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Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant
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| Veröffentlicht in: | PLOS ONE 12(2017,12) Artikel-Nummer e0186324, 25 Seiten |
|---|---|
| Personen und Körperschaften: | , |
| Titel: | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant/ Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils |
| Format: | E-Book-Kapitel |
| Sprache: | Englisch |
| veröffentlicht: |
December 7, 2017
|
| Gesamtaufnahme: |
: PLOS ONE, 12(2017,12) Artikel-Nummer e0186324, 25 Seiten
, volume:12 |
| Schlagwörter: | |
| Quelle: | Verbunddaten SWB Lizenzfreie Online-Ressourcen |
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| 245 | 1 | 0 | |a Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant |c Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils |
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| 520 | |a The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs), coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner. Here, we show that simple linear models can reliably predict the data generated by the ENCODE and Roadmap Epigenomics consortia. Further, we demonstrate that a small number of marks can predict all other marks with high average correlation across the genome, systematically revealing the substantial information compression that is present in different cell lines. We find that the linear models for activating marks are typically cell line-independent, while those for silencing marks are predominantly cell line-specific. Of particular note, a nuclear receptor corepressor, transducin beta-like 1 X-linked receptor 1 (TBLR1), was highly predictive of other marks in two hematopoietic cell lines. The methodology presented here shows how the potentially vast complexity of TFs, coregulators, and epigenetic marks at eukaryotic genes is highly redundant and that the information present can be compressed onto a much smaller subset of marks. These findings could be used to efficiently characterize cell lines and tissues based on a small number of diagnostic marks and suggest how the DNA microstates, which regulate the expression of individual genes, can be specified. | ||
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| 650 | 4 | |a Epigenesis, Genetic | |
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| contents | The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs), coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner. Here, we show that simple linear models can reliably predict the data generated by the ENCODE and Roadmap Epigenomics consortia. Further, we demonstrate that a small number of marks can predict all other marks with high average correlation across the genome, systematically revealing the substantial information compression that is present in different cell lines. We find that the linear models for activating marks are typically cell line-independent, while those for silencing marks are predominantly cell line-specific. Of particular note, a nuclear receptor corepressor, transducin beta-like 1 X-linked receptor 1 (TBLR1), was highly predictive of other marks in two hematopoietic cell lines. The methodology presented here shows how the potentially vast complexity of TFs, coregulators, and epigenetic marks at eukaryotic genes is highly redundant and that the information present can be compressed onto a much smaller subset of marks. These findings could be used to efficiently characterize cell lines and tissues based on a small number of diagnostic marks and suggest how the DNA microstates, which regulate the expression of individual genes, can be specified. |
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| spelling | Ahsendorf, Tobias VerfasserIn (DE-588)1020727934 (DE-627)689002106 (DE-576)361892853 aut, Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils, December 7, 2017, 25, Text txt rdacontent, Computermedien c rdamedia, Online-Ressource cr rdacarrier, Gesehen am 03.04.2018, The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs), coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner. Here, we show that simple linear models can reliably predict the data generated by the ENCODE and Roadmap Epigenomics consortia. Further, we demonstrate that a small number of marks can predict all other marks with high average correlation across the genome, systematically revealing the substantial information compression that is present in different cell lines. We find that the linear models for activating marks are typically cell line-independent, while those for silencing marks are predominantly cell line-specific. Of particular note, a nuclear receptor corepressor, transducin beta-like 1 X-linked receptor 1 (TBLR1), was highly predictive of other marks in two hematopoietic cell lines. The methodology presented here shows how the potentially vast complexity of TFs, coregulators, and epigenetic marks at eukaryotic genes is highly redundant and that the information present can be compressed onto a much smaller subset of marks. These findings could be used to efficiently characterize cell lines and tissues based on a small number of diagnostic marks and suggest how the DNA microstates, which regulate the expression of individual genes, can be specified., Cell Line, Epigenesis, Genetic, Gene Silencing, Histone Code, Humans, Models, Theoretical, Transcription Factors, Eils, Roland 1965- VerfasserIn (DE-588)1020648287 (DE-627)691291705 (DE-576)361718195 aut, Enthalten in PLOS ONE San Francisco, California, US : PLOS, 2006 12(2017,12) Artikel-Nummer e0186324, 25 Seiten Online-Ressource (DE-627)523574592 (DE-600)2267670-3 (DE-576)281331979 1932-6203 nnns, volume:12 year:2017 number:12 extent:25, http://dx.doi.org/10.1371/journal.pone.0186324 Verlag Resolving-System kostenfrei Volltext, http://dx.doi.org/10.1371/journal.pone.0186324 LFER, LFER 2018-04-10T00:00:00Z |
| spellingShingle | Ahsendorf, Tobias, Eils, Roland, Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant, The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs), coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner. Here, we show that simple linear models can reliably predict the data generated by the ENCODE and Roadmap Epigenomics consortia. Further, we demonstrate that a small number of marks can predict all other marks with high average correlation across the genome, systematically revealing the substantial information compression that is present in different cell lines. We find that the linear models for activating marks are typically cell line-independent, while those for silencing marks are predominantly cell line-specific. Of particular note, a nuclear receptor corepressor, transducin beta-like 1 X-linked receptor 1 (TBLR1), was highly predictive of other marks in two hematopoietic cell lines. The methodology presented here shows how the potentially vast complexity of TFs, coregulators, and epigenetic marks at eukaryotic genes is highly redundant and that the information present can be compressed onto a much smaller subset of marks. These findings could be used to efficiently characterize cell lines and tissues based on a small number of diagnostic marks and suggest how the DNA microstates, which regulate the expression of individual genes, can be specified., Cell Line, Epigenesis, Genetic, Gene Silencing, Histone Code, Humans, Models, Theoretical, Transcription Factors |
| swb_id_str | 501649239 |
| title | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant |
| title_auth | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant |
| title_full | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils |
| title_fullStr | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils |
| title_full_unstemmed | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils |
| title_in_hierarchy | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant / Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils, |
| title_short | Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant |
| title_sort | transcription factors coregulators and epigenetic marks are linearly correlated and highly redundant |
| topic | Cell Line, Epigenesis, Genetic, Gene Silencing, Histone Code, Humans, Models, Theoretical, Transcription Factors |
| topic_facet | Cell Line, Epigenesis, Genetic, Gene Silencing, Histone Code, Humans, Models, Theoretical, Transcription Factors |
| url | http://dx.doi.org/10.1371/journal.pone.0186324 |