Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5

AbstractRotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells at the left LRO margin. Ciliary activity of the calcium channel Pkd2 is crucial for flow sensing. How this flow signal is further processed and relayed to the laterality-determining Nodal cascade in the left lateral plate mesoderm (LPM) is largely unknown. We previously showed that flow down-regulates mRNA expression of the Nodal inhibitor Dand5 in left sensory cells. De-repression of the co-expressed Nodal, complexed with the TGFß growth factor Gdf3, drives LPM Nodal cascade induction. Here, we show that post-transcriptional repression of dand5 is a central process in symmetry breaking of Xenopus, zebrafish and mouse. The RNA binding protein Bicc1 was identified as a post-transcriptional regulator of dand5 and gdf3 via their 3′-UTRs. Two distinct Bicc1 functions on dand5 mRNA were observed at pre- and post-flow stages, affecting mRNA stability or flow induced translational inhibition, respectively. To repress dand5, Bicc1 co-operates with Dicer1, placing both proteins in the process of flow sensing. Intriguingly, Bicc1 mediated translational repression of a dand5 3′-UTR mRNA reporter was responsive to pkd2, suggesting that a flow induced Pkd2 signal triggers Bicc1 mediated dand5 inhibition during symmetry breakage.

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Bicc1 and dicer regulate left-right patterning through post-transcriptional control of the Nodal-inhibitor dand5

10.1101/2020.01.29.924456 ◽

2020 ◽

Author(s):

Markus Maerker ◽

Maike Getwan ◽

Megan E. Dowdle ◽

José L. Pelliccia ◽

Jason C. McSheene ◽

...

Keyword(s):

Symmetry Breaking ◽

Transcriptional Control ◽

Rna Binding ◽

Rna Binding Protein ◽

Sensory Cells ◽

Dependent Manner ◽

Lateral Plate Mesoderm ◽

Lateral Plate ◽

Central Process ◽

Flow Sensing

AbstractRotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells at the left LRO margin. How the flow signal is processed and relayed to the laterality-determining Nodal cascade in the left lateral plate mesoderm (LPM) is largely unknown. We previously showed that flow down-regulates mRNA expression of the Nodal inhibitor Dand5 in left sensory cells. De-repression of the co-expressed Nodal drives LPM Nodal cascade induction. Here, we identify the mechanism of dand5 downregulation, finding that its posttranscriptional repression is a central process in symmetry breaking. Specifically, the RNA binding protein Bicc1 interacts with a proximal element in the 3’-UTR of dand5 to repress translation in a dicer1-dependent manner. The bicc1/dicer1 module acts downstream of flow, as LRO ciliation was not affected upon its loss. Loss of bicc1 or dicer1 was rescued by parallel knockdown of dand5, placing both genes in the process of flow sensing.

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Transcriptional Control of Clostridium autoethanogenum using CRISPRi

Synthetic Biology ◽

10.1093/synbio/ysab008 ◽

2021 ◽

Author(s):

Nick Fackler ◽

James Heffernan ◽

Alex Juminaga ◽

Damien Doser ◽

Shilpa Nagaraju ◽

...

Keyword(s):

Transcriptional Repression ◽

Transcriptional Control ◽

Genome Engineering ◽

Low Cost ◽

Pathway Engineering ◽

Industrial Emissions ◽

Gas Fermentation ◽

Control Gene Expression ◽

Clostridium Autoethanogenum ◽

Commercial Process

Abstract Gas fermentation by Clostridium autoethanogenum is a commercial process for the sustainable biomanufacturing of fuels and valuable chemicals using abundant, low cost C1 feedstocks (CO and CO2) from sources such as inedible biomass, unsorted and non-recyclable municipal solid waste, and industrial emissions. Efforts towards pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods. To increase the pace of progress, here we developed an inducible CRISPR interference (CRISPRi) system for C. autoethanogenum and applied that system towards transcriptional repression of genes with ostensibly crucial functions in metabolism.

