New deals on the transcriptional and post-transcriptional regulation of TRP channel target genes during the angiogenesis of glioma

A substantial fraction of the metazoan transcriptome undergoes circadian oscillations in many cells and tissues. Based on the transcription feedback loops important for circadian timekeeping, it is commonly assumed that this mRNA cycling reflects widespread transcriptional regulation. To address this issue, we directly measured the circadian dynamics of mouse liver transcription using Nascent-Seq (genome-wide sequencing of nascent RNA). Although many genes are rhythmically transcribed, many rhythmic mRNAs manifest poor transcriptional rhythms, indicating a prominent contribution of post-transcriptional regulation to circadian mRNA expression. This analysis of rhythmic transcription also showed that the rhythmic DNA binding profile of the transcription factors CLOCK and BMAL1 does not determine the transcriptional phase of most target genes. This likely reflects gene-specific collaborations of CLK:BMAL1 with other transcription factors. These insights from Nascent-Seq indicate that it should have broad applicability to many other gene expression regulatory issues.

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Abstract WP424: Let7i Microrna Regulates Immune Response in Patients with Ischemic Stroke

Stroke ◽

10.1161/str.48.suppl_1.wp424 ◽

2017 ◽

Vol 48 (suppl_1) ◽

Author(s):

Glen C Jickling ◽

Bradley P Ander ◽

Natasha Shroff ◽

Boryana Stamova ◽

Cheryl Dykstra-Aiello ◽

...

Keyword(s):

Immune Response ◽

Transcriptional Regulation ◽

Ischemic Stroke ◽

Brain Injury ◽

Acute Ischemic Stroke ◽

Target Genes ◽

Luciferase Assay ◽

Ischemic Brain Injury ◽

Ischemic Brain ◽

Post Transcriptional Regulation

Background and Purpose: The immune system responds rapidly following ischemic brain injury and can contribute to the final extent of brain damage. microRNA are differentially expressed in leukocytes following ischemic stroke and may regulate the immune response to ischemic brain injury. In this study we evaluate microRNA let7i-5p in ischemic stroke and its regulation of leukocytes. Methods: A total of 212 patients were studied; 106 with acute ischemic stroke and 106 risk factor matched controls. . RNA from circulating leukocytes was isolated from blood collected in PaxGene tubes. Let7i-5p miRNA expression was assessed by Taqman qRT-PCR. Given microRNAs act to destabilize and degrade their target mRNA, mRNA that inversely correlated with let7i were identified. To demonstrate let7i post-transcriptional regulation of target genes, a 3’UTR luciferase assay was performed. Target protein expression was assessed by ELISA. Results: Let7i was decreased in patients with acute ischemic stroke (fold change -1.70, p<0.00001). A modest inverse correlation between let7i and NIH Stroke Scale at admission (r= -0.32, p=0.02), infarct volume (r= -0.21, p=0.04) and plasma MMP9 (r= -0.46, p=0.01) was identified. The decrease in let7i was associated with increased expression of several of its messenger RNA targets including CD86, CXCL8 and HMGB1. In vitro studies confirm let7i post-transcriptional regulation of target genes CD86, CXCL8 and HMGB1. Functional analysis predicted let7i regulates pathways involved in leukocyte activation, recruitment, and proliferation including canonical pathways CD86 signaling in T helper cells, HMGB1 signaling, and CXCL8 signaling. Conclusions: Let7i is decreased in circulating leukocytes of patients with acute ischemic stroke. Mechanisms by which let7i regulates inflammatory response post-stroke include targeting CD86, CXCL8 and HMGB1.

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A synthetic oestrogen antagonist, tamoxifen, inhibits oestrogen-induced transcriptional, but not post-transcriptional, regulation of gene expression

Biochemical Journal ◽

10.1042/bj3130269 ◽

1996 ◽

Vol 313 (1) ◽

pp. 269-274 ◽

Cited By ~ 12

Author(s):

Yukitomo ARAO ◽

Etsuko YAMAMOTO ◽

Naoto MIYATAKE ◽

Yuichi NINOMIYA ◽

Taisuke UMEHARA ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Regulation ◽

Oestrogen Receptor ◽

Target Genes ◽

Limit Of Detection ◽

Regulation Of Gene Expression ◽

Rapid Loss ◽

Mrna Stabilization ◽

Transcription Inhibitor ◽

Post Transcriptional Regulation

Oestrogen (E2) regulates the expression of its target genes at transcriptional and post-transcriptional levels. To clarify the mechanism of E2-induced post-transcriptional regulation, with attention to the involvement of the oestrogen receptor (ER), we studied the effect of tamoxifen (TAM), a synthetic E2 antagonist that inhibits ER-mediated transcription, on E2-induced transcriptional and post-transcriptional regulation of the chicken ovalbumin (OVA) gene in chick oviducts. Run-on analysis with oviduct nuclei isolated from E2-treated chicks showed that TAM treatment completely blocked E2-induced transcription of the OVA gene within 24 h without affecting ER gene expression. Likewise, the rate of transcription fell to below the limit of detection after E2 withdrawal from the chicks. Reflecting the transcription rate, OVA mRNA accumulated linearly in E2-treated chicks, and E2 withdrawal caused a rapid loss of OVA mRNA. However, in the chicks treated with TAM and E2, OVA mRNA was degraded slowly over 48 h with a half-life of 24 h, suggesting that TAM does not inhibit E2-induced mRNA stabilization. Moreover, E2-induced mRNA stabilization was observed even when transcription of the OVA gene was blocked by a transcription inhibitor. Western-blot analysis showed that the remaining OVA mRNA was translatable. Thus the present study indicates that E2 regulates expression of the OVA gene via distinct pathways at transcriptional and post-transcriptional levels.

