Publications
Department of Medicine faculty members published more than 3,000 peer-reviewed articles in 2022.
2006
2006
2006
2006
Identifying the sequences that direct the spatial and temporal expression of genes and defining their function in vivo remains a significant challenge in the annotation of vertebrate genomes. One major obstacle is the lack of experimentally validated training sets. In this study, we made use of extreme evolutionary sequence conservation as a filter to identify putative gene regulatory elements, and characterized the in vivo enhancer activity of a large group of non-coding elements in the human genome that are conserved in human-pufferfish, Takifugu (Fugu) rubripes, or ultraconserved in human-mouse-rat. We tested 167 of these extremely conserved sequences in a transgenic mouse enhancer assay. Here we report that 45% of these sequences functioned reproducibly as tissue-specific enhancers of gene expression at embryonic day 11.5. While directing expression in a broad range of anatomical structures in the embryo, the majority of the 75 enhancers directed expression to various regions of the developing nervous system. We identified sequence signatures enriched in a subset of these elements that targeted forebrain expression, and used these features to rank all approximately 3,100 non-coding elements in the human genome that are conserved between human and Fugu. The testing of the top predictions in transgenic mice resulted in a threefold enrichment for sequences with forebrain enhancer activity. These data dramatically expand the catalogue of human gene enhancers that have been characterized in vivo, and illustrate the utility of such training sets for a variety of biological applications, including decoding the regulatory vocabulary of the human genome.
View on PubMed2006
2006
2006
2006
Although quantitative identification and viable enrichment of natural regulatory T cells (T-regs) in humans are problematic, such steps would greatly facilitate the analysis of these cells in disease states. In an attempt to identify markers that are sensitive and specific for human T-regs, we analyzed the expression of fourteen intracellular and cell surface markers on human CD4(+) cells. Many markers were partially selective for CD25(hi) T-regs, but consistent and specific discrimination of functional T-regs was only made possible by focus on CD127, the alpha chain of the IL-7 receptor. Although most CD4(+) human T cells express CD127, T-regs exhibiting suppressive activity in vitro display distinctly lower surface expression of this marker, irrespective of their level of CD25 expression. Sorted cells with the surface phenotype CD4(+)CD25(+)CD127(low) had higher levels of intracellular FOXP3 and CTLA-4 and, as determined by functional assays, were suppressive, hypoproliferative, and poorly responsive to TCR signaling. The CD4(+)CD25(+)CD127(low) phenotype was also found to be characteristic of T-regs found in mice and in rhesus macaques. This surface phenotype should allow for quantitative studies of regulatory T cells in disease states as well as for enrichment of live regulatory T cells for functional analyses and/or expansion in vitro.
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