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Arginine Methyltransferases as Regulators of RNA-Binding Protein Activities in Pathogenic Kinetoplastids

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.692668 ◽

2021 ◽

Vol 8 ◽

Author(s):

Gustavo D. Campagnaro ◽

Edward Nay ◽

Michael J. Plevin ◽

Angela K. Cruz ◽

Pegine B. Walrad

Keyword(s):

Gene Expression ◽

Transcriptional Control ◽

Rna Binding ◽

Methylation Status ◽

Regulation Of Gene Expression ◽

Structural Features ◽

Arginine Methylation ◽

Diverse Range ◽

Host Interaction ◽

Intronless Genes

A large number of eukaryotic proteins are processed by single or combinatorial post-translational covalent modifications that may alter their activity, interactions and fate. The set of modifications of each protein may be considered a “regulatory code”. Among the PTMs, arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), can affect how a protein interacts with other macromolecules such as nucleic acids or other proteins. In fact, many RNA-binding (RBPs) proteins are targets of PRMTs. The methylation status of RBPs may affect the expression of their bound RNAs and impact a diverse range of physiological and pathological cellular processes. Unlike most eukaryotes, Kinetoplastids have overwhelmingly intronless genes that are arranged within polycistronic units from which mature mRNAs are generated by trans-splicing. Gene expression in these organisms is thus highly dependent on post-transcriptional control, and therefore on the action of RBPs. These genetic features make trypanosomatids excellent models for the study of post-transcriptional regulation of gene expression. The roles of PRMTs in controlling the activity of RBPs in pathogenic kinetoplastids have now been studied for close to 2 decades with important advances achieved in recent years. These include the finding that about 10% of the Trypanosoma brucei proteome carries arginine methylation and that arginine methylation controls Leishmania:host interaction. Herein, we review how trypanosomatid PRMTs regulate the activity of RBPs, including by modulating interactions with RNA and/or protein complex formation, and discuss how this impacts cellular and biological processes. We further highlight unique structural features of trypanosomatid PRMTs and how it contributes to their singular functionality.

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Riboregulators in plant development

Biochemical Society Transactions ◽

10.1042/bst0351638 ◽

2007 ◽

Vol 35 (6) ◽

pp. 1638-1642 ◽

Cited By ~ 18

Author(s):

P. Laporte ◽

F. Merchan ◽

B.B. Amor ◽

S. Wirth ◽

M. Crespi

Keyword(s):

Large Scale ◽

Transcriptional Control ◽

Rna Binding ◽

Bioinformatic Analysis ◽

Nodule Development ◽

Small Interfering Rnas ◽

Cortical Cells ◽

Protein Coding ◽

Early Nodulin ◽

Model Plant Arabidopsis Thaliana

npcRNA (non-protein-coding RNAs) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small RNAs [miRNAs (microRNAs)/siRNAs (small interfering RNAs)] that are involved in various developmental processes in plants and animals. In addition, several other npcRNAs encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. Much less is known about the mechanism of action of these other classes of riboregulators also present in the cell. The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells that express the npcRNA MtENOD40 (Medicago truncatula early nodulin 40). We have identified a novel RBP (RNA-binding protein), MtRBP1 (M. truncatula RBP 1), which interacts with the MtENOD40 RNA, and is exported into the cytoplasm during legume nodule development in the region expressing MtENOD40. A direct involvement of the MtENOD40 RNA in the relocalization of this RBP into cytoplasmic granules could be demonstrated, revealing a new RNA function in the cell. To extend these results, we searched for npcRNAs in the model plant Arabidopsis thaliana whose genome is completely known. We have identified 86 novel npcRNAs from which 27 corresponded to antisense RNAs of known coding regions. Using a dedicated ‘macroarray’ containing these npcRNAs and a collection of RBPs, we characterized their regulation in different tissues and plants subjected to environmental stresses. Most of the npcRNAs showed high variations in gene expression in contrast with the RBP genes. Recent large-scale analysis of the sRNA component of the transcriptome revealed an enormous diversity of siRNAs/miRNAs in the Arabidopsis genome. Bioinformatic analysis revealed that 34 large npcRNAs are precursors of siRNAs/miRNAs. npcRNAs, which are a sensitive component of the transcriptome, may reveal novel riboregulatory mechanisms involved in post-transcriptional control of differentiation or environmental responses.