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Dynamic regulation of small RNAs in anthocyanin accumulation during blueberry fruit maturation

Scientific Reports ◽

10.1038/s41598-021-93141-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xiaobai Li ◽

Yan Hong ◽

Aaron Jackson ◽

Fangqi Guo

Keyword(s):

Transcriptional Regulation ◽

Small Rnas ◽

Indole Acetic Acid ◽

Target Genes ◽

Anthocyanin Biosynthesis ◽

Fruit Maturation ◽

Dynamic Regulation ◽

Protein Levels ◽

Post Transcriptional Regulation ◽

Insight Into

AbstractBlueberry is rich in anthocyanins which accumulate during fruit maturation. Previous studies mostly focus on their translational/transcriptional regulation, but usually underestimate their post-transcriptional regulation, e.g. small RNAs. This study aimed to identify sRNAs and their potential pathways associated with anthocyanin biosynthesis. During three typical phases of fruit maturation (green, pink, and blue), we investigated dynamic changes of sRNA by deep sequencing sRNA and examined the interaction of sRNAs with their target genes by degradome and RLM-PCR. During maturation, up-regulation of VcmiRNA156 and VcmiR393 resulted in down-regulation of VcSPLs and VcTIR1/AFBs, respectively. An important gene of anthocyanin biosynthesis, VcDFR, was substantially down-regulated at both the mRNA and protein levels, and potentially responded to regulation of VcSPLs and VcTIR1/AFBs. Additionally, indole acetic acid (IAA) and abscisic acid (ABA) were involved in the regulation of anthocyanin biosynthesis by interacting with VcmiR393-TIR1/AFBs and VcmiRNA319-VcMYBs respectively. This information provides another insight into blueberry anthocyanin biosynthesis.

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Post-transcriptional regulation of target genes by the sRNA FnrS in Neisseria gonorrhoeae

Microbiology ◽

10.1099/mic.0.000484 ◽

2017 ◽

Vol 163 (7) ◽

pp. 1081-1092 ◽

Cited By ~ 4

Author(s):

Pooja Tanwer ◽

Susanne Bauer ◽

Elisabeth Heinrichs ◽

Gurudutta Panda ◽

Daman Saluja ◽

...

Keyword(s):

Transcriptional Regulation ◽

Neisseria Gonorrhoeae ◽

Target Genes ◽

Post Transcriptional Regulation

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miR8181 is Involved in the Cell Growth and Development Regulation of Saccharina Japonica

10.21203/rs.3.rs-62332/v1 ◽

2020 ◽

Author(s):

Xiaoqi Yang ◽

Xiu liang Wang ◽

Jian ting Yao ◽

Wei Li ◽

Delin Duan

Keyword(s):

Transcriptional Regulation ◽

Cell Growth ◽

Blue Light ◽

Cleavage Site ◽

Growth And Development ◽

Target Genes ◽

Saccharina Japonica ◽

Degradome Sequencing ◽

Post Transcriptional Regulation ◽

Development Regulation

Abstract Background: Aureochrome, a blue-light receptor found in photosynthetic stramenopiles, plays an important role in brown algal growth and development. Aureochrome preserves the reversed effector-sensor domain for blue light reception and acts as the candidate optogenetic tool for light induced post-transcriptional regulation, but the inner rapid regulation of aureochrome remains to be studied. MicroRNA (miRNAs) of plant can cleavage the specific base-pairing site of mRNA by RNA interference mechanism, and such post-transcriptional regulation of miRNAs to photoreceptor has received attention due to the flexible regulation pathway. However, the targeting relationship between aureochrome and miRNA is unclear.Results: In this study, the potential regulatory network between miRNAs and aureochrome were explored by transcriptome and sRNA sequencing in Saccharina japonica. Our results found that 18 miRNAs perfectly paired with aureochrome. Among the screened miRNAs, miR8181-x was negatively correlated with aureochrome5 with high credibility and exhibited tissue-specific expression in S. japonica. Degradome sequencing detected the exact cleavage site of miR8181-x on aureochrome5, confirming their targeting regulation relationship. Among the 54 target genes of miR8181-x, nine genes of ABC transporters, E3 ubiquitin-protein protein ligase, Hsp90, Mx1, PetC, EF2, GSA, HAD-superfamily hydrolase and SET2 that exhibited similar expression with aureochrome5 competed with the same binding site, thus constructing the competing endogenous RNA network. Functional analysis of miR8181-x target genes revealed that regulation of cell differentiation and development was enriched, indicating the potential role of miR8181-x in the regulation of growth and development.Conclusion: Our study found that miR8181-x negatively regulated the expression of aureochrome5. The exact cleavage site in aureochrome5 were verified by degradome sequencing, confirming the targeting relationships. Functional enrichment of miR8181-x target genes revealed that miR8181-x involved in the cell growth and development regulation of S. japonica.

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