis of a Regulatory Landscape in Mammals and Birds

Hintermann

Guerreiro

Bolt

et al. 2021

Preprint

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Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk rely more on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CRE sequences, an observation supported by a genome-wide comparative approach.

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MESOMELIC DYSPLASIAS ASSOCIATED WITH THEHOXDLOCUS ARE CAUSED BY REGULATORY REALLOCATIONS

Cited by 6 publications

References 69 publications

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

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

baredSC: Bayesian Approach to Retrieve Expression Distribution of Single-Cell

Developmental and Evolutionary Comparative Analysis of a Regulatory Landscape in Mammals and Birds

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