Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences

Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle

BACKGROUND

Gene regulation by transcription factors (TF) is species, tissue and time specific. To better understand how the genetic code controls gene expression in bovine muscle we associated gene expression data from developing Longissimus thoracis et lumborum skeletal muscle with bovine promoter sequence information.

RESULTS

We created a highly conserved genome-wide promoter landscape comprising 87,408 interactions relating 333 TFs with their 9,242 predicted target genes (TGs). We discovered that the complete set of predicted TGs share an average of 2.75 predicted TF binding sites (TFBSs) and that the average co-expression between a TF and its predicted TGs is higher than the average co-expression between the same TF and all genes. Conversely, pairs of TFs sharing predicted TGs showed a co-expression correlation higher that pairs of TFs not sharing TGs. Finally, we exploited the co-occurrence of predicted TFBS in the context of muscle-derived functionally-coherent modules including cell cycle, mitochondria, immune system, fat metabolism, muscle/glycolysis, and ribosome. Our findings enabled us to reverse engineer a regulatory network of core processes, and correctly identified the involvement of E2F1, GATA2 and NFKB1 in the regulation of cell cycle, fat, and muscle/glycolysis, respectively.

CONCLUSION

The pivotal implication of our research is two-fold: (1) there exists a robust genome-wide expression signal between TFs and their predicted TGs in cattle muscle consistent with the extent of promoter sharing; and (2) this signal can be exploited to recover the cellular mechanisms underpinning transcription regulation of muscle structure and development in bovine. Our study represents the first genome-wide report linking tissue specific co-expression to co-regulation in a non-model vertebrate.

Evolution of gene regulation--on the road towards computational inferences

If fragments of DNA are transcribed (expressed), they deserve to be called (parts of) a gene. Whether transcription takes place depends on the 'gene regulatory network'. This network is defined as the complex interplay of the sequence, biochemical modifications and structure of the chromosomal DNA with the regulatory proteins/RNA (transcription factors, co-factors, regulating RNA and the transcriptional apparatus itself). Gene regulatory networks play a role in various stages of development as well as in the maintenance of the organism; in this review we will concentrate on the former. Their evolutionary reconstruction is daunting (to say the least), and bioinformatics tools are in their infancy. However, gain of understanding offers a reward beyond itself, since evolutionary considerations can enable discoveries in the first place, e.g. the computational identification of conserved transcription factor binding sites. We discuss the evolution of gene regulation in the context of the 'Genetic Theory of Morphological Evolution' as described by Carroll, identifying those parts of the theory that are relevant for bioinformatics, and their implications. We discuss the important question of how bioinformatics analysis results on the evolution of gene regulation may be validated. Finally, we briefly exemplify use of the UCSC genome browser, exploiting its pre-computed alignments to describe the evolution of gene regulation.

Evolutionary tinkering with conserved components of a transcriptional regulatory network

A surprising level of evolutionary plasticity is revealed by analysis of differences between related yeasts in the mechanisms regulating the essential cellular process of ribosomal gene expression.

Gene expression variation between species is a major contributor to phenotypic diversity, yet the underlying flexibility of transcriptional regulatory networks remains largely unexplored. Transcription of the ribosomal regulon is a critical task for all cells; in S. cerevisiae the transcription factors Rap1, Fhl1, Ifh1, and Hmo1 form a multi-subunit complex that controls ribosomal gene expression, while in C. albicans this regulation is under the control of Tbf1 and Cbf1. Here, we analyzed, using full-genome transcription factor mapping, the roles, in both S. cerevisiae and C. albicans, of each orthologous component of this complete set of regulators. We observe dramatic changes in the binding profiles of the generalist regulators Cbf1, Hmo1, Rap1, and Tbf1, while the Fhl1-Ifh1 dimer is the only component involved in ribosomal regulation in both fungi: it activates ribosomal protein genes and rDNA expression in a Tbf1-dependent manner in C. albicans and a Rap1-dependent manner in S. cerevisiae. We show that the transcriptional regulatory network governing the ribosomal expression program of two related yeast species has been massively reshaped in cis and trans. Changes occurred in transcription factor wiring with cellular functions, movements in transcription factor hierarchies, DNA-binding specificity, and regulatory complexes assembly to promote global changes in the architecture of the fungal transcriptional regulatory network.

Conserved metabolic machineries direct energy production and investment in most life forms. However, variation in the transcriptional regulation of the genes that encode this machinery has been observed and shown to contribute to phenotypic differences between species. Here, we show that the regulatory circuits governing the expression of central metabolic components (in this case the ribosomes) in different yeast species have an unexpected level of evolutionary plasticity. Most transcription factors involved in the regulation of expression of ribosomal genes have in fact been reused in new ways during the evolutionary time separating S. cerevisiae and C. albicans to generate global changes in transcriptional network structures and new ribosomal regulatory complexes.

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

Regulatory regions with similar transcriptional output often have little overt sequence similarity, both within and between genomes. Although cis- and trans-regulatory changes can contribute to sequence divergence without dramatically altering gene expression outputs, heterologous DNA often functions similarly in organisms that share little regulatory sequence similarities (e.g. human DNA in fish), indicating that trans-regulatory mechanisms tend to diverge more slowly and can accommodate a variety of cis-regulatory configurations. This capacity to 'tinker' with regulatory DNA probably relates to the complexity, robustness and evolvability of regulatory systems, but cause-and-effect relationships among evolutionary processes and properties of regulatory systems remain a topic of debate. The challenge of understanding the concrete mechanisms underlying cis-regulatory evolution - including the conservation of function without the conservation of sequence - relates to the challenge of understanding the function of regulatory systems in general. Currently, we are largely unable to recognize functionally similar regulatory DNA.

Evolution of transcriptional control in mammals

Changes in gene expression directed by transcriptional regulators can give rise to new phenotypes. While gene expression profiles can be maintained across large evolutionary distances, transcription factor-DNA interactions diverge rapidly. The application of new genome-wide methodologies has begun refining our global understanding of when and where mammalian transcription factors interact with DNA, thereby providing new insight into the mechanisms of transcriptional evolution. The interplay between cis and trans regulation of gene expression is an increasingly active area of investigation, and recent studies suggest that mutations in cis-regulatory DNA can explain many inter-species differences in gene expression.