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Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing
Disconnected interacting protein 2 homolog A (DIP2A) is highly expressed in nervous system and respiratory system of developing embryos. However, genes regulated by Dip2a in developing brain and lung have not been systematically studied. Transcriptome of brain and lung in embryonic 19.5 day (E19.5)...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619597/ https://www.ncbi.nlm.nih.gov/pubmed/31291246 http://dx.doi.org/10.1371/journal.pone.0213702 |
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author | Sah, Rajiv Kumar Yang, Analn Bah, Fatoumata Binta Adlat, Salah Bohio, Ameer Ali Oo, Zin Mar Wang, Chenhao Myint, May Zun Zaw Bahadar, Noor Zhang, Luqing Feng, Xuechao Zheng, Yaowu |
author_facet | Sah, Rajiv Kumar Yang, Analn Bah, Fatoumata Binta Adlat, Salah Bohio, Ameer Ali Oo, Zin Mar Wang, Chenhao Myint, May Zun Zaw Bahadar, Noor Zhang, Luqing Feng, Xuechao Zheng, Yaowu |
author_sort | Sah, Rajiv Kumar |
collection | PubMed |
description | Disconnected interacting protein 2 homolog A (DIP2A) is highly expressed in nervous system and respiratory system of developing embryos. However, genes regulated by Dip2a in developing brain and lung have not been systematically studied. Transcriptome of brain and lung in embryonic 19.5 day (E19.5) were compared between wild type and Dip2a(-/-) mice. An average of 50 million reads per sample was mapped to the reference sequence. A total of 214 DEGs were detected in brain (82 up and 132 down) and 1900 DEGs in lung (1259 up and 641 down). GO enrichment analysis indicated that DEGs in both Brain and Lung were mainly enriched in biological processes ‘DNA-templated transcription and Transcription from RNA polymerase II promoter’, ‘multicellular organism development’, ‘cell differentiation’ and ‘apoptotic process’. In addition, COG classification showed that both were mostly involved in ‘Replication, Recombination, and Repair’, ‘Signal transduction and mechanism’, ‘Translation, Ribosomal structure and Biogenesis’ and ‘Transcription’. KEGG enrichment analysis showed that brain was mainly enriched in ‘Thyroid cancer’ pathway whereas lung in ‘Complement and Coagulation Cascades’ pathway. Transcription factor (TF) annotation analysis identified Zinc finger domain containing (ZF) proteins were mostly regulated in lung and brain. Interestingly, study identified genes Skor2, Gpr3711, Runx1, Erbb3, Frmd7, Fut10, Sox11, Hapln1, Tfap2c and Plxnb3 from brain that play important roles in neuronal cell maturation, differentiation, and survival; genes Hoxa5, Eya1, Errfi1, Sox11, Shh, Igf1, Ccbe1, Crh, Fgf9, Lama5, Pdgfra, Ptn, Rbp4 and Wnt7a from lung are important in lung development. Expression levels of the candidate genes were validated by qRT-PCR. Genome wide transcriptional analysis using wild type and Dip2a knockout mice in brain and lung at embryonic day 19.5 (E19.5) provided a genetic basis of molecular function of these genes. |
format | Online Article Text |
id | pubmed-6619597 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-66195972019-07-25 Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing Sah, Rajiv Kumar Yang, Analn Bah, Fatoumata Binta Adlat, Salah Bohio, Ameer Ali Oo, Zin Mar Wang, Chenhao Myint, May Zun Zaw Bahadar, Noor Zhang, Luqing Feng, Xuechao Zheng, Yaowu PLoS One Research Article Disconnected interacting protein 2 homolog A (DIP2A) is highly expressed in nervous system and respiratory system of developing embryos. However, genes regulated by Dip2a in developing brain and lung have not been systematically studied. Transcriptome of brain and lung in embryonic 19.5 day (E19.5) were compared between wild type and Dip2a(-/-) mice. An average of 50 million reads per sample was mapped to the reference sequence. A total of 214 DEGs were detected in brain (82 up and 132 down) and 1900 DEGs in lung (1259 up and 641 down). GO enrichment analysis indicated that DEGs in both Brain and Lung were mainly enriched in biological processes ‘DNA-templated transcription and Transcription from RNA polymerase II promoter’, ‘multicellular organism development’, ‘cell differentiation’ and ‘apoptotic process’. In addition, COG classification showed that both were mostly involved in ‘Replication, Recombination, and Repair’, ‘Signal transduction and mechanism’, ‘Translation, Ribosomal structure and Biogenesis’ and ‘Transcription’. KEGG enrichment analysis showed that brain was mainly enriched in ‘Thyroid cancer’ pathway whereas lung in ‘Complement and Coagulation Cascades’ pathway. Transcription factor (TF) annotation analysis identified Zinc finger domain containing (ZF) proteins were mostly regulated in lung and brain. Interestingly, study identified genes Skor2, Gpr3711, Runx1, Erbb3, Frmd7, Fut10, Sox11, Hapln1, Tfap2c and Plxnb3 from brain that play important roles in neuronal cell maturation, differentiation, and survival; genes Hoxa5, Eya1, Errfi1, Sox11, Shh, Igf1, Ccbe1, Crh, Fgf9, Lama5, Pdgfra, Ptn, Rbp4 and Wnt7a from lung are important in lung development. Expression levels of the candidate genes were validated by qRT-PCR. Genome wide transcriptional analysis using wild type and Dip2a knockout mice in brain and lung at embryonic day 19.5 (E19.5) provided a genetic basis of molecular function of these genes. Public Library of Science 2019-07-10 /pmc/articles/PMC6619597/ /pubmed/31291246 http://dx.doi.org/10.1371/journal.pone.0213702 Text en © 2019 Sah et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Sah, Rajiv Kumar Yang, Analn Bah, Fatoumata Binta Adlat, Salah Bohio, Ameer Ali Oo, Zin Mar Wang, Chenhao Myint, May Zun Zaw Bahadar, Noor Zhang, Luqing Feng, Xuechao Zheng, Yaowu Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing |
title | Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing |
title_full | Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing |
title_fullStr | Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing |
title_full_unstemmed | Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing |
title_short | Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing |
title_sort | transcriptome profiling of mouse brain and lung under dip2a regulation using rna-sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619597/ https://www.ncbi.nlm.nih.gov/pubmed/31291246 http://dx.doi.org/10.1371/journal.pone.0213702 |
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