Project description:Here we describe an additional member of the Vitamin K-dependent protease family comprising the Gla-EGF1-EGF2-SP domain architecture. These proteases were found in different vertebrate classes including jawless fish, cartilaginous fish, bony fish, reptiles, birds and marsupials but not in other mammals. We have investigated for the first time the homolog of the garter snake Thamnophis sirtalis and thus called these proteases ‘sirtilins’.

2019-02-22 | PXD010679 | Pride

Thamnophis elegans

Project description:Thamnophis elegans Transcriptome or Gene expression

| PRJNA183122 | ENA

Reorganization of HoxD regulatory landscapes during the evolution of a snake-like body plan (ChIP-seq)

Project description:While the vertebrate body plan is highly conserved amongst all species of this taxon, extreme variations thereof can be documented in snakes, which display both an absence of limbs and an unusually elongated trunk. As Hox genes are strong candidates both for the making and the evolution of this body plan, their comparative study in such a morphologically diverged group is informative regarding their potential causative importance in these processes. In this work we use an interspecies comparative approach where different aspects of regulation at the HoxD locus are investigated. We find that although spatial collinearity and associated epigenetic mark dynamics are conserved in the corn snake, other regulatory modalities have been largely restructured. A BAC transgenic approach indeed revealed that, while the majority of mesodermal enhancers in vertebrates appear to be mostly located outside of the cluster, the corn snake contains most mesodermal trunk enhancers within the HoxD cluster. We also find that, despite the absence of limbs and an altered Hoxd gene regulation in external genitalia, the bimodal chromatin structure at the corn snake HoxD locus is maintained. The analysis of particular enhancer sequences initially defined in the mouse and further isolated at the snake orthologous locus showed differences in their specificities for the limb and genital bud expression. Of particular interest, a snake counterpart of a mouse limb-only enhancer sequence evolved into a genital-only enhancer. Such a regulatory exaptation suggests that enhancer versatility may have been an important factor to accompany the transition towards the snake body plan. These results show that vertebrate morphological evolution is likely to have been associated with extensive reorganization at the HoxD regulatory landscapes while respecting a very conserved general regulatory framework.

2016-11-05 | GSE79047 | GEO

Genetic Adaptation of C. elegans to Environment Changes II: Multigenerational Analysis of Genome-wide Chromatin Remodeling

Project description:Chemical modifications to the tails of histone proteins act as gene regulators that play a pivotal role in adaptive responses to environmental stress. Determining the short and long term kinetics of histone marks is essential for understanding their functions in adaptation. We used Caenorhabditis elegans as a model organism to study the histone modification kinetics in response to environmental stress, taking advantage of their ability to live in both terrestrial and aquatic environments. We investigated the multigenerational genome-wide dynamics of five histone marks (H3K4me3, H3K27me3, H4K20me1, H3K36me1, and H3K9me3) by maintaining P0 animals on terrestrial (agar plates), F1 in aquatic cultures, and F2 back on terrestrial environments. We determined the distributions of histone marks in the gene promoter regions and found that H4K20me1, H3K36me1, and H3K9me3 showed up to eleven-fold differences in density, whereas H3K4me3 and H3K27me3 remained highly constant during adaptation from terrestrial to aquatic environments. Furthermore, we predicted that up to five combinations of histone marks can co-occupy single gene promoters and confirmed the colocalization of these histone marks by structured illumination microscopy. The co-occupancy increases with environment changes and different co-occupancy patterns contribute to variances in gene expressions and thereby presents a supporting evidence for the histone code hypothesis.

2021-07-09 | GSE103775 | GEO