TABLE 2.
Comparison of results obtained with mRNA 3′‐end sequencing methods, including median poly(A) tail length and correlations between poly(A) tail length and mRNA expression, half‐life, and translational efficiency
| Model | Method | Median poly(A) | Correlation with expression | Correlation with half‐life | Correlation with translation efficiency | |
|---|---|---|---|---|---|---|
| Total [nt] | Intragenic [nt] | |||||
| HeLa | TAIL‐Seq (Chang et al., 2014) | 59 | 60 | R p = 0.058noncano | ||
| PAL‐Seq (Subtelny et al., 2014) | 67.5 | 82.6 | R s = −0.053 | R s = −0.048 | R s = −0.1 | |
| Poly(A)‐Seq (Yu et al., 2020) | 95.5 | |||||
| HeLa S3 | FLAM‐Seq (Legnini et al., 2019) | 81 | 87 | R p = −0.18 | R p = −0.13 | R p = −0.1 |
| HEK923T | PAL‐Seq (Subtelny et al., 2014) | 75.3 | 88.4 | R s = −0.23 | R s = 0.07 | |
| HCT116 | Poly(A)‐Seq (Yu et al., 2020) | 101.5 | ||||
| K562 | DRS (Maier et al., 2020) | 94.75 | R s = 0.48 | |||
| Human iPSC | FLAM‐Seq (Legnini et al., 2019) | 97 | 111.5 | R p = −0.19 | ||
| Cerebral organoids | FLAM‐Seq (Legnini et al., 2019) | 104 | 121.5 | R p = −0.32 | ||
| NIH3T3 | TAIL‐Seq (Chang et al., 2014) | 60 | 61 | R p = 0.076 | R p = 0.364 | R p = 0.009 |
| PAL‐Seq (Subtelny et al., 2014) | 95.7 | 107.8 | R s = −0.23 | R s = −0.16 | R s = −0.04 | |
| Mouse liver | PAL‐Seq (Subtelny et al., 2014) | 66.6 | 75.3 | R s = 0.085 | R s = 0 | |
| Mouse | Nano3P‐Seq (Begik et al., 2021) | 100.7 | 106.4 | |||
| Rat liver | PAIso‐Seq (Y. Liu, Nie, et al., 2019) | 63 | ||||
| Arabidopsis leaf | PAL‐Seq (Subtelny et al., 2014) | 50.7 | 58.1 | |||
| Arabidopsis | DRS (Parker et al., 2020) | 68 | R s = −0.34 | |||
| Drosophila S2 | PAL‐Seq (Subtelny et al., 2014) | 50.4 | 63.3 | |||
|
Drosophila Immature oocyte Mature oocyte Activated egg |
mTAIL‐Seq (Lim et al., 2016) |
60 75 73 |
58 76 70 |
NA R s = 0.306 R s = 0.638 |
||
| S. cerevisiae | PAL‐Seq (Subtelny et al., 2014) | 26.7 | 33.1 | R s = −0.44 |
R s = 0.048 R s = −0.094 R s = 0.044 R s = −0.11 R s = 0.045 R s = −0.44 R s = 0.23 R s = −0.35 |
R s = −0.12 |
| DRS (Tudek et al., 2021) | 40 | R p = −0.53 |
R p = −0,22 R p = −0.39 |
|||
| Nano3P‐Seq (Begik et al., 2021) | 22.3 | 24.8 | ||||
| S. pombe | PAL‐Seq (Subtelny et al., 2014) | 28.2 | 32.8 | R s = −0.31 | R s = −0.15 | |
| Mouse germinal vesicle stage oocytes | PAIso‐Seq (Y. Liu, Nie, et al., 2019) | 55.3 | 55.7 | |||
| Danio rerio | Nano3P‐Seq (Begik et al., 2021) | 74.5 | 63.6 | |||
|
Danio rerio embryo: 2 hpf 4 hpf 6 hpf |
PAL‐Seq (Subtelny et al., 2014) |
23.1 42.2 58.1 |
29.4 44 58.9 |
R s = −0.13 R s = −0.011 R s = −0.25 |
R s = 0.77 R s = 0.62 R s = 0.13 |
|
|
X. laevis embryo: Stage 3–4 Stage 9 Stage 12–12.5 |
PAL‐Seq (Subtelny et al., 2014) |
21.7 35.4 44.5 |
25.4 38.1 49.2 |
R s = 0.63 R s = 0.65 R s = 0.13 |
||
|
C. elegans L4 larval stage |
mTAIL‐Seq (Lima et al., 2017) | 57 | 82 | R s = −0.24 |
R = −0.32 Fop instead of TE |
|
| FLAM‐Seq (Legnini et al., 2019) | 51 | 59 | R p = −0.19 | |||
|
C. elegans adult stage |
FLAM‐Seq (Legnini et al., 2019) | 44.5 | 49.5 | R p = −0.21 | ||
Abbreviations: DRS, Nanopore direct RNA sequencing; F op, frequency of optimal codons; R p, Pearson's correlation coefficient; R s, Spearman's correlation coefficient; TE, translational efficiency.
Note: In the case of poly(A) tail length, in poly(A)‐Seq, FLAM‐Seq, and PAIso‐Seq, the mean of medians for replicates is given.