Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues
<p>Abstract</p> <p>Background</p> <p>More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts – NATs), some of which may play a key role in a range of human diseases. To date, several databases of <it>in sili...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2009-07-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/324 |
| _version_ | 1811259904303824896 |
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| author | Kendrick Howard Tanney Austin Oliver Gavin R Grigoriadis Anita Smalley Matt J Jat Parmjit Neville A Munro |
| author_facet | Kendrick Howard Tanney Austin Oliver Gavin R Grigoriadis Anita Smalley Matt J Jat Parmjit Neville A Munro |
| author_sort | Kendrick Howard |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts – NATs), some of which may play a key role in a range of human diseases. To date, several databases of <it>in silico </it>defined human sense-antisense (SAS) pairs have appeared, however no study has focused on differential expression of SAS pairs in breast tissue. We therefore investigated the expression levels of sense and antisense transcripts in normal and malignant human breast epithelia using the Affymetrix HG-U133 Plus 2.0 and Almac Diagnostics Breast Cancer DSA microarray technologies as well as massively parallel signature sequencing (MPSS) data.</p> <p>Results</p> <p>The expression of more than 2500 antisense transcripts were detected in normal breast duct luminal cells and in primary breast tumors substantially enriched for their epithelial cell content by DSA microarray. Expression of 431 NATs were confirmed by either of the other two technologies. A corresponding sense transcript could be identified on DSA for 257 antisense transcripts. Of these SAS pairs, 163 have not been previously reported. A positive correlation of differential expression between normal and malignant breast samples was observed for most SAS pairs. Orientation specific RT-QPCR of selected SAS pairs validated their expression in several breast cancer cell lines and solid breast tumours.</p> <p>Conclusion</p> <p>Disease-focused and antisense enriched microarray platforms (such as Breast Cancer DSA) confirm the assumption that antisense transcription in the human breast is more prevalent than previously anticipated. Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated. Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.</p> |
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| id | doaj.art-6868d1e91bf24195b802f1934c9deaee |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T18:39:41Z |
| publishDate | 2009-07-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-6868d1e91bf24195b802f1934c9deaee2022-12-22T03:20:50ZengBMCBMC Genomics1471-21642009-07-0110132410.1186/1471-2164-10-324Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissuesKendrick HowardTanney AustinOliver Gavin RGrigoriadis AnitaSmalley Matt JJat ParmjitNeville A Munro<p>Abstract</p> <p>Background</p> <p>More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts – NATs), some of which may play a key role in a range of human diseases. To date, several databases of <it>in silico </it>defined human sense-antisense (SAS) pairs have appeared, however no study has focused on differential expression of SAS pairs in breast tissue. We therefore investigated the expression levels of sense and antisense transcripts in normal and malignant human breast epithelia using the Affymetrix HG-U133 Plus 2.0 and Almac Diagnostics Breast Cancer DSA microarray technologies as well as massively parallel signature sequencing (MPSS) data.</p> <p>Results</p> <p>The expression of more than 2500 antisense transcripts were detected in normal breast duct luminal cells and in primary breast tumors substantially enriched for their epithelial cell content by DSA microarray. Expression of 431 NATs were confirmed by either of the other two technologies. A corresponding sense transcript could be identified on DSA for 257 antisense transcripts. Of these SAS pairs, 163 have not been previously reported. A positive correlation of differential expression between normal and malignant breast samples was observed for most SAS pairs. Orientation specific RT-QPCR of selected SAS pairs validated their expression in several breast cancer cell lines and solid breast tumours.</p> <p>Conclusion</p> <p>Disease-focused and antisense enriched microarray platforms (such as Breast Cancer DSA) confirm the assumption that antisense transcription in the human breast is more prevalent than previously anticipated. Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated. Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.</p>http://www.biomedcentral.com/1471-2164/10/324 |
| spellingShingle | Kendrick Howard Tanney Austin Oliver Gavin R Grigoriadis Anita Smalley Matt J Jat Parmjit Neville A Munro Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues BMC Genomics |
| title | Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues |
| title_full | Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues |
| title_fullStr | Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues |
| title_full_unstemmed | Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues |
| title_short | Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues |
| title_sort | identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues |
| url | http://www.biomedcentral.com/1471-2164/10/324 |
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