Tag Archives: genes

CD 14 now also on the vitamin+allergy list

Just for curiosity I am collecting a list of allergy genes that are vitamin D dependent. The list is already rather long but now there is a prominent addition: CD14. Known as asthma gene for many years the vitamin D dependency isn’t such clear. A clever analysis, however, now shows that there is an intermediate step involved Continue reading CD 14 now also on the vitamin+allergy list

Another layer of complexity in gene regulation

Yesterday evening I attended an excellent presentation by Nikolaus Rajewksy about microRNAs, small noncoding RNAs that are thought to have a role in posttranscriptional regulation. Nikolaus just moved 3 months ago from New York to follow Jens Reich at MDC in Berlin). Basically, he talked about his recent “l(ou)sy” paper and the “SNP” paper after giving a rather detailed history about the development of the field. It started in 1950 with Jacob and Monod, 1960 Britten and Davidson, 1970 Haywood (who even quit science after being dissappointed), finally to 1990 when the Ambros and Ruvkun labs discovered nematode microRNAs. Current research is mainly done in the Tuschl, Batel, Cohen, Lander and Rajewsky labs who produce the bulk of the 800 papers or so published in 2006.
Approximately 30% of genes are influenced by microRNAs, the total number of microRNA sites is under heavy debate (~22,000) as well as the number of human microRNAs (328); each microRNA regulates ~200 genes. Unfortunately there is still no highthroughput technique to detect targets. There is also no good prediction by free energy and even mismatches in the 5 prime of mRNA are possible (individual predictions can be obtained at Pictar that uses a hidden Markov model).
If I understood that correctly, miRNA are the feedback mechanism on RNA level (with transcription factors at the DNA level). He mentioned 3 classes known so far in humans: oncomiRNA, miRNA 375 myotrophin, and miRNA 122 acting on cholesterol (quite interesting as being described recently in the NEJM. The experimental knockdown of liver specific mouse microRNA shows ~300 up- and ~300 down regulated genes. Upregulated genes have in approximately 50% of cases one miRNA nucleus, downregulated ones have even less than average binding sites. There is no overrepresented GO category in upregulated genes but cholesterol is highly significant in downregulated genes whatever that means. Action of miRNA seem to heavily context dependent giving us many more questions than answers. Yea, yea.

Why dog and cat can´t marry

or in more scientific terms: Why are F1 hybrids so often sterile or lethal? The Dobzhansky-Muller theory says that there is an incompatibility between genes with reduced fitness that have diverged between species. So far nobody has ever observed a D-M gene but a new Science paper describes two genes that separate D. simulans and D. melanogaster: lhr (lethal hybrid rescue) and hmr (hybrid male rescue). Yea, Yea.

What could have been learned from linkage studies

What makes the difference between genetic linkage and association studies? Simply speaking, for linkage you need to inherit a particular marker allele from your parents where it does not matter if a child in another family inherits another allele (pending it shares it with its affected sibling). With association studies this matters.

As we found with the much relaxed linkage strategy so many minor diverse loci, I assume a rather heterogeneous origin of complex diseases. There is no doubt about the importance of genes, but about the sharing of the same genetic abnormality. An (anonymous) position paper on basic Asthma Research Strategy II in Clin Exp All 2006; 36: 1326 says

The average size of effect on asthma and related traits from common SNPs is small. For instance, seven common SNPs in the IL13 gene jointly accounted for only 0,5% of the variance of total IgE … With a heritability of circa 60% for total IgE this implies that hundreds of genes, each with small effects, may be involved in IgE regulation.

Families presenting with a complex system disease will all have unique patterns how they arrive at the same clinical endpoint. Alpha-delta-gamma asthma, theta-kappa-jota schizophrenia or $%&# diabetes – are they combining lets say 3000 variations in 300 genes of 30 metabolic-signalling pathways to 1 disease of variable onset, severity and prognosis? Yea, yea.