Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1
Eukaryotic non-coding regulatory features contribute significantly to cellular plasticity which on aberration leads to cellular malignancy. Enhancers are cis-regulatory elements that contribute to the development of resistance to endocrine therapy in estrogen receptor (ER)-positive breast cancer lea...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2023-04-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.1177/11779322231167971 |
| _version_ | 1797839252378091520 |
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| author | N Sreekar Smeeta Shrestha |
| author_facet | N Sreekar Smeeta Shrestha |
| author_sort | N Sreekar |
| collection | DOAJ |
| description | Eukaryotic non-coding regulatory features contribute significantly to cellular plasticity which on aberration leads to cellular malignancy. Enhancers are cis-regulatory elements that contribute to the development of resistance to endocrine therapy in estrogen receptor (ER)-positive breast cancer leading to poor clinical outcome. ER is vital for therapeutic targets in ER-positive breast cancer. Here, we review and report the different regulatory features present on ER with the objective to delineate potential mechanisms which may contribute to development of resistance. The UCSC Genome Browser, data mining, and bioinformatics tools were used to review enhancers, transcription factors (TFs), histone marks, long non-coding RNAs (lncRNAs), and variants residing in the non-coding region of the ER gene. We report 7 enhancers, 3 of which were rich in TF-binding sites and histone marks in a cell line-specific manner. Furthermore, some enhancers contain estrogen resistance variants and sites for lncRNA. Our review speculates putative models suggesting potential aberrations in gene regulation and expression if these regulatory landscapes and assemblies are altered. This review gives an interesting perspective in designing integrated in vitro studies including non-coding elements to study development of endocrine resistance in ER-positive breast cancer. |
| first_indexed | 2024-04-09T15:54:59Z |
| format | Article |
| id | doaj.art-4d0d4b8409bc4090bfa248ac10bedf23 |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-04-09T15:54:59Z |
| publishDate | 2023-04-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-4d0d4b8409bc4090bfa248ac10bedf232023-04-25T17:33:44ZengSAGE PublishingBioinformatics and Biology Insights1177-93222023-04-011710.1177/11779322231167971Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1N SreekarSmeeta ShresthaEukaryotic non-coding regulatory features contribute significantly to cellular plasticity which on aberration leads to cellular malignancy. Enhancers are cis-regulatory elements that contribute to the development of resistance to endocrine therapy in estrogen receptor (ER)-positive breast cancer leading to poor clinical outcome. ER is vital for therapeutic targets in ER-positive breast cancer. Here, we review and report the different regulatory features present on ER with the objective to delineate potential mechanisms which may contribute to development of resistance. The UCSC Genome Browser, data mining, and bioinformatics tools were used to review enhancers, transcription factors (TFs), histone marks, long non-coding RNAs (lncRNAs), and variants residing in the non-coding region of the ER gene. We report 7 enhancers, 3 of which were rich in TF-binding sites and histone marks in a cell line-specific manner. Furthermore, some enhancers contain estrogen resistance variants and sites for lncRNA. Our review speculates putative models suggesting potential aberrations in gene regulation and expression if these regulatory landscapes and assemblies are altered. This review gives an interesting perspective in designing integrated in vitro studies including non-coding elements to study development of endocrine resistance in ER-positive breast cancer.https://doi.org/10.1177/11779322231167971 |
| spellingShingle | N Sreekar Smeeta Shrestha Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 Bioinformatics and Biology Insights |
| title | Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 |
| title_full | Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 |
| title_fullStr | Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 |
| title_full_unstemmed | Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 |
| title_short | Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1 |
| title_sort | bioinformatic evaluation of features on cis regulatory elements at 6q25 1 |
| url | https://doi.org/10.1177/11779322231167971 |
| work_keys_str_mv | AT nsreekar bioinformaticevaluationoffeaturesoncisregulatoryelementsat6q251 AT smeetashrestha bioinformaticevaluationoffeaturesoncisregulatoryelementsat6q251 |