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Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells
Open accessAbstract
Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3'-untranslated region (UTR) and CpG di-nucleotides in the 5'-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.
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“In silico analysis showed several ARE 1 (AUUUA) and ARE 4 (12-mer A/U, max.one mismatch) sites (33) as well as a potential miR-27a/b binding site.”
From MicroRNA-27b Contributes to Lipopolysaccharide-mediated Peroxisome Proliferator-activated Receptor γ (PPARγ) mRNA Destabilization (2010) · cites this paper as [33]
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“This result is in agreement with that previously observed in mESCs 54,55 , thus suggesting the bona fide of the experiment.”
From Intragenic DNA methylation prevents spurious transcription initiation (2017) · cites this paper as [54]
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Prete, V., Pietro, P. D., Abate, A. C., Venturini, E., Iside, C., Vecchione, C., & Carrizzo, A. (2025) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00231.2025 · Cited by 4
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Quantifying BRCA1 and BRCA2 mRNA Isoform Expression Levels in Single Cells
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“Research has identified several possible causes for this discrepancy, including alternate rates of protein generation and decay [3], [4], [5], varying reactions to environmental stimuli [6], [7], or simply systematic experimentation error bias [8], [9].”
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InfluentialQuantifying broken detailed balance in transcription
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“To obtain values for the mRNA degradation rate, d , we cross-referenced gene names with the mouse mRNA degradation rate dataset from [72].”
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BackgroundPredicting cell population-specific gene expression from genomic sequence
Michielsen, L., Reinders, M. J. T., & Mahfouz, A. E. (2024) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2024.1347276 · Cited by 6
“…We decreased the number of half-life time features from eight to fi ve; the three features we removed (5 ′ UTR, ORF, and 3 ′ UTR GC content) correlated less with half-life time, so we removed them to make the model less complex (Sharova et al., 2009; Spies et al., 2013; Agarwal and Shendure, 2020).”
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“This is remarkable because natural mRNA is highly unstable (Yang et al., 2003), with an average half-life in mammals of about 7 h (Sharova et al., 2008).”
MiRNA-Mediated Regulation of S100B: A Review
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“The half-life of S100 β mRNA may be as long as 24 h [25], indicating a potential “stationary target” for mRNA-targeting medications.”
Jana, S., Dines, M., Lalzar, M., & Lamprecht, R. (2023) · Molecular Neurobiology · doi:10.1007/s12035-022-03191-w · Cited by 3
“Since the half-life of mRNA is relatively short [50], this alteration represents changes in the long-lasting transcriptional program.”
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“Half-lives (τ1/2) of individual mRNAs have been successfully measured in mouse embryonic stem cells (19).”
Gene-specific transcript buffering revealed by perturbation of coactivator complexes
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“Furthermore, we assumed that the 24-hour auxin treatment was sufficiently long relative to the typical mRNA half-life, which is on the order of hours ( 28 , 29 ), allowing cells to attain a quasi-equilibrium state after perturbation.”
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G2M splits mouse embryonic stem cells into naïve and formative pluripotency statesPreprint
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“0503871 ∙ b̀ + 1 In order to determine the appropriate value of Is, several values were assigned to Is, and mRNA half-lives in the Std condition were compared with the previously reported mRNA half-lives [32] (Fig.”
BackgroundMethodResultInfluentialNuclear poly(A) tail size is regulated by Cnot1 during the serum responsePreprint
Singhania, R., Thorn, G. J., Williams, K., Gandhi, R. D., Daher, C., Barthet-Barateig, A., Parker, H. N., Utami, W., Al-Siraj, M., Barrett, D. A., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/773432 · Cited by 5
“In contrast, most mRNAs involved in maintenance functions, such as the general factors required for basal transcription, translation, energy metabolism and protein degradation are quite stable, making them impervious to short term down regulation [1-5].”
