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Status |
Public on Apr 10, 2023 |
Title |
Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [RNA-seq] |
Organism |
Ambystoma mexicanum |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
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.
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Overall design |
Comparative gene expression profiling analysis of RNA-seq data for mature UA vs Hand, and mature UA vs UA BLs in different time points.
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Contributor(s) |
Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei J, Tanaka EM |
Citation missing |
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Submission date |
Nov 09, 2022 |
Last update date |
Oct 04, 2023 |
Contact name |
Jingkui Wang |
E-mail(s) |
jingkui.wang@imp.ac.at
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Organization name |
Research Institute of Molecular Pathology (IMP)
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Lab |
Tanaka
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Street address |
Campus-Vienna-Biocenter 1
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City |
Vienna |
ZIP/Postal code |
1030 |
Country |
Austria |
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Platforms (2) |
GPL27159 |
Illumina NovaSeq 6000 (Ambystoma mexicanum) |
GPL32846 |
NextSeq 2000 (Ambystoma mexicanum) |
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Samples (16)
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This SubSeries is part of SuperSeries: |
GSE217594 |
Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration |
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Relations |
BioProject |
PRJNA899787 |