Table 1. Half-life Comparison between this study and previous studies*
|
ORF |
Gene |
Microarray Half-life (min) |
Northern Half-life (min) |
|
YCR040W |
mata1 |
8 |
5 (1) |
|
YNL145W |
mfa2 |
32 |
3 (1) |
|
YKL178C |
ste3 |
6 |
4 (1) |
|
YOR204W |
ded1 |
15 |
4 (1) |
|
YLR420W |
ura4 |
15 |
4 (2) |
|
YFL009W |
cdc4 |
34 |
5 (1) |
|
YDR224C |
htb1 |
7 |
5 (1) |
|
YAL040C |
cln3 |
18 |
5 (3) |
|
YKL216W |
ura1 |
13 |
7 (2) |
|
YEL021W |
ura3 |
32 |
3 (1) |
|
YOR063W |
rpl3 |
8 |
11 (1) |
|
YKL211C |
trp3 |
17 |
12 (4) |
|
YML106W |
ura5 |
8 |
4 (5) |
|
YOR202W |
his3 |
23 |
7 (1) |
|
YCL030C |
his4 |
5 |
13 (2) |
|
YJR060W |
cbf1 |
11 |
15 (3) |
|
YEL009C |
gcn4 |
19 |
16 (2) |
|
YER165W |
pab1 |
15 |
11 (1) |
|
YHL033C |
rpl8a |
17 |
20 (6) |
|
YLL045C |
rpl8b |
21 |
20 (6) |
|
YPL090C |
rps6a |
22 |
20 (6) |
|
YBR181C |
rps6b |
24 |
20 (6) |
|
YLR264W |
rps28b |
21 |
20 (6) |
|
YGL030W |
rpl30 |
22 |
20 (6) |
|
YCR031C |
rps14a |
35 |
25 (3) |
|
YJL191W |
rps14b |
27 |
25 (3) |
|
YML024W |
rps17a |
29 |
28 (1) |
|
YMR205C |
pfk2 |
31 |
29 (7) |
|
YFL039C |
act1 |
46 |
40 (6) |
|
YGL103W |
rpl28 |
39 |
43 (1) |
|
YLR044C |
pdc1 |
27 |
43 (7) |
|
YCR012W |
pgk1 |
70 |
45 (1) |
|
YGR204W |
ade3 |
26 |
50 (3) |
|
YAL038W |
cdc19 |
72 |
67 (7) |
*
Several short-lived mRNAs (via Northern) have considerably longer halftimes
according to microarray analysis. The
factors that we have identified that can contribute are: i. Most of the data
points are at the longer times; thus noise in these data points will be fit and
may obscure a faster decay; ii. The decay is always assumed to go to zero (for
maximal consistency of data treatment) whereas background and low levels of
residual expression can result in non-zero backgrounds and sub-optimal fits;
iii. There will be greater uncertainty in low abundance mRNAs, in general. iv.
Some of the Northern data may be incorrect.
Note that not all of the fast decaying mRNAs give poor fits or
agreement. Nevertheless, future studies
should include additional short time points to maximize precision for the
short-lived mRNAs. In addition, more
accurate halftimes for many of the mRNAs can be obtained by fitting the data
individually with more weighting and endpoints for each mRNA.
Reference:
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2. Peltz, S. W., He, F., Welch, E. & Jacobson, A. (1994) Prog Nucleic Acid Res Mol Biol 47, 271-98.
3. Peltz, S. W. & Jacobson, A. (1993), 291-398. Control of
messenger RNA stability, Academic Press Inc.
4. Braus, G. H. (1991) Microbiol
Rev 55, 349-70.
5. Zuk, D. & Jacobson, A. (1998) Embo J 17, 2914-25.
6. Li, B., Nierras, C. R. & Warner, J. R. (1999) Mol Cell Biol 19, 5393-404.
7. Moore, P. A., Sagliocco, F. A., Wood, R. M. & Brown, A.
J. (1991) Mol Cell Biol 11, 5330-7.