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Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation

Development ◽

10.1242/dev.126.6.1129 ◽

1999 ◽

Vol 126 (6) ◽

pp. 1129-1138 ◽

Cited By ~ 1

Author(s):

Y.S. Lie ◽

P.M. Macdonald

Keyword(s):

Translational Control ◽

Untranslated Region ◽

Rna Binding ◽

Mrna Translation ◽

Posterior Pole ◽

Translational Repression ◽

Yeast Two Hybrid ◽

Functional Interaction ◽

Translational Repressor ◽

Two Hybrid

The product of the oskar gene directs posterior patterning in the Drosophila oocyte, where it must be deployed specifically at the posterior pole. Proper expression relies on the coordinated localization and translational control of the oskar mRNA. Translational repression prior to localization of the transcript is mediated, in part, by the Bruno protein, which binds to discrete sites in the 3′ untranslated region of the oskar mRNA. To begin to understand how Bruno acts in translational repression, we performed a yeast two-hybrid screen to identify Bruno-interacting proteins. One interactor, described here, is the product of the apontic gene. Coimmunoprecipitation experiments lend biochemical support to the idea that Bruno and Apontic proteins physically interact in Drosophila. Genetic experiments using mutants defective in apontic and bruno reveal a functional interaction between these genes. Given this interaction, Apontic is likely to act together with Bruno in translational repression of oskar mRNA. Interestingly, Apontic, like Bruno, is an RNA-binding protein and specifically binds certain regions of the oskar mRNA 3′ untranslated region.

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Abstract 217: Quaking Post-Transcriptionally Guides Monocyte Adhesion and Differentiation into the Pro-Inflammatory Macrophage

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.35.suppl_1.217 ◽

2015 ◽

Vol 35 (suppl_1) ◽

Author(s):

Ruben G de Bruin ◽

Lily Shiue ◽

Anjana Djarmshi ◽

Hetty C de Boer ◽

Wai Yi Leung ◽

...

Keyword(s):

Transcriptional Control ◽

Rna Binding ◽

Inflammatory Diseases ◽

Human Monocyte ◽

Human Macrophage ◽

Monocyte Adhesion ◽

Sequence Elements ◽

Bound Sequence ◽

Novel Target ◽

And Function

A hallmark of inflammatory diseases is the excessive recruitment and influx of monocytes to sites of tissue damage and their ensuing differentiation into macrophages. Numerous stimuli are known to induce new transcription necessary for macrophage identity, but post-transcriptional control of human macrophage differentiation is less well understood. Here, we detail our discovery that levels of the RNA-binding protein Quaking (QKI) are low in monocytes of early atherosclerotic lesions, but abundant in macrophages of advanced plaques. Specific depletion of QKI protein impaired monocyte adhesion, migration and differentiation into macrophages, and lesion formation. RNA-seq and microarray analysis of human monocyte and macrophage transcriptomes, including those of a unique QKI haploinsufficient patient, reveal developmental changes in RNA levels and alternative splicing of RNA transcripts enriched in QKI-bound sequence elements. The importance of these transcripts and requirement for QKI during differentiation illustrates a central role for QKI in post-transcriptionally guiding macrophage identity and function. These studies implicate QKI as a novel target for therapeutic intervention in inflammatory diseases.

