Epigenetic modification maintains intrinsic limb-cell identity in Xenopus limb bud regeneration.
Many amphibians can regenerate limbs, even in adulthood. If a limb is amputated, the stump generates a blastema that makes a complete, new limb in a process similar to developmental morphogenesis. The blastema is thought to inherit its limb-patterning properties from cells in the stump, and it retains the information despite changes in morphology, gene expression, and differentiation states required by limb regeneration. We hypothesized that these cellular properties are maintained as epigenetic memory through histone modifications. To test this hypothesis, we analyzed genome-wide histone modifications in Xenopus limb bud regeneration. The trimethylation of histone H3 at lysine 4 (H3K4me3) is closely related to an open chromatin structure that allows transcription factors access to genes, whereas the trimethylation of histone H3 at lysine 27 (H3K27me3) is related to a closed chromatin state that blocks the access of transcription factors. We compared these two modification profiles by high-throughput sequencing of samples prepared from the intact limb bud and the regenerative blastema by chromatin immunoprecipitation. For many developmental genes, histone modifications at the transcription start site were the same in the limb bud and the blastema, were stable during regeneration, and corresponded well to limb properties. These results support our hypothesis that histone modifications function as a heritable cellular memory to maintain limb cell properties, despite dynamic changes in gene expression during limb bud regeneration in Xenopus.
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
Shinichi
S
Hayashi
Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Japan.
Akane
A
Kawaguchi
Laboratory of Genome Informatics, Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan; Data Integration and Analysis Facility, National Institute for Basic Biology, Okazaki, Japan.
Ikuo
I
Uchiyama
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
Aiko
A
Kawasumi-Kita
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
Takuya
T
Kobayashi
Data Integration and Analysis Facility, National Institute for Basic Biology, Okazaki, Japan.
Hiroyo
H
Nishide
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
Rio
R
Tsutsumi
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
Kazuhiko
K
Tsuru
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
Takeshi
T
Inoue
Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Japan.
Hajime
H
Ogino
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
Kiyokazu
K
Agata
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
Koji
K
Tamura
Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan. Electronic address: yokoyoko@hirosaki-u.ac.jp.
Hitoshi
H
Yokoyama
D000241:Adenosine / Q000031:analogs & derivatives; D000818:Animals; D030801:Animals, Genetically Modified; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D044127:Epigenesis, Genetic / Q000502:physiology*; D005455:Fluorescent Antibody Technique; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D042421:Histone Code / Q000502:physiology*; D006657:Histones / Q000378:metabolism; D017403:In Situ Hybridization; D018878:Limb Buds / Q000502:physiology*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012038:Regeneration / Q000502:physiology*; D017422:Sequence Analysis, DNA; D014981:Xenopus / Q000502:physiology*
D017931:DNA Primers; D006657:Histones; C048460:3-deazaneplanocin; D000241:Adenosine
Cellular memory; Epigenetic modification; Histone; Limb regeneration