BackgroundExon-intron architecture determines mRNA stability by dictating m6A depositionPreprint
Uzonyi, A., Slobodin, B., & Schwartz, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.29.498130 · Cited by 3
“The primary feature with which these ‘fixed’ decay rates correlated was exon density, in line also with prior studies (Agarwal and Shendure, 2020; Clark et al., 2012; Sharova et al., 2009; Spies et al., 2013).”
BackgroundResultInfluentialCompetition between transcription and loop extrusion modulates promoter and enhancer dynamicsPreprint
Sexton, T., Platania, A., Erb, C., Barbieri, M., Molcrette, B., Grandgirard, E., de Kort, M. A. C., Meaburn, K. J., Taylor, T., Shchuka, V. M., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3164817/v1 · Cited by 3
Rose, A. B., Baer, A., Shaker, I., Monroe, J. G., Korf, I. F., & Rose, L. S. (2025) · Scientific Reports · doi:10.1038/s41598-025-99739-6 · Cited by 2
How cells tame noise while maintaining ultrasensitive transcriptional responses
Jeong, E. M., Chung, C. Y., & Kim, J. K. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013217 · Cited by 2
“…with a biologically relevant binding rate k f Ω –1 = 6 × 10 –6 ∼ 6 × 10 –5 ymol –1 min –1 [24,29,30], where Ω = 10 7 aL is the volume of the cell [23], and the mRNA half-life is 0.5 ~ 16.4 hours (i.e., 30 ~ 984 min; Table 2) [31,32], the Fano factor is greater than 40 (Fig 1e, gray box).”
InfluentialMintcheva, J., Tseng, T.-L., Goumenaki, P., Neuschulz, A., Senoussi, A., Lelek, S., Lim, K. L., Ming, Z., Schäfer, R., Hnatiuk, A., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72781-2 · Cited by 2
“The average half-life amounted to 2.5h ( τ [0.5h,48 h], R 2 >0.7), slightly shorter than reported average half-lives in mammalian cells 35,36 .”
InfluentialShea, E. N., Olafson, H. R., Muscato, D. R., Adams, L. M., Valero, M. C., McKee, K., Shen, X., Dougherty, P. G., Hicks, A. N., Liu, N., et al. (2026) · Molecular Therapy · doi:10.1016/j.ymthe.2026.04.060 · Cited by 2
Tani, H. (2026) · IUBMB Life · doi:10.1002/iub.70122 · Cited by 2
Xiao, Q., Liu, Y., Zhang, D., Li, C., Yang, Q., Lu, D., Zhang, W., Rosenecker, J., Zou, Q., Li, Y., et al. (2022) · Journal of Visualized Experiments · doi:10.3791/64288 · Cited by 3
Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms
Uriu, K., Hernandez-Sanchez, J. P., & Kojima, S. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00451-4 · Cited by 2
A POLYMORPHISM ANALYSIS OF DYSFERLIN GENE LOCUS IN CHICKEN GENE POOL
Barkova, O. Y. (2021) · Sel skokhozyaistvennaya Biologiya · doi:10.15389/agrobiology.2021.4.641eng · Cited by 2
“По результатам полногеномного анализа стабильность мРНК положительно коррелировала с числом интронов у мыши и человека (27-30).”
Alicea, B., Suhr, S. T., & Cibelli, J. B. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/006213 · Cited by 2
Origins and impacts of new mammalian exonsPreprint
Merkin, J. J., Chen, P., Alexis, M. S., Hautaniemi, S., & Burge, C. B. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/009282 · Cited by 2
Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNAPreprint
Alicea, B. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/006775 · Cited by 2
“Patterns of decay across three or four samples across time can be assessed using linear and nonlinear statistical curve-fitting techniques [13, 14], which when applied in tandem at a time-scale of days can reveal finer-scale fluctuations not due to intrinsic noise.”
