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Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [ATAC-seq]

ABSTRACT: Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [ATAC-seq]

PROVIDER: PRJNA691875 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13428031_1.fastq.gz	Fastqsanger.gz
	SRR13428031_2.fastq.gz	Fastqsanger.gz
	SRR13428032_1.fastq.gz	Fastqsanger.gz
	SRR13428032_2.fastq.gz	Fastqsanger.gz
	SRR13428033_1.fastq.gz	Fastqsanger.gz

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Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [ATAC-seq]

Project description:Understanding the origin of morphological diversity across vertebrates is central to evolutionary developmental biology. cis-regulatory elements (CRE) such as enhancers and promoters interpret precise spatiotemporal cues to control and coordinate gene expression. To get insights into both conserved and species-specific variations during early limb patterning and outgrowth, we leverage genome-wide comprehensive assessment of chromatin accessibility and transcriptional changes during mouse forelimb and chicken wing bud development. Our analysis reveals temporal modulation of chromatin accessibility and expression as well as their temporal relationship during the progression of mouse forelimb and chicken wing bud development. Transcription factor binding site enrichment analysis and putative TF occupancy as inferred by integrating TF binding motifs and chromatin accessibility information reveal temporal TF-DNA interactions during forelimb/wing bud patterning. Finally, the integration of accessibility, expression, and TF binding site information allowed to identify candidate gene targets of HAND2 and GLI3 that include conserved as well as species-specific transcriptional regulator-gene interactions.

2021-07-31 | GSE164736 | GEO

Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [RNA-seq]

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Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development

Project description:Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development

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Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [RNA-seq]

Project description:Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development [RNA-seq]

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Shifts in pigeon limb identity reveal conserved genetic networks

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Project description:Shifts in pigeon limb identity reveal conserved genetic networks

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Chromatin remodeling and expression dynamics reveal conserved and species-specific regulation during mouse and chicken limb development

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-07-31 | GSE164738 | GEO

Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development.

Project description:Chromatin remodeling and genomic alterations impact spatio-temporal regulation of gene expression, which is central to embryonic development. The analysis of mouse and chicken limb development provides important insights into the morphoregulatory mechanisms, however little is known about the regulatory differences underlying their morphological divergence. Here, we identify the underlying shared and species-specific epigenomic and genomic variations. In mouse forelimb buds, we observe striking synchrony between the temporal dynamics of chromatin accessibility and gene expression, while their divergence in chicken wing buds uncovers species-specific regulatory heterochrony. In silico mapping of transcription factor binding sites and computational footprinting establishes the developmental time-restricted transcription factor-DNA interactions. Finally, the construction of target gene networks for HAND2 and GLI3 transcriptional regulators reveals both conserved and species-specific interactions. Our analysis reveals the impact of genome evolution on the regulatory interactions orchestrating vertebrate limb bud morphogenesis and provides a molecular framework for comparative Evo-Devo studies.

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Shifts in pigeon limb identity reveal conserved genetic networks

Project description:The goal of this study is to identify genetic network changes that accompany shifts in limb identity.

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Multi-species atlas resolves an axolotl limb development and regeneration paradox

Project description:Humans and other tetrapods are considered to require apical-ectodermal-ridge, AER, cells for limb development, and AER-like cells are suggested to be re-formed to initiate limb regeneration. Paradoxically, the presence of AER in the axolotl, the primary regeneration model organism, remains controversial. Here, by leveraging a single-cell transcriptomics-based multi-species atlas, composed of axolotl, human, mouse, chicken, and frog cells, we first established that axolotls contain cells with AER characteristics. Surprisingly, further analyses and spatial transcriptomics revealed that axolotl limbs do not fully re-form AER cells during regeneration. Moreover, the axolotl mesoderm displays part of the AER machinery, revealing a novel program for limb (re)growth. These results clarify the debate about the axolotl AER and the extent to which the limb developmental program is recapitulated during regeneration.

2023-09-20 | GSE243225 | GEO

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