Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Abstract

We demonstrate that the binding sites for highly conserved transcription factors vary extensively between human and mouse. We mapped the binding of four tissue-specific transcription factors (FOXA2, HNF1A, HNF4A, HNF6) to 4,000 orthologous gene pairs in hepatocytes purified from human and mouse livers. Despite the conserved function of these factors, from 41% to 89% of their binding events appear to be species-specific. When the same protein binds the promoters of orthologous genes, approximately two-thirds of the binding sites do not align.Elements of transcriptional regulation have central roles in evolution [1][2][3] . In many cases, conserved biological processes are controlled by evolutionarily conserved regulatory programs while evolving phenotypes are associated with cross-species variation in transcription regulation 4 . However, in the absence of suitable genome-wide data, it is unclear what fraction of all protein-DNA interactions are under either positive or negative selective pressure 1 . A preliminary effort to compare genome-wide binding sites for two stem cell-specific transcription factors in human and mouse has suggested that large differences exist between mouse and human 5, 6 yet because the data were obtained using different To compare systematically the binding of transcriptional regulators to promoter regions across species, we designed carefully matched ChIP-chip experiments 7 in human and mouse. We created custom DNA microarrays that array ten kilobases of sequence surrounding the known transcription start sites of over 4,000 orthologous pairs of mouse and human genes. These genes were selected because their orthology could be unambiguously assigned and oligonucleotides could be designed to represent the putative regulatory regions at high density ( Figure 1A, Supplementary Methods). Forty-seven hand-curated, tissuespecific genes were included in the array design as controls.Chromatin immunoprecipitations were performed independently in primary hepatocytes directly isolated from mouse and human liver using antibodies against four tissue-specific transcription factors (FOXA2, HNF1A, HNF4A, HNF6) involved in liver development and regulation ( Figure 1B, Table S1) 7 . Hepatocytes were chosen as a representative tissue for these experiments because (1) they are functionally and structurally conserved among mammals 8 ; (2) their gene expression programs are similar across species (Table S1); (3) their gene expression patterns are largely unperturbed by isolation procedures 9 ; and (4) the transcription factors responsible for hepatocyte development and function are highly conserved 8 . We amplified and fluorescently labeled the DNA from these binding experiments, hybridized it to the microarrays, and then scored binding events 10 .Several possible outcomes can be distinguished when comparing a binding event in one species with the data from the second species (Figure 1). First, one can determine if a particular transcription factor binds anywhere within the arrayed region of the human ...

Conservation analysis predicts in vivo occupancy of glucocorticoid receptor-binding sequences at glucocorticoid-induced genes

“…However, it should be noted that we restricted our analysis to positionally conserved sites, and that these sites found in the mouse genome may actually be conserved in sequence but shifted location within the human genome. Indeed, occupancy of some regulatory factors has been shown to shift in location between mouse and human genomes (12). Moreover, GBSs that are not conserved between mouse and human may be conserved in genomes of other species, and extending our study beyond the current pairwise analysis may be informative.…”

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

“…We found that comparative genomics resulted in many functionally meaningful sites for transcription factors Mef2, Twist and Snail outside ChIPbound regions, probably representing targets from diverse conditions not surveyed experimentally. Similarly, ChIP resulted in many additional sites outside those recovered by comparative genomics: some of these may have been replaced by functionally equivalent non-orthologous sequence, rendering them apparently non-conserved in sequence alignments [122][123][124] ; others may have species-or lineagespecific roles, thus lacking sufficient signal for their comparative detection; finally, some bound sites may be biochemically active yet selectively neutral 125 . It is worth noting, however, that ChIP-bound motifs that were not conserved showed decreased enrichment in muscle/ mesoderm development where the factors are known to act, suggesting that potential lineage-specific roles may lie outside the regulators' conserved functions.…”

A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs

“…In fact, for one of their transcription factors, CEPBA, only 0.3% of binding sites were conserved across all five species (Schmidt et al 2010). Transcription factor binding site (TFBS) ''turnover'' and sequence mutation of binding sites are two mechanisms that may explain this high degree of species-specific binding (Odom et al 2007;Schmidt et al 2010). These results raise an important question: How sensitive are alignment-based conservation approaches in predicting regulatory elements?…”