Detecting Differential Transcription Factor Activity from ATAC-Seq Data
Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summari...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2018-05-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1420-3049/23/5/1136 |
| _version_ | 1818976887033036800 |
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| author | Ignacio J. Tripodi Mary A. Allen Robin D. Dowell |
| author_facet | Ignacio J. Tripodi Mary A. Allen Robin D. Dowell |
| author_sort | Ignacio J. Tripodi |
| collection | DOAJ |
| description | Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases. |
| first_indexed | 2024-12-20T16:18:59Z |
| format | Article |
| id | doaj.art-0f75646673bd4064844333c3f560b2cc |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-20T16:18:59Z |
| publishDate | 2018-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-0f75646673bd4064844333c3f560b2cc2022-12-21T19:33:41ZengMDPI AGMolecules1420-30492018-05-01235113610.3390/molecules23051136molecules23051136Detecting Differential Transcription Factor Activity from ATAC-Seq DataIgnacio J. Tripodi0Mary A. Allen1Robin D. Dowell2Computer Science, University of Colorado, Boulder, CO 80305, USABioFrontiers Institute, University of Colorado, Boulder, CO 80303, USAComputer Science, University of Colorado, Boulder, CO 80305, USATranscription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases.http://www.mdpi.com/1420-3049/23/5/1136transcription factorperturbationRNA-seqDNase I cleavageATAC-seqopen chromatinmotifDAStk |
| spellingShingle | Ignacio J. Tripodi Mary A. Allen Robin D. Dowell Detecting Differential Transcription Factor Activity from ATAC-Seq Data Molecules transcription factor perturbation RNA-seq DNase I cleavage ATAC-seq open chromatin motif DAStk |
| title | Detecting Differential Transcription Factor Activity from ATAC-Seq Data |
| title_full | Detecting Differential Transcription Factor Activity from ATAC-Seq Data |
| title_fullStr | Detecting Differential Transcription Factor Activity from ATAC-Seq Data |
| title_full_unstemmed | Detecting Differential Transcription Factor Activity from ATAC-Seq Data |
| title_short | Detecting Differential Transcription Factor Activity from ATAC-Seq Data |
| title_sort | detecting differential transcription factor activity from atac seq data |
| topic | transcription factor perturbation RNA-seq DNase I cleavage ATAC-seq open chromatin motif DAStk |
| url | http://www.mdpi.com/1420-3049/23/5/1136 |
| work_keys_str_mv | AT ignaciojtripodi detectingdifferentialtranscriptionfactoractivityfromatacseqdata AT maryaallen detectingdifferentialtranscriptionfactoractivityfromatacseqdata AT robinddowell detectingdifferentialtranscriptionfactoractivityfromatacseqdata |