Transcription factors without footprints
| العنوان: | Transcription factors without footprints |
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| المؤلفون: | Nicole Rusk |
| المصدر: | Nature Methods. 11:988-989 |
| بيانات النشر: | Springer Science and Business Media LLC, 2014. |
| سنة النشر: | 2014 |
| مصطلحات موضوعية: | Sequence analysis, genetic processes, DNA Footprinting, information science, DNA footprinting, Genomics, Biology, environment and public health, Biochemistry, Article, Footprint, chemistry.chemical_compound, Humans, ComputerSystemsOrganization_SPECIAL-PURPOSEANDAPPLICATION-BASEDSYSTEMS, Molecular Biology, Transcription factor, Epigenomics, Genetics, Hardware_MEMORYSTRUCTURES, Base Sequence, DNA, Sequence Analysis, DNA, Cell Biology, Chromatin, body regions, ComputingMethodologies_PATTERNRECOGNITION, chemistry, health occupations, Transcription Factors, Biotechnology |
| الوصف: | Genomic footprinting has emerged as an unbiased discovery method for transcription factor (TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin. This phenomenon is interpreted to imply protection of the critical nucleotides by the stably bound protein factor. However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a time scale of seconds. We show that TFs with short DNA residence times have no footprints at bound motif elements. Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor binding site, rather than from the protein occupying specific nucleotides. These findings suggest a revised understanding of TF footprinting, and reveal limitations in comprehensive reconstruction of the TF regulatory network using this approach. |
| تدمد: | 1548-7105 1548-7091 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ccb8210b2c0cc1cf501ab55e3077e4e1Test https://doi.org/10.1038/nmeth.3128Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....ccb8210b2c0cc1cf501ab55e3077e4e1 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15487105 15487091 |
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