Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs

Regulation of human CYP11B1 and CYP11B2 promoters by transposable elements and conserved cis elements

CYP11B1 and CYP11B2 responsible for the final steps of cortisol and aldosterone synthesis, respectively, are believed to be duplicate genes with distinctive promoters. Our sequence analysis uncovers that these two genes share great homology in the proximal upstream regions, but insertion of Alu and L1 elements drives promoters divergent. Each CYP11B promoter contains two Alu elements embedded in a truncated L1 element, breaking L1 into three disconnected fragments. Alu functions as an enhancer in both genes regardless of orientation and copy number. Insertion of Alu upstream of a SV40 promoter also elevates promoter activity. However, the effect of Alu on CYP11B1 is blocked by a second L1 element (CYP11B1-L1.2) inserted between the first one and the conserved proximal upstream region. Although CYP11B1-L1.2 is 5'-truncated and lacks a functional ORF, replacing it with a fluorescent gene demonstrates that the element can be transcribed from the CYP11B1 core promoter in an opposite direction and a smaller magnitude compared to CYP11B1. Deletion of CYP11B1-L1.2 greatly increases CYP11B1 promoter activity and restores the enhancing effect of Alu. The Ad5 and SF-1 binding elements conserved in the proximal core promoter play a role in basal expression of both genes. Mutation of the Ad5 site reduces promoter activity to the minimal level. ERRα is the transcription factor interacting with Ad5 during basal expression. The core promoters of both genes are also conserved in mouse and rat despite the fact that the sites corresponding to cre, Ad5, and SF-1 in rodent Cyp11b1 promoters deviate from consensus.

A deterministic motif finding algorithm with application to the human genome

MOTIVATION

We present a novel algorithm, MaMF, for identifying transcription factor (TF) binding site motifs. The method is deterministic and depends on an indexing technique to optimize the search process. On common yeast datasets, MaMF performs competitively with other methods. We also present results on a challenging group of eight sets of human genes known to be responsive to a diverse group of TFs. In every case, MaMF finds the annotated motif among the top scoring putative motifs. We compared MaMF against other motif finders on a larger human group of 21 gene sets and found that MaMF performs better than other algorithms. We analyzed the remaining high scoring motifs and show that many correspond to other TFs that are known to co-occur with the annotated TF motifs. The significant and frequent presence of co-occurring transcription factor binding sites explains in part the difficulty of human motif finding. MaMF is a very fast algorithm, suitable for application to large numbers of interesting gene sets.

Correlation between alterations in nucleosomal organization of LINEs in the promoter of cytochrome P450 2B1/2 gene and induction of CYP 2B1/2B2 mRNA expression by phenobarbitone in rat liver

Mammalian genome contains a high proportion of repetitive DNA with a sizeable fraction of Long Interspersed Nuclear Elements (LINEs). LINEs have been functionally implicated in the organization and evolution of mammalian genome. However, functions of LINEs in the promoter region and gene expression are poorly understood. Here, we report two small, conserved LINE sequences (3P and 5P) that occur as multiple copies of inverted repeats in the rat Cytochrome P450 2B1/2B2 (CYP 2B1/2) gene promoter. Using 3P or 5P as a single primer, the CYP 2B1/2 promoter DNA was amplified by PCR from the rat genome. Phenobarbitone (PB), a prototype xenobiotic drug, strongly induced CYP 2B1/2 mRNA expression in the rat liver. 3P and 5P LINE sequences showed an alteration in the nucleosomal organization in the CYP 2B1/2 promoter after 2, 4, and 6 h of PB induction, and the promoter was mostly devoid of nucleosomes during the induction. Reorganization of nucleosomes associated with these LINE sequences were strongly correlated with induction of CYP 2B1/2 mRNA expression by PB in vivo. Our results strongly suggest that these LINE sequences in CYP 2B1/2 gene promoter(s) may facilitate transcriptional activation of the gene(s) by PB through retention and reorganization of nucleosomes. This might be a novel function of LINEs in the mammalian genome that correlates the chromatin structure with gene expression during drug metabolism.

Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements

Background

The primate-specific Alu elements, which originated 65 million years ago, exist in over a million copies in the human genome. These elements have been involved in genome shuffling and various diseases not only through retrotransposition but also through large scale Alu-Alu mediated recombination. Only a few subfamilies of Alus are currently retropositionally active and show insertion/deletion polymorphisms with associated phenotypes. Retroposition occurs by means of RNA intermediates synthesised by a RNA polymerase III promoter residing in the A-Box and B-Box in these elements. Alus have also been shown to harbour a number of transcription factor binding sites, as well as hormone responsive elements. The distribution of Alus has been shown to be non-random in the human genome and these elements are increasingly being implicated in diverse functions such as transcription, translation, response to stress, nucleosome positioning and imprinting.

Results

We conducted a retrospective analysis of putative functional sites, such as the RNA pol III promoter elements, pol II regulatory elements like hormone responsive elements and ligand-activated receptor binding sites, in Alus of various evolutionary ages. We observe a progressive loss of the RNA pol III transcriptional potential with concomitant accumulation of RNA pol II regulatory sites. We also observe a significant over-representation of Alus harboring these sites in promoter regions of signaling and metabolism genes of chromosome 22, when compared to genes of information pathway components, structural and transport proteins. This difference is not so significant between functional categories in the intronic regions of the same genes.

Conclusions

Our study clearly suggests that Alu elements, through retrotransposition, could distribute functional and regulatable promoter elements, which in the course of subsequent selection might be stabilized in the genome. Exaptation of regulatory elements in the preexisting genes through Alus could thus have contributed to evolution of novel regulatory networks in the primate genomes. With such a wide spectrum of regulatory sites present in Alus, it also becomes imperative to screen for variations in these sites in candidate genes, which are otherwise repeat-masked in studies pertaining to identification of predisposition markers.