Genome-Wide Transcript Profiling Reveals Novel Breast Cancer-Associated Intronic Sense RNAs Article Swipe
Sang Woo Kim
,
Elane Fishilevich
,
Gustavo Arango-Argoty
,
Yuefeng Lin
,
Guodong Liu
,
Zhihua Li
,
A. Paula Monaghan
,
Mark Nichols
,
Bino John
·
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0120296
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0120296
Non-coding RNAs (ncRNAs) play major roles in development and cancer progression. To identify novel ncRNAs that may identify key pathways in breast cancer development, we performed high-throughput transcript profiling of tumor and normal matched-pair tissue samples. Initial transcriptome profiling using high-density genome-wide tiling arrays revealed changes in over 200 novel candidate genomic regions that map to intronic regions. Sixteen genomic loci were identified that map to the long introns of five key protein-coding genes, CRIM1, EPAS1, ZEB2, RBMS1, and RFX2. Consistent with the known role of the tumor suppressor ZEB2 in the cancer-associated epithelial to mesenchymal transition (EMT), in situ hybridization reveals that the intronic regions deriving from ZEB2 as well as those from RFX2 and EPAS1 are down-regulated in cells of epithelial morphology, suggesting that these regions may be important for maintaining normal epithelial cell morphology. Paired-end deep sequencing analysis reveals a large number of distinct genomic clusters with no coding potential within the introns of these genes. These novel transcripts are only transcribed from the coding strand. A comprehensive search for breast cancer associated genes reveals enrichment for transcribed intronic regions from these loci, pointing to an underappreciated role of introns or mechanisms relating to their biology in EMT and breast cancer.
Related Topics
Concepts
Biology
Transcriptome
Gene
Genetics
Intron
Genome
Breast cancer
Gene expression profiling
Computational biology
Coding region
Gene expression
Cancer
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pone.0120296
- https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0120296&type=printable
- OA Status
- gold
- Cited By
- 3
- References
- 40
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2095217206
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2095217206Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1371/journal.pone.0120296Digital Object Identifier
- Title
-
Genome-Wide Transcript Profiling Reveals Novel Breast Cancer-Associated Intronic Sense RNAsWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2015Year of publication
- Publication date
-
2015-03-23Full publication date if available
- Authors
-
Sang Woo Kim, Elane Fishilevich, Gustavo Arango-Argoty, Yuefeng Lin, Guodong Liu, Zhihua Li, A. Paula Monaghan, Mark Nichols, Bino JohnList of authors in order
- Landing page
-
https://doi.org/10.1371/journal.pone.0120296Publisher landing page
- PDF URL
-
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0120296&type=printableDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0120296&type=printableDirect OA link when available
- Concepts
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Biology, Transcriptome, Gene, Genetics, Intron, Genome, Breast cancer, Gene expression profiling, Computational biology, Coding region, Gene expression, CancerTop concepts (fields/topics) attached by OpenAlex
- Cited by
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3Total citation count in OpenAlex
- Citations by year (recent)
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2020: 1, 2017: 1, 2016: 1Per-year citation counts (last 5 years)
- References (count)
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40Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.and | 8, 31, 78, 115, 201 |
| abstract_inverted_index.are | 117, 162 |
| abstract_inverted_index.for | 131, 172, 179 |
| abstract_inverted_index.key | 18, 71 |
| abstract_inverted_index.map | 54, 64 |
| abstract_inverted_index.may | 16, 128 |
| abstract_inverted_index.the | 66, 82, 86, 91, 103, 154, 166 |
| abstract_inverted_index.RFX2 | 114 |
| abstract_inverted_index.RNAs | 1 |
| abstract_inverted_index.ZEB2 | 89, 108 |
| abstract_inverted_index.cell | 135 |
| abstract_inverted_index.deep | 138 |
| abstract_inverted_index.five | 70 |
| abstract_inverted_index.from | 107, 113, 165, 183 |
| abstract_inverted_index.loci | 60 |
| abstract_inverted_index.long | 67 |
| abstract_inverted_index.only | 163 |
| abstract_inverted_index.over | 47 |
| abstract_inverted_index.play | 3 |
| abstract_inverted_index.role | 84, 190 |
| abstract_inverted_index.situ | 99 |
| abstract_inverted_index.that | 15, 53, 63, 102, 125 |
