Functional diversification of shh paralog enhancers

Genome Biology | Abstract | gb-2007-8-6-r106 | Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction: "We demonstrate that the sonic hedgehog a (shha) paralogs sonic hedgehog b (tiggy winkle hedgehog; shhb) genes of fishes have a modified ar-C enhancer which specifies a diverged function at the embryonic midline. We have identified several conserved motifs indicative of putative transcription factor binding sites by a local alignment of ar-C enhancers of numerous vertebrate sequences. To trace the evolutionary changes among paralog enhancers, phylogenomic reconstruction was carried out and lineage-specific motif changes were identified. The relevance of the motif composition to observed developmental differences was studied through transgenic functional analyses. Altering and exchanging motifs between paralog enhancers resulted in the reversal of enhancer specificity in the floor plate and notochord. A model reconstructing enhancer divergence during vertebrate evolution was developed."
Comments (by sterding):
1. Enhancers ar-C in two paralogs of zebrafish shh gene are diverse in sequence conservation (fig.1) and in functionality (fig. 3); ar-C in shha enhances the expression of reporter gene in notochord, while reporter with ar-C in sshb shows expression in floor plate, additionally.

2. Local alignment of ar-C shows that 4 conserved motifs(C1,C2,C3,C4) in shha, while only 2 of them(C1,C3) present in sshb branch (fig. 4).

3. Experiment with mutation in specific motif shows that C1 are critical for notochord specificity, C3 is not so important from current result; C2 and C4 are floor plate repressor (fig. 5,6).

a -22k CNE Controls Ifng Gene Expression by T Cells and NK Cells

"Chromatin dynamics that regulate Ifng gene expression are incompletely understood. By using cross-species comparative sequence analyses, we have identified conserved noncoding sequences (CNSs) upstream of the Ifng gene, one of which, located −22 kb from the transcriptional start site, contains clustered consensus binding sequences of transcription factors that function in T cell differentiation. CNS−22 was uniquely associated with histone modifications typical of accessible chromatin in both T helper 1 (Th1) and Th2 cells and demonstrated significant and selective T-bet (T-box transcription factor expressed in T cells, Tbx21)-dependent binding and enhancer activity in Th1 cells. Deletion of CNS−22 in the context of an Ifng reporter transgene ablated T cell receptor-dependent and -independent Ifng expression in Th1 effectors and similarly blocked expression by cytotoxic T lymphocytes and natural killer cells. Thus, a single distal element may be essential for Ifng gene expression by both innate and adaptive immune effector cell lineages."

The first marsupial genome sequence [Nature Rev Gen]

"One surprising finding from comparing the opossum and human genomes is that most sequence innovation in the human genome following the eutherian split from the metatherian lineage has occurred in non-coding sequences (20% being lineage-specific in eutherians), rather than in coding sequences (only 1% are absent in metatherians). Many of these non-coding sequences are in regions surrounding important developmental genes, indicating that they are functional regulatory elements. The authors found a high degree of overlap between eutherian-specific sequences and transposable elements (16%), which might have served as a driving force in the evolution of the eutherian genome." The first marsupial genome sequence : Article : Nature Reviews Genetics