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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq]

ABSTRACT: A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq]

PROVIDER: PRJNA562519 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10046030_1.fastq.gz	Fastqsanger.gz
	SRR10046030_2.fastq.gz	Fastqsanger.gz
	SRR10046031_1.fastq.gz	Fastqsanger.gz
	SRR10046031_2.fastq.gz	Fastqsanger.gz
	SRR10046032_1.fastq.gz	Fastqsanger.gz

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [RNA-seq]

Project description:We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq]

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development

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

2019-09-17 | GSE136445 | GEO

High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

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Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration

Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.

2016-06-01 | E-GEOD-74415 | biostudies-arrayexpress

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Deep evolutionary origin of limb and fin regeneration.

Project description:Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-sequencing (RNA-seq) analysis of Polypterus and axolotl blastemas to provide support for a common origin of paired appendage regeneration in Osteichthyes (bony vertebrates). We show that, in addition to polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of 2 other nonteleost actinopterygians: the American paddlefish (Chondrostei) and the spotted gar (Holostei). Furthermore, we assessed regeneration in 4 teleost species and show that, with the exception of the blue gourami (Anabantidae), 3 species were capable of regenerating fins after endoskeleton amputation: the white convict and the oscar (Cichlidae), and the goldfish (Cyprinidae). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a shared genetic program of appendage regeneration. Comparison of RNA-seq data from early Polypterus blastema to single-cell RNA-seq data from axolotl limb bud and limb regeneration stages shows that Polypterus and axolotl share a regeneration-specific genetic program. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in Osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.

| S-EPMC6660751 | biostudies-literature

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