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RNA-Binding Proteins HuB, HuC, and HuD are Distinctly Regulated in Dorsal Root Ganglia Neurons from STZ-Sensitive Compared to STZ-Resistant Diabetic Mice

International Journal of Molecular Sciences ◽

10.3390/ijms20081965 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1965 ◽

Cited By ~ 1

Author(s):

Cosmin Cătălin Mustăciosu ◽

Adela Banciu ◽

Călin Mircea Rusu ◽

Daniel Dumitru Banciu ◽

Diana Savu ◽

...

Keyword(s):

Gene Expression ◽

Body Weight ◽

Sensory Neurons ◽

Dorsal Root Ganglia ◽

Dorsal Root ◽

Transcriptional Control ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Diabetic Mice

The neuron-specific Elav-like Hu RNA-binding proteins were described to play an important role in neuronal differentiation and plasticity by ensuring the post-transcriptional control of RNAs encoding for various proteins. Although Elav-like Hu proteins alterations were reported in diabetes or neuropathy, little is known about the regulation of neuron-specific Elav-like Hu RNA-binding proteins in sensory neurons of dorsal root ganglia (DRG) due to the diabetic condition. The goal of our study was to analyze the gene and protein expression of HuB, HuC, and HuD in DRG sensory neurons in diabetes. The diabetic condition was induced in CD-1 adult male mice with single-intraperitoneal injection of streptozotocin (STZ, 150 mg/kg), and 8-weeks (advanced diabetes) after induction was quantified the Elav-like proteins expression. Based on the glycemia values, we identified two types of responses to STZ, and mice were classified in STZ-resistant (diabetic resistant, glycemia < 260 mg/dL) and STZ-sensitive (diabetic, glycemia > 260 mg/dL). Body weight measurements indicated that 8-weeks after STZ-induction of diabetes, control mice have a higher increase in body weight compared to the diabetic and diabetic resistant mice. Moreover, after 8-weeks, diabetic mice (19.52 ± 3.52 s) have longer paw withdrawal latencies in the hot-plate test than diabetic resistant (11.36 ± 1.92 s) and control (11.03 ± 1.97 s) mice, that correlates with the installation of warm hypoalgesia due to the diabetic condition. Further on, we evidenced the decrease of Elav-like gene expression in DRG neurons of diabetic mice (Elavl2, 0.68 ± 0.05 fold; Elavl3, 0.65 ± 0.01 fold; Elavl4, 0.53 ± 0.07 fold) and diabetic resistant mice (Ealvl2, 0.56 ± 0.07 fold; Elavl3, 0.32 ± 0.09 fold) compared to control mice. Interestingly, Elav-like genes have a more accentuated downregulation in diabetic resistant than in diabetic mice, although hypoalgesia was evidenced only in diabetic mice. The Elav-like gene expression changes do not always correlate with the Hu protein expression changes. To detail, HuB is upregulated and HuD is downregulated in diabetic mice, while HuB, HuC, and HuD are downregulated in diabetic resistant mice compared to control mice. To resume, we demonstrated HuD downregulation and HuB upregulation in DRG sensory neurons induced by diabetes, which might be correlated with altered post-transcriptional control of RNAs involved in the regulation of thermal hypoalgesia condition caused by the advanced diabetic neuropathy.

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PRMT7 regulates RNA-binding capacity and protein stability in Leishmania parasites

Nucleic Acids Research ◽

10.1093/nar/gkaa211 ◽

2020 ◽

Vol 48 (10) ◽

pp. 5511-5526

Author(s):

Tiago R Ferreira ◽

Adam A Dowle ◽

Ewan Parry ◽

Eliza V C Alves-Ferreira ◽

Karen Hogg ◽

...

