A genome-wide study of transcription in yeast redefines the concept of promoters
Genes that contain instructions for making proteins make up less than 2% of the human genome. Yet, for unknown reasons, most of our genome is transcribed into RNA. The same is true for many other organisms that are easier to study than humans. Researchers in the groups of Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and Wolfgang Huber at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, have now unravelled how yeast generates its transcripts and have come a step closer to understanding their function. The study, published online in Nature, redefines the concept of promoters (the start sites of transcription) contradicting the established notion that they support transcription in one direction only. The results are also representative of transcription in humans.
Investigating all transcripts produced in a yeast cell, the scientists found that most regions of the yeast genome produce several transcripts starting at the same promoter. These transcripts are interleaved and overlapping on the DNA. In contrast to what was previously thought, the vast majority of promoters seem to initiate transcription in both directions.
Not all of the produced transcripts are stable, many are degraded rapidly making it difficult to observe what they do. While some of the RNA molecules might be 'transcriptional noise' without function, other transcripts control the expression of genes and production of proteins. The act of transcription itself is also likely to play an important role in regulation of gene expression. Transcribing one stretch of DNA might either help or in other cases interfere with the transcription of a gene close by. Moreover, transcripts without a current purpose can serve as 'raw material for evolution' and acquire new functions over time.
The results shed light on the complex organisation of the yeast genome and the insights gained extend to transcription in humans. A better understanding of transcription mechanisms could find application in new technologies to tune gene regulation in the future.
The above, for example suggests "branch points" of a biophysical phase space of 2 sheeted surface of n functional dimensions. This is only one recent example. But it is quite obvious that there are a whole domain of instances wherein we find such a multi functional phase space embedded within the proteome. It is likewise becoming demonstrable that there obtains a similar ordering in many extreme regimes of the physics of the abiotic. For example, it has recently been shown that the superconductivity/permittivity band gap may coexist in certain alloys rather than being separate phases.
Transport properties of high transition temperature (high-Tc) superconductors apparently demonstrate two distinct relaxation rates in the normal state. We propose that this superficial inconsistence can be resolved with an effective carrier (quasiparticle) density n almost linear in temperature T. Experimental evidence both for and against this explanation is analyzed and we conclude that this offers a clear yet promising scenario. Band structure calculation was utilized to determine the Fermi surface topology of the cuprate superconductor versus doping. The results demonstrate that an electron-like portion of the Fermi surface exists in a wide range of doping levels even for a p-type superconductor, exemplified by La2−xSrxCuO4−δ (LSCO). Such electron-like segments have also been confirmed in recent photoemission electron spectroscopy. The Coulomb interaction between electron-like and hole-like quasiparticles then forms a bound state, similar to that of an exciton. As a result the number of charge carriers upon cooling temperature is decreased. A quantum mechanical calculation of scattering cross section demonstrates that a T2 relaxation rate is born out of an electron–hole collision process. Above the pseudogap temperature T* the normal state of high-Tc cuprates is close to a two-component Fermi liquid. It, however, assumes non-Fermi-liquid behavior below T*.
This bridging of the abiotic domain to the biotic domain represents a boundary layer whereby a kind of potential shockwave forcing curvature operates. That is, scientists may, by forcing an ordinary physical phase into an extreme configuration "mimic" a rather ordinary biophysical condition. (For instance, quasi-crystals and the Bose Einstein state also immediately come to mind.)
Now, the movement across this boundary may also be seen as a multi-sheeted Riemann surface. Photosynthesis represents one such sheet in this overarching manifold; whereas, technological intervention creating such extreme regimes would represent another higher order sheet whereby the noetic domain reorders the characteristic biophysical space. Likewise, noesis (technological creativity) may operate upon the boundary between the biophysical to noetic domains as is evident in the history of advances in agronomy and medicine, inter alia.
As I have referenced elsewhere, it is via a combination of Riemann's method that accurately predicted sonic shockwave theory, and Cantor's transfinite sequencing of nested manifolds, that this functional interplay among Vernadsky's identification of three qualitatively distinct domains comes into focus. This overview represents a long term project orientation for science.