Table 2.
Calculation of the average meeting point of rightward and leftward replication forks progressing along CCSER1βa and of the proportion of rightward (leftward) forks reaching the IZ located in 3′ (5′) of CCSER1βa. To reach the 3′ (5′) IZ, rightward (leftward) forks coming from the 5′ (3′) IZ must have travelled a minimum of 621 kb (i.e., CCSER1βa length) before the 3′ (5′) IZ fired, that is, at the latest, before S4. Only rightward (leftward) forks emanating from the 5′ (3′) IZ at the beginning of S-phase (S1 fraction), which could theoretically travel 663 (628) kb by the end of the third quarter of S-phase, fulfil these criteria. These forks accounted for 26.3 (5.7) % of total rightward (leftward) forks, while the 3′ (5′) IZ fired after S3 33.2 (2.9) % of the time. The 5′ and 3′ IZs were considered to be fully efficient. Replication fork velocity was assumed to be constant throughout S-phase. fS1 (fS1′), fS2 (fS2′), fS3 (fS3′) and fS4 (fS4′) replication timing values correspond to the percentage of BrdU-labelled DNA relative to total S-phase in S1, S2, S3 and S4 fractions, respectively, at the position of the 5′ (3′) IZ (data from Figure 2F in (46); average percentage from two independent experiments). vRF, velocity of rightward forks; vLF, velocity of leftward forks
| Parameter | Value | Comments | |
|---|---|---|---|
| Doubling time | 744 min | Data from Supplementary Figure 5D in (46) | |
| % of cells in S phase | 62.5 | Data from Supplementary Figure 5E in (46) | |
| Estimated S-phase duration | 465 min | = % of cells in S phase*doubling time | |
| Median velocity of rightward forks emanating from the IZ located in 5′ of CCSER1βa | 1.9 kb/min | vRF; see Supplementary Figure S1D | |
| Theoretical distance travelled by rightward forks emanating from the IZ located in 5′ of CCSER1βa starting in | S1 | 884 kb | dS1 = 1*S-phase duration*vRF |
| S2 | 663 kb | dS2 = 0.75*S-phase duration*vRF | |
| S3 | 442 kb | dS3 = 0.5*S-phase duration*vRF | |
| S4 | 221 kb | dS4 = 0.25*S-phase duration*vRF | |
| % of rightward forks emanating from the IZ located in 5′ of CCSER1βa starting in | S1 | 26.3 | fS1; data from Figure 2F in (46) |
| S2 | 53.2 | fS2; data from Figure 2F in (46) | |
| S3 | 17.6 | fS3; data from Figure 2F in (46) | |
| S4 | 2.9 | fS4; data from Figure 2F in (46) | |
| Average distance potentially travelled by rightward forks emanating from the IZ located in 5′ of CCSER1βa | 669 kb | dIZ1 = dS1*fS1+dS2*fS2+dS3*fS3+dS4*fS4 | |
| Median velocity of leftward forks emanating from the IZ located in 3′ of CCSER1βa | 1.8 kb/min | vLF. See Supplementary Figure S1D | |
| Theoretical distance travelled by lefttward forks emanating from the IZ located in 3′ of CCSER1βa starting in | S1 | 837 kb | dS1′ = 1*S-phase duration*vLF |
| S2 | 628 kb | dS2′ = 0.75*S-phase duration*vLF | |
| S3 | 419 kb | dS3′ = 0.5*S-phase duration*vLF | |
| S4 | 209 kb | dS4′ = 0.25*S-phase duration*vLF | |
| % of leftward forks emanating from the IZ located in 3′ of CCSER1βa starting in | S1 | 5.7 | fS1′; data from Figure 2F in (46) |
| S2 | 20.1 | fS2′; data from Figure 2F in (46) | |
| S3 | 41.0 | fS3′; data from Figure 2F in (46) | |
| S4 | 33.2 | fS4′; data from Figure 2F in (46) | |
| Average distance potentially travelled by leftward forks emanating from the IZ located in 3′ of CCSER1βa | 415 kb | dIZ2 = dS1′*fS1′+dS2′*fS2′+dS3′*fS3′+dS4′*fS4′ | |
| CCSER1βa length | 621 kb | Data from Supplementary Figure 5A in (46) | |
| Average meeting point of rightward and leftward progressing forks (distance from CCSER1βa TSS) | 383 kb | = dIZ1/(dIZ1+dIZ2)*length(CCSER1βa) | |
| % of rightward forks emanating from the IZ located in 5′ of CCSER1βa able to reach the IZ located in 3′ of CCSER1βa | 8.7 | =fS1*fS4′*100 | |
| % of leftward forks emanating from the IZ located in 3′ of CCSER1βa able to reach the IZ located in 5′ of CCSER1βa | 0.17 | =fS4*fS1′*100 | |