An in vivo method to study post‐transcriptional regulation in germ stem cells

AbstractBackgroundQuiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcriptome level, how post-transcriptional regulation contributes to their chemoresistance remains unknown.ResultsWe induced chemoresistant and quiescent (G0) leukemic cells by serum-starvation or chemotherapy treatment. To study post-transcriptional regulation in G0 leukemic cells, we systematically analyzed their transcriptome, translatome, and proteome. We find that our resistant G0 cells recapitulate gene expression profiles of in vivo chemoresistant leukemic and G0 models. In G0 cells, canonical translation initiation is inhibited; yet we find that inflammatory genes are highly translated, indicating alternative post-transcriptional regulation. Importantly, AU-rich elements (AREs) are significantly enriched in the up-regulated G0 translatome and transcriptome. Mechanistically, we find the stress-responsive p38 MAPK-MK2 signaling pathway stabilizes ARE mRNAs by phosphorylation and inactivation of mRNA decay factor, tristetraprolin (TTP) in G0. This permits expression of ARE-bearing TNFα and DUSP1 that promote chemoresistance. Conversely, inhibition of TTP phophorylation by p38 MAPK inhibitors and non-phosphorylatable TTP mutant decreases ARE mRNAs and sensitizes leukemic cells to chemotherapy. Furthermore, co-inhibiting p38 MAPK and TNFα—prior to or along with chemotherapy—substantially reduced chemoresistance in primary leukemic cells ex vivo and in vivo.ConclusionsThese studies uncover post-transcriptional regulation underlying chemoresistance in leukemia. Our data reveal the p38 MAPK-MK2-TTP axis as a key regulator of expression of ARE bearing mRNAs that promote chemoresistance. By disrupting this pathway, we developed an effective combination therapy against chemosurvival.

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Essential Cytoplasmic Role of the Histone Lysine Methyltransferase Setdb1 in Post-Transcriptional Regulation in Embryonic Stem Cells

10.21203/rs.3.rs-145869/v1 ◽

2021 ◽

Author(s):

Roberta Rapone ◽

Laurence Del Maestro ◽

Costas Bouyioukos ◽

Sonia Albini ◽

Paola Cruz-Tapias ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Transcriptional Regulation ◽

Mrna Stability ◽

Regulation Of Gene Expression ◽

Embryonic Stem ◽

Histone Lysine ◽

Histone Lysine Methyltransferase ◽

Lysine Methyltransferase ◽

Post Transcriptional Regulation

Abstract Embryonic stem cells (ESCs) fate is regulated both at transcriptional and post-transcriptional levels. Indeed, several studies showed that, in addition to gene transcription, mRNA stability and protein synthesis are finely tuned and strongly control the ESCs pluripotency and fate changes. An increasing number of RNA-binding proteins (RBPs) involved in post-transcriptional and translational regulation of gene expression has been identified as regulators of ESC identity. The major lysine methyltransferase Setdb1 is essential for the self-renewal and viability of ESCs. Setdb1 was primarily known to methylate the lysine 9 of histone 3 (H3K9) in the nucleus, where it regulates chromatin functions. However, Setdb1 is also massively localized in the cytoplasm, including in mouse ESCs, where its role remains unknown. Here we show that the cytoplasmic Setdb1 (cSetdb1) is essential for the survival of mESCs. Functional assays further demonstrate that cSetdb1 regulates gene expression post-transcriptionally, affecting the abundance of mRNAs and the rate of newly synthetized proteins. A yeast-two-hybrid assay shows that cSetdb1 interacts with several regulators of mRNA stability and protein translation machinery, such as the ESCs-specific E3 ubiquitin ligase and mRNA silencer Trim71/Lin41. Finally, proteomic analyses reveal that cSetdb1 is required for the integrity of Trim71 complexes involved in mRNA metabolism and translation. Altogether, our data uncover the essential cytoplasmic function of a firstly supposed nuclear “histone” lysine methyltransferase, Setdb1, and provide new insights into the cytoplasmic/post-transcriptional regulation of gene expression mediated by a key epigenetic regulator.

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Transcriptional and post-transcriptional regulation of the genes encoding cytochromes P-450c and P-450d in vivo and in primary hepatocyte cultures.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)68357-7 ◽

1988 ◽

Vol 263 (18) ◽

pp. 8671-8676 ◽

Cited By ~ 4

Author(s):

D S Pasco ◽

K W Boyum ◽

S N Merchant ◽

S C Chalberg ◽

J B Fagan

Keyword(s):

Transcriptional Regulation ◽

Primary Hepatocyte ◽

Hepatocyte Cultures ◽

Primary Hepatocyte Cultures ◽

Genes Encoding ◽

Post Transcriptional Regulation

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Post-transcriptional regulation of TNF gene expression in vivo

Arthritis Research & Therapy ◽

10.1186/ar-1999-66730 ◽

1999 ◽

Vol 3 (1) ◽

Author(s):

Andy Clark

Keyword(s):

Gene Expression ◽

Transcriptional Regulation ◽

Tnf Gene ◽

Post Transcriptional Regulation

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Transcriptional and Post-transcriptional Regulation of Drosophila Germline Stem Cells and Their Differentiating Progeny

Transcriptional and Translational Regulation of Stem Cells - Advances in Experimental Medicine and Biology ◽

10.1007/978-94-007-6621-1_4 ◽

2013 ◽

pp. 47-61 ◽

Cited By ~ 10

Author(s):

Helen White-Cooper ◽

Simona Caporilli

Keyword(s):

Stem Cells ◽

Transcriptional Regulation ◽

Germline Stem Cells ◽

Post Transcriptional Regulation

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A post-transcriptional regulatory code for mRNA stability during the zebrafish maternal-to-zygotic transition

10.1101/292441 ◽

2018 ◽

Author(s):

Charles E. Vejnar ◽

Mario Abdel Messih ◽

Carter M. Takacs ◽

Valeria Yartseva ◽

Panos Oikonomou ◽

...

Keyword(s):

Transcriptional Regulation ◽

Mrna Stability ◽

Binding Proteins ◽

Regulatory Elements ◽

Dependent Manner ◽

A Genome ◽

Maternal To Zygotic Transition ◽

Post Transcriptional Regulation ◽

Genome Activation

AbstractPost-transcriptional regulation is crucial to shape gene expression. During the Maternal-to-Zygotic Transition (MZT), thousands of maternal transcripts are regulated upon fertilization and genome activation. Transcript stability can be influenced by cis-elements and trans-factors, but how these inputs are integrated to determine the overall mRNA stability is unclear. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. To identify cis-regulatory elements, we performed a massively parallel reporter assay for stability-influencing sequences, which revealed that 3’-UTR poly-U motifs are associated with mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC and CUGC elements emerged as the main destabilizing motifs in the embryo, with miR-430 and AREs causing mRNA deadenylation in a genome activation-dependent manner. To identify the trans-factors interacting with these cis-elements, we comprehensively profiled RNA-protein interactions and their associated regulatory activities across the transcriptome during the MZT. We find that poly-U binding proteins are preferentially associated with 3’-UTR sequences and stabilizing motifs, and that antagonistic sequence contexts for poly-C and poly-U binding proteins shape the binding landscape and magnitude of regulation across the transcriptome. Finally, we integrate these regulatory motifs into a machine learning model that accurately predicts the stability of mRNA reporters in vivo. Our findings reveal how mechanisms of post-transcriptional regulation are coordinated to direct changes in mRNA stability within the early zebrafish embryo.

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