Identification of active miRNA promoters from nuclear run-on RNA sequencing

Bitter

Proc. Natl. Acad. Sci. U.S.A.

et al. 2019

Liver fibrosis interferes with normal liver function and facilitates hepatocellular carcinoma (HCC) development, representing a major threat to human health. Here, we present a comprehensive perspective of microRNA (miRNA) function on targeting the fibrotic microenvironment. Starting from a murine HCC model, we identify a miRNA network composed of 8 miRNA hubs and 54 target genes. We show that let-7, miR-30, miR-29c, miR-335, and miR-338 (collectively termed antifibrotic microRNAs [AF-miRNAs]) down-regulate key structural, signaling, and remodeling components of the extracellular matrix. During fibrogenic transition, these miRNAs are transcriptionally regulated by the transcription factor Pparγ and thus we identify a role of Pparγ as regulator of a functionally related class of AF-miRNAs. The miRNA network is active in human HCC, breast, and lung carcinomas, as well as in 2 independent mouse liver fibrosis models. Therefore, we identify a miRNA:mRNA network that contributes to formation of fibrosis in tumorous and nontumorous organs of mice and humans.

Section: Af-mirnas Are Down-regulated and Fibrosis-associated Genes Arementioning

confidence: 99%

Identification of Ppar γ -modulated miRNA hubs that target the fibrotic tumor microenvironment

Bitter

Proc. Natl. Acad. Sci. U.S.A.

et al. 2019

“…Analogous to regulation of protein-coding genes, expression of miRNAs is regulated at both transcriptional and post-transcriptional levels ( Ha and Kim, 2014 ). Transcription of pri-miRNAs is developmentally regulated as shown by in situ hybridization and transcriptome analysis in Drosophila ( Aboobaker et al, 2005 ; Graveley et al, 2011 ; Brown et al, 2014 ; Liu et al, 2017 ). On the other hand, recent studies also revealed a variety of mechanisms post-transcriptionally regulating miRNA processing in a gene-specific or global manner.…”

Section: Introductionmentioning

confidence: 99%

Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development

Zhou

Lim

Kaur

et al. 2018

eLife

Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5’ nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/–309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.

“…miRNA is typically generated from long primary miRNA, which is transcribed by RNA polymerase II and is rapidly cleaved to produce precursor miRNA by Drosha. Compared to the knowledge of miRNAs regulating gene expression, the understanding of miRNA transcriptional initiation is lagging far behind, mainly due to the fact that miRNA transcription start sites (TSSs) are largely unknown [20]. Addressing this issue is more complex for baculovirus miRNAs because most viral early transcripts are initiated at early promoter sequences by host cell RNA polymerase, while viral late transcripts are initiated at late promoter sequences by viral RNA polymerase.…”

Section: Resultsmentioning

confidence: 99%

Characterization of miRNAs encoded by Autographa californica nucleopolyhedrovirus

Wang¹,

Xing

Peng³

et al. 2020

Preprint

Two Autographa californica nucleopolyhedrovirus (AcMNPV) encoded miRNAs, AcMNPV-miR-1 and -miR-3, have been reported in 2013 and 2019. Here, we present an integrated investigation of AcMNPV-encoded miRNAs. Six candidate miRNAs were predicted through small RNA deep sequencing and bioinformatics, of which, five validated by experiments. Three miRNAs perfectly matched the coding sequence of viral genes. The other two are located in coding sequences of viral genes. Targets in both virus and host were predicted and subsequently tested using dual-luciferase reporter assay. The validated targets were found mainly in AcMNPV, except for the targets of AcMNPV-miR-4, which are all host genes. Based on reporter assays, the five miRNAs predominantly function by down-regulating their targets, though individual target is slightly up-regulated. The transcription start sites of these miRNAs were analyzed. Our results suggest that AcMNPV-encoded miRNAs function as fine modulators of the interactions between host and virus by regulating viral and/or host genes. Author summaryVirus-encoded miRNAs have been widely reported as modulators participating in almost all biological processes. However, among Baculoviridae, which consists of a large family of dsDNA viruses that infect numerous beneficial insects and agricultural pests, only several have been reported encoding miRNAs. To clarify the roles of AcMNPV-encoded miRNAs in host-pathogen interactions, we employed RNA deep sequencing and series of experimental approaches identifying AcMNPV-encoded miRNAs, followed by target validation and function deduction. Among them, AcMNPV-miR-1 and AcMNPV-miR-3 have been reported in 2013 and 2019, respectively. This study reveals the sites of these miRNAs in the genome, both in coding sequences and complements, suggesting diverse functions. These miRNAs target genes in the virus itself and in the host, largely by suppressing expression, with some enhancing it. The transcription initiations of the miRNAs were analyzed. Our results provide some insight into the finely regulated process of baculovirus infection. baculovirus molecular biology, was also reported encoding miRNAs, AcMNPV-miR-1 and AcMNPV-miR-3 in 2013 [8, 12] by us, respectively.AcMNPV-miR-1 can down-regulate viral gene ac94, reducing the production of infectious budded virions (BVs) and accelerating the formation of occlusion-derived virions (ODVs) [8]. In 2016, we further reported two more target genes (ac95 and ac18) of AcMNPV-miR-1, and depicted the function pathway of this miRNA [13]. As for AcMNPV-miR-3, it mainly down-regulates viral gene ac101, meanwhile, it also regulates other five viral genes [12]. All these findings indicate that baculovirus-encoded miRNAs play roles in multiple aspects of virus infection.Here, we provide an integrated characterization of these miRNAs which AcMNPV encoded. The investigation for AcMNPV-encoded miRNAs and their functions began with sequencing four small RNA samples collected from Sf9 cells infected with AcMNPV at three different time intervals...