BackgroundA novel regulatory pathway recognizes and degrades transcripts with long 3′ untranslated regionsPreprint
Daly, C. W. P., Kristjánsdóttir, K., West, J. D., Vu, L. T., Fogarty, E. A., Geißler, R., McDermott, C., Venkataramany, A., & Grimson, A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.11.584429 · Cited by 2
“…3′UTR length correlates with decreased transcript abundance, although this correlation is inconsistent between different cell types (Yang et al. 2003; Sharova et al. 2009; Spies et al. 2013) , perhaps reflecting differences in 3′UTR isoforms and/or alternative complements of trans factors.”
BackgroundResultDevelopmental dynamics and axonal transport of cerebral cortex projection neuron mRNAs in vivoPreprint
Veeraraghavan, P., Tillman, D. E., Ross, M. I., & Macklis, J. D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.23.650263 · Cited by 2
RNA AS A BIOMARKER IN CLINICAL LABORATORY DIAGNOSTICS
MUDROV, V. P. (2024) · Лабораторная медицина · doi:10.58953/15621790_2024_15_1-2_13 · Cited by 1
The advantage of periodic over constant signalling in microRNA-mediated regulation
Ferro, E., Szischik, C. L., Ventura, A. C., & Bosia, C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf867 · Cited by 2
Tsachaki, M., Peltret, M., Laplace, T. B., Vaxelaire-Hily, E., Mosbaoui, F., Aillerie, C., Schmid, A., Galea, A., Contarin, F., Duarte, L., et al. (2026) · New Biotechnology · doi:10.1016/j.nbt.2026.03.008 · Cited by 1
Zhu, W. (2015) · UKnowledge (University of Kentucky) · Cited by 1
Puszyński, K., Jonak, K., Kurpas, M. K., Janus, P., & Szołtysek, K. (2014) · IWBBIO · Cited by 1
Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each
Dogar, A. M., Pauchard-Batschulat, R., Grisoni-Neupert, B., Richman, L., Paillusson, A., Pradervand, S., Hagenbüchle, O., Ambrosini, G., Schmid, C. D., Bücher, P., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0206823 · Cited by 1
Nguyen, T. T., & Seoighe, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079627 · Cited by 1
“related to physiological function [8,12].”
BackgroundKhan, H. A., Alrokayan, S., Alhomida, A. S., & Khan, I. (2016) · Biomedical Research-tokyo · Cited by 1
The Effects of Rosiglitazone on the Neonatal Rat Cardiomyocyte Transcriptome: A Temporal Analysis
da Silveira, W. A., Vazquez-Hidalgo, E., Bartolotta, E. A., Renaud, L., Paolini, P. J., & Hardiman, G. (2019) · Pharmacogenomics · doi:10.2217/pgs-2019-0077 · Cited by 1
Mušo, M., Dumbell, R., Pulit, S. L., Sinnott-Armstrong, N., Laber, S., Zolkiewski, L., Bentley, L., Claussnitzer, M., & Cox, R. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194640 · Cited by 1
Dynamic Analysis and Control of the Hepatitis C Virus
Castaño-Arcila, M., Ramírez-Hurtado, A., León, C. E. G.-D., & Rodríguez-González, J. (2020) · IFAC-PapersOnLine · doi:10.1016/j.ifacol.2020.12.425 · Cited by 1
“9⇥ 10 2 (h 1) Sharova et al. (2009) μP2 6.19⇥ 10 2 (h 1) Sharova et al. (2009) μP3 6.19⇥ 10 2(h 1) Sharova et al. (2009) μP4 3.75⇥ 10 2 (h 1) Sharova et al. (2009) μP5 6.08⇥ 10 2(h 1) Sharova et al. (2009) μP6 6.08⇥ 10 2(h 1) Sharova et al. (2009) μP7 2.39⇥ 10 2 (h 1) Sharova et al. (2009) μm1 9.27⇥ 10 2 (h 1) Sharova…”
InfluentialSeeking a Role for Translational Control by Alternative Polyadenylation in Saccharomyces cerevisiae
Turner, R. E., & Beilharz, T. H. (2021) · Microorganisms · doi:10.3390/microorganisms9091885 · Cited by 1
“Some studies have suggested that the presence of regulatory elements plays a larger role in 3′ UTR regulation than the length of the 3′ UTR itself [18].”