| abstract_inverted_index.well | 110 |
| abstract_inverted_index.were | 61 |
| abstract_inverted_index.with | 81, 149 |
| abstract_inverted_index.EPAS1 | 116 |
| abstract_inverted_index.RFX2. | 79 |
| abstract_inverted_index.These | 159 |
| abstract_inverted_index.ZEB2, | 76 |
| abstract_inverted_index.cells | 120 |
| abstract_inverted_index.genes | 176 |
| abstract_inverted_index.known | 83 |
| abstract_inverted_index.large | 143 |
| abstract_inverted_index.loci, | 185 |
| abstract_inverted_index.major | 4 |
| abstract_inverted_index.novel | 13, 49, 160 |
| abstract_inverted_index.roles | 5 |
| abstract_inverted_index.their | 197 |
| abstract_inverted_index.these | 126, 157, 184 |
| abstract_inverted_index.those | 112 |
| abstract_inverted_index.tumor | 30, 87 |
| abstract_inverted_index.using | 39 |
| abstract_inverted_index.(EMT), | 97 |
| abstract_inverted_index.CRIM1, | 74 |
| abstract_inverted_index.EPAS1, | 75 |
| abstract_inverted_index.RBMS1, | 77 |
| abstract_inverted_index.arrays | 43 |
| abstract_inverted_index.breast | 21, 173, 202 |
| abstract_inverted_index.cancer | 9, 22, 174 |
| abstract_inverted_index.coding | 151, 167 |
| abstract_inverted_index.genes, | 73 |
| abstract_inverted_index.genes. | 158 |
| abstract_inverted_index.ncRNAs | 14 |
| abstract_inverted_index.normal | 32, 133 |
| abstract_inverted_index.number | 144 |
| abstract_inverted_index.search | 171 |
| abstract_inverted_index.tiling | 42 |
| abstract_inverted_index.tissue | 34 |
| abstract_inverted_index.within | 153 |
| abstract_inverted_index.Initial | 36 |
| abstract_inverted_index.Sixteen | 58 |
| abstract_inverted_index.biology | 198 |
| abstract_inverted_index.cancer. | 203 |
| abstract_inverted_index.changes | 45 |
| abstract_inverted_index.genomic | 51, 59, 147 |
| abstract_inverted_index.introns | 68, 155, 192 |
| abstract_inverted_index.regions | 52, 105, 127, 182 |
| abstract_inverted_index.reveals | 101, 141, 177 |
| abstract_inverted_index.strand. | 168 |
| abstract_inverted_index.(ncRNAs) | 2 |
| abstract_inverted_index.analysis | 140 |
| abstract_inverted_index.clusters | 148 |
| abstract_inverted_index.deriving | 106 |
| abstract_inverted_index.distinct | 146 |
| abstract_inverted_index.identify | 12, 17 |
| abstract_inverted_index.intronic | 56, 104, 181 |
| abstract_inverted_index.pathways | 19 |
| abstract_inverted_index.pointing | 186 |
| abstract_inverted_index.regions. | 57 |
| abstract_inverted_index.relating | 195 |
| abstract_inverted_index.revealed | 44 |
| abstract_inverted_index.samples. | 35 |
| abstract_inverted_index.candidate | 50 |
| abstract_inverted_index.important | 130 |
| abstract_inverted_index.performed | 25 |
| abstract_inverted_index.potential | 152 |
| abstract_inverted_index.profiling | 28, 38 |
| abstract_inverted_index.Consistent | 80 |
| abstract_inverted_index.Non-coding | 0 |
| abstract_inverted_index.Paired-end | 137 |
| abstract_inverted_index.associated | 175 |
| abstract_inverted_index.enrichment | 178 |
| abstract_inverted_index.epithelial | 93, 122, 134 |
| abstract_inverted_index.identified | 62 |
| abstract_inverted_index.mechanisms | 194 |
| abstract_inverted_index.sequencing | 139 |
| abstract_inverted_index.suggesting | 124 |
| abstract_inverted_index.suppressor | 88 |
| abstract_inverted_index.transcript | 27 |
| abstract_inverted_index.transition | 96 |
| abstract_inverted_index.development | 7 |
| abstract_inverted_index.genome-wide | 41 |
| abstract_inverted_index.maintaining | 132 |
| abstract_inverted_index.mesenchymal | 95 |
| abstract_inverted_index.morphology, | 123 |
| abstract_inverted_index.morphology. | 136 |
| abstract_inverted_index.transcribed | 164, 180 |
| abstract_inverted_index.transcripts | 161 |
| abstract_inverted_index.development, | 23 |
| abstract_inverted_index.high-density | 40 |
| abstract_inverted_index.matched-pair | 33 |
| abstract_inverted_index.progression. | 10 |
| abstract_inverted_index.comprehensive | 170 |
| abstract_inverted_index.hybridization | 100 |
| abstract_inverted_index.transcriptome | 37 |
| abstract_inverted_index.down-regulated | 118 |
| abstract_inverted_index.protein-coding | 72 |
| abstract_inverted_index.high-throughput | 26 |
| abstract_inverted_index.underappreciated | 189 |
| abstract_inverted_index.cancer-associated | 92 |
| cited_by_percentile_year.max | 94 |
| cited_by_percentile_year.min | 89 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 9 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.7900000214576721 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.59130573 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |