HI HexiRPA000010
DN (Velculescu VE, 1997) Characterization of the Yeast Transcriptome @Cell #20060730
DA 2006.07.30
CP Cell. 1997 Jan 24;88(2):243-51.
TI Characterization of the yeast transcriptome.
AU Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW.
IN Program in Human Genetics and Molecular Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.
AB We have analyzed the set of genes expressed from the yeast genome, herein called the transcriptome, using serial analysis of gene expression. Analysis of 60,633 transcripts revealed 4,665 genes, with expression levels ranging from 0.3 to over 200 transcripts per cell. Of these genes, 1981 had known functions, while 2684 were previously uncharacterized. The integration of positional information with gene expression data allowed for the generation of chromosomal expression maps identifying physical regions of transcriptional activity and identified genes that had not been predicted by sequence information alone. These studies provide insight into global patterns of gene expression in yeast and demonstrate the feasibility of genome-wide expression studies in eukaryotes.
PM PMID: 9008165 [PubMed - indexed for MEDLINE]
CA Velculescu VE, velculescu@jhmi.edu, from the Johns Hopkins Oncology
CT Contents:
1. States of yeast cells in SAGE libraries:
a. log phase : 20,184 (3,298 unique genes)
b. S phase-arrested : 20,034
c. G2/M phase-arrested : 20,415
??How about the cross section of each cell? sample in a certain cell every 5 min?
2. the transcript expression level per gene: 0.3 ~ 200
a. those have coregulated divergent promoters : similar expression. e.g. histone H3 and H4
b. Regions within 10kb of telomeres / nontelomeric regions : 3.2 tags per gene / 12.4 tags.
3. Mushegian and Koonin, 1996: a minimal set of 250 genes required for prokaryotic cellular life. (196 hologous genes in yeast, >90% identified.)
4. Limitations of SAGE:
a. transcripts of lack an NIaIII site would not be detected.
b. the transcripts found at least 0.3 copies per cell
c. some mRNA sequence of yeast are unavailable. (misassigned)
NT Notes:
1. log phase: Bacterial growth From Wikipedia, the free encyclopedia
Bacterial growth is the process in which from a bacterial cell, two clone daughter cells are produced. Hence, through cell division, local doubling of the bacterial population occurs. However, in each generation not all bacteria survive. Hence, at best, bacterial growth is only temporarily adhering to an exponential growth model. The measurement of a bacterial growth curve was traditionally a part of the training of all microbiologists.
In autecological studies, bacterial growth can be modeled with four different phases: lag phase (A), exponential or log phase (B), stationary phase (C), and death phase (D).
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L | B / \ D
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T
Growth is shown as L = log(numbers) where numbers is the number of colony forming units per ml, versus T (time.)
During lag phase, bacteria adapt themselves to growth conditions. It is the period where the individual bacteria are maturing and not yet able to divide.
During the exponential phase, the number of new bacteria appearing per unit time is proportional to the present population. This gives rise to the classic exponential growth curve, in which the logarithm of the population density rises linearly with time (see figure). The actual rate of this growth (i.e. the slope of the line in the figure) depends upon the growth conditions. Exponential growth cannot continue indefinitely, however, because the medium is soon depleted of nutrients.
3. During stationary phase, the growth rate slows as a result of nutrient depletion. This phase is reached as the bacteria begin to exhaust the resources that are available to them.
4 At death phase, bacteria run out of nutrients and die.
In reality, these phases are not so well defined, and the curve is much more continuous.
Bacterial growth can be suppressed with bacteriostats, without necessarily killing the bacteria.
In a synecological, a true-to-nature situation, where more than one bacterial species is present, the growth of microbes is more dynamic and continual.
2. S phase-arrested: from Wikipedia
Although the various stages of interphase are not usually morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for entry into the next stage. It should be remembered that, throughout interphase, the cell carries out its normal metabolic activities and is actively engaging in transcription and translation of its genome.
In G1 phase, the cell carries on its usual metabolic activities while preparing to duplicate its DNA. These preparations often include growing by increasing the amount of cytoplasm and the number of important organelles such as mitochondria. (This is particularly important in organisms and cell types that divide their cytoplasm unevenly, as in budding yeast.) In G1 a diploid cell (such as a human cell) has a complement of 2N chromosomes, where N is the gene copy number; in sexually reproducing organisms this amounts to one chromosome inherited from each parent. The actual quantity of DNA is described as 2c, where the "c" value is measured in picograms and 1c is equal to the quantity of DNA in a single haploid genome. The end of G1 is demarcated by a "point of no return" beyond which the cell is committed to dividing; in yeast this is called START and in multicellular eukaryotes it is termed the restriction point.
In S phase, the cell duplicates its DNA.
In G2 phase, the cell continues with growth and metabolism in preparation for undergoing mitosis. In this quantity of DNA within the cell has increased to 4c, but the cell is still considered diploid.
In M phase the cell segregates its chromosomes so that both daughter cells receive a total complement of 2N. The four stages of mitosis - prophase, metaphase, anaphase, and telophase - also progress in a sequential and directional fashion, like the cell cycle as a whole. Telophase, the final stage of mitosis, is accompanied by cytokinesis; when the cytoplasm is completely divided, the cycle is complete and the new daughter cells are said to be in G1 again. The exact mechanism of cytokinesis is highly organism- and cell type-dependent; for example, in plant cells surrounded by a rigid cell wall, cytokinesis occurs via the formation of a cell plate, while animal cells are "pinched" in two by a ring formed from a structural protein called actin.
Although the illustration assigns the four stages of the cell cycle roughly equal durations, a cell actually spends a very small amount of its time in G2 phase, and even less time in M phase. The overall duration of the cell cycle depends on the organism and type of cell.
The term "post-mitotic" is sometimes used to refer to both quiescent and senescent cells. Nonproliferative cells in multicellular eukaryotes generally enter the quiescent G0 state from G1 and may remain quiescent for long periods of time, possibly indefinitely (as is often the case for neurons). This is very common for cells that are fully differentiated. Cellular senescence is a state that occurs in response to DNA damage or degradation that would make a cell's progeny nonviable; it is often a biochemical alternative to the self-destruction of such a damaged cell by apoptosis.
3. Rot Curve:?
SP Sentence Patterns from Paper:
1. Tables incuding XX are available from the authors upon request.
2. This work was supported by grants ...
3. We thank members of our laboratories for helpful discussions and critical reading of the manuscript.
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