BackgroundАНАЛИЗ ПОЛИМОРФИЗМА ГЕНА ДИСФЕРЛИНА У ГЕНОФОНДНЫХ ПОРОД КУР
Всероссийский НИИ генетики и разведения сельскохозяйственных животных, Ф. Ф. Ф. Ж. —. В. И. А. Л. К. Э., & БАРКОВА, O. Ю. (2021) · Sel skokhozyaistvennaya Biologiya · doi:10.15389/agrobiology.2021.4.641rus · Cited by 1
Trela, M., Witkowska‐Piłaszewicz, O., Domańska, D., Kaczmarek, M. M., Pawliński, B., Gajewski, Z., & Domino, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031235 · Cited by 1
Findlay, S. D., Bilyk, O., Lypka, K., Waskiewicz, A. J., & Postovit, L.-M. M. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/276170 · Cited by 1
“Real time PCR was conducted for short half-life controls c-Myc (MYC) and TATA-binding protein (TBP; Hs99999910_m1), and for the long half-life control beta-Actin (ACTB; Hs01060665g1) (Jeck et al., 2013; Sharova et al., 2009).”
Gupta, R. (2021) · Research Publications (Maastricht University) · doi:10.26481/dis.20210304rg · Cited by 1
Multimodal measurements of phototoxicity in nonlinear optical microscopyPreprint
Zhang, X., Dorlhiac, G., Landry, M. P., & Streets, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.27.457929 · Cited by 1
Predicting cell population-specific gene expression from genomic sequencePreprint
Michielsen, L., Reinders, M. J. T., & Mahfouz, A. E. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.06.506837 · Cited by 1
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.04.556212 · Cited by 1
The advantage of periodic over constant signalling in microRNA-mediated repressionPreprint
Ferro, E., Szischik, C. L., Ventura, A. C., & Bosia, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.18.590057 · Cited by 1
Compartmentalization of mRNA and Translation by DesmosomesPreprint
D’Alessandro, A., Badu-Nkansah, K. A., Link, S., Hlavaty, D., Bjerke, G. A., Nicchitta, C. V., Yi, R., & Lechler, T. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.17.649424 · Cited by 1
Wang, Y., Shu, Z., Cao, Z., & Grima, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.05.652189 · Cited by 1
“1”
Metadata
- Authors
- Sharova, L. V., Sharov, A. A., Nedorezov, T., Piao, Y., Shaik, N., & Ko, M. S. H.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Ko, M. S.H.
- Venue
- DNA Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-08
- Volume
- 16
- Issue
- 1
- Pages
- 45-58
- ISSN
- 1340-2838 (ISSN-L)
- 1756-1663
- PMC
- PMC2644350
- OpenAlex
- W2106014350
- Cited by
- 591
- References
- 57
- Citations by year
- 2026: 20 · 2025: 28 · 2024: 42 · 2023: 40 · 2022: 39 · 2021: 42 · 2020: 37 · 2019: 35 · 2018: 36 · 2017: 38 · 2016: 33 · 2015: 43 · 2014: 40 · 2013: 31 · 2012: 30
- FWCI
- 7.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- DNA Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute on Aging (Z01AG000656)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- mRNA half-life, mRNA stability, mouse embryonic stem cells, pluripotency, cell differentiation, gene expression regulation, exon-exon junctions, AU-rich elements, 3' untranslated region, CpG, 5' untranslated region, transcription factors, steady-state mRNA levels
- MeSH terms
- Animals, Cell Differentiation, Cells, Cultured, Half-Life, Humans, Mice, Inbred C57BL, Mice, Inbred Strains, RNA, Messenger, Oligonucleotide Array Sequence Analysis, 3' Untranslated Regions, Gene Expression Profiling, RNA Stability, Databases, Genetic, Pluripotent Stem Cells, Mice, Embryonic Stem Cells
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