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An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (4C-seq)

ABSTRACT: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (4C-seq)

PROVIDER: PRJNA497803 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8083840.fastq.gz	Fastqsanger.gz
	SRR8083850.fastq.gz	Fastqsanger.gz
	SRR8083841.fastq.gz	Fastqsanger.gz
	SRR8083851.fastq.gz	Fastqsanger.gz
	SRR8083832.fastq.gz	Fastqsanger.gz

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Similar Datasets

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (4C-seq)

Project description:Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci likely to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

2019-07-09 | GSE121564 | GEO

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

Project description:An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

| PRJNA497799 | ENA

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (ATAC-seq)

2019-07-09 | GSE121565 | GEO

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (ATAC-seq)

Project description:An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice (ATAC-seq)

| PRJNA497802 | ENA

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.

Project description:Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

| S-EPMC6606024 | biostudies-literature

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

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

2019-07-09 | GSE121566 | GEO

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs (4C-Seq)

Project description:During limb development, Hoxd genes are transcribed in two waves: Early on, when the arm and forearm are specified and subsequently, when digits form. While the latter phase is controlled by enhancers centromeric to the HoxD cluster, we show here that the early phase requires enhancers located in the opposite telomeric gene desert. The transition between the two types of regulations involves a functional switch between two distinct topological domains, as reflected by a subset of genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently shift to establish new contacts on the opposite side. This transition between two regulatory landscapes generates an intermediate area of low Hox dose developing into the wrist, the transition between our arms and our hands. This intriguing correspondence between genomic and morphological boundaries illustrates the mechanism underlying collinear Hox gene regulation in our developing appendages. Circular Chromosome Conformation Capture (4C seq) at the HoxD locus in developing proximal and distal limbs at E9.5 and E12.5

2013-06-07 | E-GEOD-45455 | biostudies-arrayexpress

DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [4C-Seq]

Project description:DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [4C-Seq]

| PRJNA677992 | ENA

Project description:An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

| PRJNA496392 | ENA

Comparative transcriptomic analysis of the proximal tibial growth plates of 14-day old Longshanks and wildtype mice

Project description:This study was undertaken to uncover the molecular pathways that underlie differences among individuals in rates of longitudinal growth and mature length of the long bones in a rodent model. To do so, the transcriptomic profiles of the proximal epiphyses of 14-day old CD-1 wildtype mice and the Longshanks mice were compared. The Longshanks mouse was selectively bred for longer tibiae in relation to body mass (see Marchini et al 2014 – BMC Evol Biol 14:258). Over 13 generations, Longshanks tibiae were 11-12% longer compared to random-bred wildtype mice (hereafter Controls) from the same genetic background (ICR or CD-1), but body mass was unchanged. By comparing the transcriptomes of samples of Control and Longshanks proximal tibiae, we sought to identify differentially expressed genes that were associated with the faster growth and longer tibia of the Longshanks mouse, as a window into the pathways that may underlie intra- and interspecific differences in limb bone size and shape. Results were further validated using qPCR and cell and tissue culture assays.

2021-12-01 | GSE189528 | GEO

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