Replication timing

E. J. White, O. Emanuelsson, D. Scalzo, T. Royce, S. Kosak, E. J. Oakeley, S. Weissman, M. Gerstein, M. Groudine, et al. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc. Natl. Acad. Sci. USA 101, 11111-17776 (2004). 

In general the cube portion might be replicated times and the star portion might be replicated times. Also, it might be possible to use a fractional factorial design of resolution less than V if the experimenter is prepared to assume that certain interactions are negligible. A central composite design in four variables is shown in Table 2.6. In this table, runs 1-16 are the cube portion, runs 17-24 are the star portion, and runs 25-27 are the center points. 

The influx Rs of cells from the pluripotent stem cell population to the committed stem cell fines is assumed mainly regulated by long-range humoral mechanisms 4>(e), implicating the cytokine G-CSF, c (/,). An intrinsic property of the hemopoietic chain is the presence of a time delay t° that arises because of finite cell maturation times and cell replication times for the neutrophil myelocytes, s (t). In fact, it is important to remember that once a cell from the pluripotent stem cell population is committed to the neutrophil lineage, it undergoes a series of nuclear divisions and enters a maturational phase for a period of time (t° 5-7 d) before release into circulation. The production function Rs has not only to be amplified, but... 

The answer is c. (Murray, pp 412-434. Scriver, pp 3-45. Sack, pp 3—29. Wilson, pp 99-121.) Despite the great length of the chromosomes of eukaryotic DNA, the actual replication time is only minutes. This is because eukaryotic DNA is replicated bidirectionally from many points of origin. The hundreds of initiation sites for DNA replication on chromosomes share a consensus sequence called an autonomous replication sequence (ARS). Thus, while the process of DNA replication in mammals is similar to that in bacteria, with DNA polymerases of similar optimal temperatures and speed, the many replication forks allow for a rapid synthesis of chromosomal DNA. Proteins such as histones, which are bound to mammalian chromosomes, inhibit DNA replication or transcription. Dissociation of the protein-DNA complex (chromatin) and unwinding of DNA supercoils (followed by chromatin reassembly) is part of the replication process. 

As already mentioned, G bands comprise two different subsets of bands, one of which is predominantly composed of LI isochores, has a higher DNA compaction relative to H3 bands and corresponds to the darkest G bands of Francke (1994). In contrast, the other subset is composed of L2 and H1 isochores, has less extreme compositional properties and corresponds to the less dark G bands of Francke (see Fig. 7.18). When we checked the replication timing of G bands using the data of Dutrillaux et al. (1976) and Biemont et al. (1978), we found that the LH- bands (or G1+G2 see Table 7.1) comprised the bands that replicate at the latest times, whereas the LP bands (or G3+G4 see Table 7.1) were the earliest replicating among the G bands (Federico et al., 2000). Fig. 7.19 summarizes all the results just presented. 

Figure 7,17. Kepliciiiion timing ofR bands. G-banded human karytilype showing the R bands identified by Sacconeet ai. (19961 as H3 (red), H3 (yellow) and H3 (white). G bands arc black, i hc replication class of R bands orDtitrillauxei al. (1976) are indicated (by Arabic numerals) on the left (H3 and H3 bands) and on the right (113" btinds) of each chromosome In some cases, the same R band corresponds to two different replication timings. (From Federico et al.. I99S).

Figure 7.19. Histograms with the replication timing of the chromosomal bands. Histograms showing the himiaii chromosomal bands as distributed in the replication classes described byDuirillau. iet al. (1976) and Biemont et al. (1978). (From Saceonc and Bernardi, 2001).

Tenzen T., Yamagata T., Fukagawa T., Sugaya K., Ando A., Inoko H., Gojobori T., Fujiyama A., Okumura K., Ikemura T. (1997). Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex. Mol. Cell Biol. 17 4043-4050. 

Watanabe Y., Fujiyama A., Ichiba Y., Hattori M., Yada T., Sakaki Y, Ikemura T. (2002). Chromosome-wide assessment of replication timing for human chromosomes 1 Iq and 21q disease-related genes in timing-switch regions. Hum. Mol. Gen. 11 13-21. 

Goldman MA, Holmquist GP, Gray MC et al. Replication timing of genes and middle repetitive... 

Selig S, Okumura K, Ward DC et al. Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J 1992 11 1217-1225. 

The organizing laboratory will collect the results, test for normality of variances and outliers, and then determine repeatability precision and reproducibility precision, either directly or from an analysis of variance (ANOVA) on the data. A one way ANOVA, with the laboratories being the factor studied, will give the repeatability variance as the within groups mean square, and the between groups mean square is the repeatability plus the number of replicates times the laboratory variance. For duplicate determinations these quantities may be obtained directly from the means of the two results and their differences, which will subtract out the laboratory bias. 

These workers incubated the salivary gland of larvae of various species of Drosophila in a solution containing -thymidine for a period of about 10-15 min, which is between one-fortieth and one-fiftieth of the total DNA replication time in polytene chromosome (10-12 h). In this case DNA synthesis was not observed... 

Dealing with Replications Time Series Considerations... 

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