Despite much research, our understanding of the rules by which cis-regulatory sequences are translated into expression levels is still lacking. We devised a method for obtaining parallel and highly accurate expression measurements of thousands of fully designed promoters, and applied it to measure the effect of systematic changes to location, number, orientation, affinity and organization of transcription factor (TF) binding sites and of nucleosome disfavoring sequences. Our analyses reveal a clear relationship between expression and binding site number, and TF-specific dependencies of expression on the distance between sites and gene starts including a striking ~10bp periodic relationship. We also demonstrate the utility of our approach for measuring TF sequence specificities and sensitivity of TF sites to surrounding sequence context, and for profiling the activity of most yeast transcription factors. Our method is readily applicable for studying both the cis and trans effects of genotype on transcriptional, post-transcriptional, and translational control.

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Mechanisms underlying the age-related decrease in the developmental capacity of thymocyte progenitors from the bone marrow (BM) were analyzed, focussing on interaction of these cells with the thymic microenvironment. We employed the experimental model in which mixtures of young and old mouse BM cells, congenic for the Thy-1 marker, were seeded onto fetal thymus (FT) explains depleted of self lymphocytes and the levels of Thy-1+ cells developing from each of the two donor types were measured. When cells from young and old BM donors were seeded simultaneously, in saturating quantities, a higher level of T cells developed from the young donors. To find out whether there were originally more thymocyte progenitors in the young BM, we carried out the competitive colonization under limiting dilution conditions and found that the advantage of the young had diminished under these conditions, thus suggesting that the age-related changes could not be related solely to quantitative differences. We then incubated the FT sequentially with old donor cells for 24 h, followed by young for an additional 48 h and found that the advantage of the young progenitors was eliminated. We thus established that the initial stage of colonization of the FT was important in determining the outcome of the subsequent development. The kinetics of simultaneous competition within the FT, however, revealed that the advantage of the young BM-derived cells became significant only from day 7 in organ culture, thus suggesting that sequential divisions of these cells were at a higher level than those of the old. Recolonization of FT explants by young or old BM-derived thymocytes obtained from the first colonization of the FT stroma showed a reduced, but still significant advantage for the young BM-derived cells over the old. Thus, we concluded that the old BM thymocyte progenitors manifested a qualitative disadvantage which became apparent during competitive colonization of the FT.

The expression of estrogen receptor (ER) in thymocytes was studied in young, middle-aged, and old (2, 12, and 24 months, respectively) female and male C57BL/6J mice. Western immunoblots prepared from the thymocytes of females of all age groups showed the presence of a 67-kD protein band, which has been associated with the apparent MW of denatured ER. Flow cytometry analysis o,f cells stained with a monoclonal anti-ER antibody (clone 13H2) disclosed ER expression in both females and males of all age groups. In vivo treatment with estradiol (E2) led to an increase in the specific activity of thymic creatine kinase (CK) in the female mice, whereas the male thymocytes responded with an increase in CK activity only on treatment with dihydrotestosterone (DHT). The data show no differences in ER expression between male and females, but the receptor appears not to be functional in males. Interestingly, when estradiol was applied to co-cultures of lymphoid-depleted fetal thymus (FT) explants and bone-marrow cells, or thymocytes, from young and old females, it resulted in increased cellularity of cultures containing cells of the young, and not those of the old. The proportion of CD4/CD8 phenotypes of the developing cells in these cultures was not affected by E2 treatment. These observations provide a new insight into ER expression and function in T-cell development in relation to gender and age.

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