Transcriptional landscapes of Axolotl (Ambystoma mexicanum)

Juan Caballero-Pérez, Annie Espinal-Centeno, Francisco Falcon, Luis F. García-Ortega, Everardo Curiel-Quesada, Andrés Cruz-Hernández, Laszlo Bako, Xuemei Chen, Octavio Martínez, Mario Alberto Arteaga-Vázquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

© 2017 Elsevier Inc. The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.
Original languageAmerican English
Pages (from-to)227-239
Number of pages13
JournalDevelopmental Biology
DOIs
StatePublished - 15 Jan 2018

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Ambystoma mexicanum
MicroRNAs
Regeneration
Untranslated RNA
Messenger RNA
Open Reading Frames
Vertebrates
Protein Isoforms
Proteins
Extremities
Genome
Gene Expression
Liver
Population

Cite this

Caballero-Pérez, J., Espinal-Centeno, A., Falcon, F., García-Ortega, L. F., Curiel-Quesada, E., Cruz-Hernández, A., ... Cruz-Ramírez, A. (2018). Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Developmental Biology, 227-239. https://doi.org/10.1016/j.ydbio.2017.08.022
Caballero-Pérez, Juan ; Espinal-Centeno, Annie ; Falcon, Francisco ; García-Ortega, Luis F. ; Curiel-Quesada, Everardo ; Cruz-Hernández, Andrés ; Bako, Laszlo ; Chen, Xuemei ; Martínez, Octavio ; Alberto Arteaga-Vázquez, Mario ; Herrera-Estrella, Luis ; Cruz-Ramírez, Alfredo. / Transcriptional landscapes of Axolotl (Ambystoma mexicanum). In: Developmental Biology. 2018 ; pp. 227-239.
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Caballero-Pérez, J, Espinal-Centeno, A, Falcon, F, García-Ortega, LF, Curiel-Quesada, E, Cruz-Hernández, A, Bako, L, Chen, X, Martínez, O, Alberto Arteaga-Vázquez, M, Herrera-Estrella, L & Cruz-Ramírez, A 2018, 'Transcriptional landscapes of Axolotl (Ambystoma mexicanum)', Developmental Biology, pp. 227-239. https://doi.org/10.1016/j.ydbio.2017.08.022

Transcriptional landscapes of Axolotl (Ambystoma mexicanum). / Caballero-Pérez, Juan; Espinal-Centeno, Annie; Falcon, Francisco; García-Ortega, Luis F.; Curiel-Quesada, Everardo; Cruz-Hernández, Andrés; Bako, Laszlo; Chen, Xuemei; Martínez, Octavio; Alberto Arteaga-Vázquez, Mario; Herrera-Estrella, Luis; Cruz-Ramírez, Alfredo.

In: Developmental Biology, 15.01.2018, p. 227-239.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Transcriptional landscapes of Axolotl (Ambystoma mexicanum)

AU - Caballero-Pérez, Juan

AU - Espinal-Centeno, Annie

AU - Falcon, Francisco

AU - García-Ortega, Luis F.

AU - Curiel-Quesada, Everardo

AU - Cruz-Hernández, Andrés

AU - Bako, Laszlo

AU - Chen, Xuemei

AU - Martínez, Octavio

AU - Alberto Arteaga-Vázquez, Mario

AU - Herrera-Estrella, Luis

AU - Cruz-Ramírez, Alfredo

PY - 2018/1/15

Y1 - 2018/1/15

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AB - © 2017 Elsevier Inc. The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.

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JF - Developmental Biology

SN - 0012-1606

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Caballero-Pérez J, Espinal-Centeno A, Falcon F, García-Ortega LF, Curiel-Quesada E, Cruz-Hernández A et al. Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Developmental Biology. 2018 Jan 15;227-239. https://doi.org/10.1016/j.ydbio.2017.08.022