Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling.
Background: Development of the cerebral cortex requires highly specific spatio-temporal regulation of gene expression. It is proposed that transcriptome profiling of the cerebral cortex at various developmental time points or regions will reveal candidate genes and associated molecular pathways in...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English English |
| Published: |
BioMed Central
2009
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| Online Access: | http://psasir.upm.edu.my/id/eprint/15711/ http://psasir.upm.edu.my/id/eprint/15711/1/Molecular%20networks%20involved%20in%20mouse%20cerebral%20corticogenesis%20and%20spatio.pdf |
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| author | Ling, King Hwa Hewitt, Chelsee Ann Beissbarth, Tim Hyde, Lavinia Banerjee, Kakoli Cheah , Pike See Cannon, Ping Z. Hahn, Christopher N. Thomas, Paul Q. Smyth, Gordon K. Tan, Seong-Seng Thomas, Tim Scott, Hamish S. |
| author_facet | Ling, King Hwa Hewitt, Chelsee Ann Beissbarth, Tim Hyde, Lavinia Banerjee, Kakoli Cheah , Pike See Cannon, Ping Z. Hahn, Christopher N. Thomas, Paul Q. Smyth, Gordon K. Tan, Seong-Seng Thomas, Tim Scott, Hamish S. |
| author_sort | Ling, King Hwa |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Background:
Development of the cerebral cortex requires highly specific spatio-temporal regulation of gene expression. It is proposed that transcriptome profiling of the cerebral cortex at various developmental time points or regions will reveal candidate genes and associated molecular pathways involved in cerebral corticogenesis.
Results:
Serial analysis of gene expression (SAGE) libraries were constructed from C57BL/6 mouse cerebral cortices of age embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4 to 6 months. Hierarchical clustering analysis of 561 differentially expressed transcripts showed regionalized, stage-specific and co-regulated expression profiles. SAGE expression profiles of 70 differentially expressed transcripts were validated using quantitative RT-PCR assays. Ingenuity pathway analyses of validated differentially expressed transcripts demonstrated that these transcripts possess distinctive functional properties related to various stages of cerebral corticogenesis and human neurological disorders. Genomic clustering analysis of the differentially expressed transcripts identified two highly transcribed genomic loci, Sox4 and Sox11, during embryonic cerebral corticogenesis. These loci feature unusual overlapping sense and antisense transcripts with alternative polyadenylation sites and differential expression. The Sox4 and Sox11 antisense transcripts were highly expressed in the brain compared to other mouse organs and are differentially expressed in both the proliferating and differentiating neural stem/progenitor cells and P19 (embryonal carcinoma) cells.
Conclusions:
We report validated gene expression profiles that have implications for understanding the associations between differentially expressed transcripts, novel targets and related disorders pertaining to cerebral corticogenesis. The study reports, for the first time, spatio-temporally regulated Sox4 and Sox11 antisense transcripts in the brain, neural stem/progenitor cells and P19 cells, suggesting they have an important role in cerebral corticogenesis and neuronal/glial cell differentiation. |
| first_indexed | 2025-11-15T08:04:10Z |
| format | Article |
| id | upm-15711 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English English |
| last_indexed | 2025-11-15T08:04:10Z |
| publishDate | 2009 |
| publisher | BioMed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-157112015-10-05T04:47:00Z http://psasir.upm.edu.my/id/eprint/15711/ Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Ling, King Hwa Hewitt, Chelsee Ann Beissbarth, Tim Hyde, Lavinia Banerjee, Kakoli Cheah , Pike See Cannon, Ping Z. Hahn, Christopher N. Thomas, Paul Q. Smyth, Gordon K. Tan, Seong-Seng Thomas, Tim Scott, Hamish S. Background: Development of the cerebral cortex requires highly specific spatio-temporal regulation of gene expression. It is proposed that transcriptome profiling of the cerebral cortex at various developmental time points or regions will reveal candidate genes and associated molecular pathways involved in cerebral corticogenesis. Results: Serial analysis of gene expression (SAGE) libraries were constructed from C57BL/6 mouse cerebral cortices of age embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4 to 6 months. Hierarchical clustering analysis of 561 differentially expressed transcripts showed regionalized, stage-specific and co-regulated expression profiles. SAGE expression profiles of 70 differentially expressed transcripts were validated using quantitative RT-PCR assays. Ingenuity pathway analyses of validated differentially expressed transcripts demonstrated that these transcripts possess distinctive functional properties related to various stages of cerebral corticogenesis and human neurological disorders. Genomic clustering analysis of the differentially expressed transcripts identified two highly transcribed genomic loci, Sox4 and Sox11, during embryonic cerebral corticogenesis. These loci feature unusual overlapping sense and antisense transcripts with alternative polyadenylation sites and differential expression. The Sox4 and Sox11 antisense transcripts were highly expressed in the brain compared to other mouse organs and are differentially expressed in both the proliferating and differentiating neural stem/progenitor cells and P19 (embryonal carcinoma) cells. Conclusions: We report validated gene expression profiles that have implications for understanding the associations between differentially expressed transcripts, novel targets and related disorders pertaining to cerebral corticogenesis. The study reports, for the first time, spatio-temporally regulated Sox4 and Sox11 antisense transcripts in the brain, neural stem/progenitor cells and P19 cells, suggesting they have an important role in cerebral corticogenesis and neuronal/glial cell differentiation. BioMed Central 2009-10 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/15711/1/Molecular%20networks%20involved%20in%20mouse%20cerebral%20corticogenesis%20and%20spatio.pdf Ling, King Hwa and Hewitt, Chelsee Ann and Beissbarth, Tim and Hyde, Lavinia and Banerjee, Kakoli and Cheah , Pike See and Cannon, Ping Z. and Hahn, Christopher N. and Thomas, Paul Q. and Smyth, Gordon K. and Tan, Seong-Seng and Thomas, Tim and Scott, Hamish S. (2009) Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Genome Biology, 10 (10). 104. ISSN 1465-6906; ESSN:1465-6914 http://www.biomedcentral.com/ 10.1186/gb-2009-10-10-r104 English |
| spellingShingle | Ling, King Hwa Hewitt, Chelsee Ann Beissbarth, Tim Hyde, Lavinia Banerjee, Kakoli Cheah , Pike See Cannon, Ping Z. Hahn, Christopher N. Thomas, Paul Q. Smyth, Gordon K. Tan, Seong-Seng Thomas, Tim Scott, Hamish S. Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. |
| title | Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. |
| title_full | Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. |
| title_fullStr | Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. |
| title_full_unstemmed | Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. |
| title_short | Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. |
| title_sort | molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of sox4 and sox11 novel antisense transcripts revealed by transcriptome profiling. |
| url | http://psasir.upm.edu.my/id/eprint/15711/ http://psasir.upm.edu.my/id/eprint/15711/ http://psasir.upm.edu.my/id/eprint/15711/ http://psasir.upm.edu.my/id/eprint/15711/1/Molecular%20networks%20involved%20in%20mouse%20cerebral%20corticogenesis%20and%20spatio.pdf |