Variation in Transcription Factor Binding Among Humans

Abstract

Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee using chromatin immunoprecipitation followed by sequencing (ChIP-Seq). The binding sites of RNA Polymerase II (PolII) and a key regulator of immune responses, NFκB (p65), were mapped in ten lymphoblastoid cell lines and 25% and 7.5% of the respective binding regions were found to differ between individuals. Binding differences were frequently associated with SNPs and genomic structural variants (SVs) and were often correlated with differences in gene expression, suggesting functional consequences of binding variation. Furthermore, comparing PolII binding between human and chimpanzee suggests extensive divergence in TF binding. Our results indicate that many differences in individuals and species occur at the level of TF binding and provide insight into the genetic events responsible for these differences. TextDifferences in gene expression have been observed in a variety of species (1-3). However, the extent to which TF binding differences occur both within individuals and closely related species and the global relationship between TF binding and genetic variation are largely unexplored (4). We used ChIP-Seq to map NFκB and PolII binding sites in ten humans: five are of European ancestry (including a parent-offspring trio), two of eastern Asian ancestry, and three of Nigerian

Involvement of RNA Polymerase III in Immune Responses

“…The NF-B family of transcription factors consists of five proteins, namely, RelA (p65), RelB, c-Rel, NF-B1 (p50/p105), and NF-B2 (p52/p100) (13). Kasowski and colleagues performed chromatin precipitation followed by deep sequencing to look at genome-wide binding of p65 protein in human lymphoblastoid cells (17). We took advantage of these data and manually inspected the presence of p65 on tRNA genes using the ENCODE transcription factor ChIP track in the UCSC genome browser (http://genome.ucsc.edu) (32,33).…”

“…In particular, elevated Pol III activity is a recurring feature of mouse and human tumors (14). Interestingly, NF-B subunit RelA/p65 has been shown to associate with Pol III-transcribed genes in human lymphoblastoid cells (17). However, its role in Pol III transcriptional regulation has not yet been determined.…”

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

“…Individuals of the same species also display considerable variation albeit at lower levels, as expected. Comparison of 10 human individuals revealed a higher fraction of shared events, but as low as 75% in the case of RNA polymerase II (Pol II) [23]. Similarly, when comparing two Saccharomyces cerevisiae strains, around 70% of the genes putatively bound by Ste12 were found to be conserved [25].…”

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach

“…Analysis of ChIP-seq data [26] revealed that the SNP was located within an NF-KB target site in LCLs ( Figure 6A) and contained an NF-KB consensus binding motif. We investigated whether the A to G substitution could modulate predicted binding affinity using a publically available database identifying binding sites of NF-KB by a combination of protein-binding microarrays and surface plasmon resonance [27].…”

“…We then proceeded to determine whether allelic differences in NF-KB binding were present ex vivo using ChIP-seq data for a panel of five LCLs heterozygous for rs11074938 [26]. This revealed that there was significantly more RELA binding to the A allele compared to the G, with on average 66.1% (SD 8.1) of reads mapping to the A allele (P =0.008) ( Figure 6C).…”