Keyword(s):

Protein Modification ◽

Transcriptional Control ◽

Leishmania Major ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Capacity ◽

Arginine Methylation ◽

Mrna Metabolism

Abstract RNA binding proteins (RBPs) are the primary gene regulators in kinetoplastids as transcriptional control is nearly absent, making Leishmania an exceptional model for investigating methylation of non-histone substrates. Arginine methylation is an evolutionarily conserved protein modification catalyzed by Protein aRginine Methyl Transferases (PRMTs). The chromatin modifier PRMT7 is the only Type III PRMT found in higher eukaryotes and a restricted number of unicellular eukaryotes. In Leishmania major, PRMT7 is a cytoplasmic protein implicit in pathogenesis with unknown substrates. Using comparative methyl-SILAC proteomics for the first time in protozoa, we identified 40 putative targets, including 17 RBPs hypomethylated upon PRMT7 knockout. PRMT7 can modify Alba3 and RBP16 trans-regulators (mammalian RPP25 and YBX2 homologs, respectively) as direct substrates in vitro. The absence of PRMT7 levels in vivo selectively reduces Alba3 mRNA-binding capacity to specific target transcripts and can impact the relative stability of RBP16 in the cytoplasm. RNA immunoprecipitation analyses demonstrate PRMT7-dependent methylation promotes Alba3 association with select target transcripts and thus indirectly stabilizes mRNA of a known virulence factor, δ-amastin surface antigen. These results highlight a novel role for PRMT7-mediated arginine methylation of RBP substrates, suggesting a regulatory pathway controlling gene expression and virulence in Leishmania. This work introduces Leishmania PRMTs as epigenetic regulators of mRNA metabolism with mechanistic insight into the functional manipulation of RBPs by methylation.

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The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2007268117 ◽

2020 ◽

Vol 117 (26) ◽

pp. 15316-15321 ◽

Cited By ~ 1

Author(s):

Xiaofeng Fang ◽

Zhe Wu ◽

Oleg Raitskin ◽

Kimberly Webb ◽

Philipp Voigt ◽

...

Keyword(s):

Noncoding Rna ◽

Transcriptional Control ◽

Rna Binding ◽

Antisense Transcription ◽

Set Domain ◽

Antisense Transcripts ◽

Polycomb Repressive Complex 2 ◽

Active Transcription ◽

Transcriptional Output

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. AtArabidopsis thaliana FLC,antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3′ processing factors, reducesFLCtranscription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over theFLCgene body. SDG26 interacts with the RNA 3′ processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repressFLC. Overall, our work provides insights into RNA-mediated chromatin silencing.

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The Role of PPARγin the Transcriptional Control by Agonists and Antagonists

PPAR Research ◽

10.1155/2012/362361 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 16

Author(s):

Tamotsu Tsukahara

Keyword(s):

Transcriptional Repression ◽

Transcriptional Control ◽

Thyroid Hormone Receptor ◽

Therapeutic Potential ◽

Current Knowledge ◽

Peroxisome Proliferator ◽

Peroxisome Proliferator Activated Receptor ◽

Cyclic Phosphatidic Acid

In recent years, peroxisome proliferator-activated receptor gamma (PPARγ) has been reported to be a target for the treatment of type II diabetes. Furthermore, it has received attention for its therapeutic potential in many other human diseases, including atherosclerosis, obesity, and cancers. Recent studies have provided evidence that the endogenously produced PPARγ antagonist, 2,3-cyclic phosphatidic acid (cPA), which is similar in structure to lysophosphatidic acid (LPA), inhibits cancer cell invasion and metastasisin vitroandin vivo. We recently observed that cPA negatively regulates PPARγ function by stabilizing the binding of the corepressor protein, silencing mediator of retinoic acid and thyroid hormone receptor. We also showed that cPA prevents neointima formation, adipocyte differentiation, lipid accumulation, and upregulation of PPARγ target gene transcription. We then analyzed the molecular mechanism of cPA's action on PPARγ. In this paper, we summarize the current knowledge on the mechanism of PPARγ-mediated transcriptional activity and transcriptional repression in response to novel lipid-derived ligands, such as cPA.

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