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Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [ATAC-seq]

ABSTRACT: Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [ATAC-seq]

PROVIDER: PRJNA899788 | ENA |

REPOSITORIES: ENA

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Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

Project description:Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

| PRJNA899785 | ENA

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [RNA-seq]

Project description:Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [RNA-seq]

| PRJNA899787 | ENA

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [Cut&Tag]

Project description:Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [Cut&Tag]

| PRJNA899786 | ENA

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [ATAC-seq]

Project description:The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program. Profiling chromatin accessibility (ACRs) of Axoltol limb connective tissue cells, and compare among developmental limb buds, and mature limb at different segments and regeneration time points.

2023-04-10 | GSE217592 | GEO

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [Cut&Tag]

Project description:The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program. Profiling histone marks of Axoltol limb connective tissue cells, and comparing among limb different limb segments and mature vs regeneration time points.

2023-04-10 | GSE217591 | GEO

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [RNA-seq]

Project description:The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program. We performed Differential Gene expression analysis using data obtained from RNA-seq of two mature limb segments (mature arm vs hand). Therefore, we performed libraries from the mature arm and 5, 9, 13 dpa regenerating arm blastema.

2023-04-10 | GSE217593 | GEO

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

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

2023-04-10 | GSE217594 | GEO

A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors

Project description:Discovery of genes driving axolotl limb regeneration has been challenging due to limited genomic resources. We assembled 42 RNA-Seq samples totaling approximately 1.3 billion 100 base paired-end reads using Trinity (Grabherr M.G. et al, Nature Biotechnology, 2011; Haas B.J. et al, Nature Protocols, 2013): https://github.com/trinityrnaseq/trinityrnaseq/wiki). We created a transcriptome with complete sequence information for most axolotl genes, identified transcriptional profiles that distinguish blastemas from differentiated limb tissues, and uncovered functional roles for cirbp and kazald1 in limb regeneration.

2016-12-15 | GSE92429 | GEO

Single-nucleus multiome (RNA+ATAC) sequencing of the axolotl pallium

Project description:In order to understand the genomic and transcriptomic variability of the axolotl pallium, as well as reconstruct their intrinsic gene regulatory networks, we performed single-nucleus multiome sequencing (RNA and open chromatin) of whole axolotl pallium.

2022-07-20 | E-MTAB-11666 | biostudies-arrayexpress

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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