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:

 

1.            Herrick, D., Parker, R. & Jacobson, A. (1990) Mol Cell Biol 10, 2269-84.

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.