Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).
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.
1] Molecular, Cellular and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH, USA [2] Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH, USA.
Wilberforce Zachary
WZ
Ouma
1] Molecular, Cellular and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH, USA [2] Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH, USA.
Maria Katherine
MK
Mejia-Guerra
Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey.
Alper
A
Yilmaz
Oh no sequences! Research group, Era7 Information Technologies SLU, Granada, Spain.
Pablo
P
Pareja-Tobes
1] Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA [2] Department Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
Wei
W
Li
1] Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA [2] Department Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
Andrea I
AI
Doseff
1] Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH, USA [2] Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
Erich
E
Grotewold
D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002877:Chromosomes, Human / Q000235:genetics; D006801:Humans; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1
D051792:Basic Helix-Loop-Helix Proteins; D011518:Proto-Oncogene Proteins; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; C067143:TAL1 protein, human