Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).
In: Scientific Reports, 2015-03-06, S. 8635
Online
academicJournal
Zugriff:
Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigated an average of 40% of reads fail to align to the corresponding genome, with some datasets having as much as 80% of reads failing to align. We describe here the provenance of previously unaligned reads in ChIP-Seq experiments from animals and plants. We show that a substantial portion corresponds to sequences of bacterial and metazoan origin, irrespective of the ChIP-Seq chromatin source. Unforeseen was the finding that 30%-40% of unaligned reads were actually alignable. To validate these observations, we investigated the characteristics of the previously unaligned reads corresponding to TAL1, a human TF involved in lineage specification of hemopoietic cells. We show that, while unmapped ChIP-Seq read datasets contain foreign DNA sequences, additional TFBSs can be identified from the previously unaligned ChIP-Seq reads. Our results indicate that the re-evaluation of previously unaligned reads from ChIP-Seq experiments will significantly contribute to TF target identification and determination of emerging properties of GRNs. [ABSTRACT FROM AUTHOR]
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Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).
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Autor/in / Beteiligte Person: | Ouma, Wilberforce Zachary ; Mejia-Guerra, Maria Katherine ; Yilmaz, Alper ; Pareja-Tobes, Pablo ; Li, Wei ; Doseff, Andrea I. ; Grotewold, Erich |
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Zeitschrift: | Scientific Reports, 2015-03-06, S. 8635 |
Veröffentlichung: | 2015 |
Medientyp: | academicJournal |
ISSN: | 2045-2322 (print) |
DOI: | 10.1038/srep08635 |
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