scholarly journals C. elegans LIN-28 controls temporal cell-fate progression by regulating LIN-46 expression via the 5’UTR of lin-46 mRNA

2019 ◽  
Author(s):  
Orkan Ilbay ◽  
Charles Nelson ◽  
Victor Ambros
Keyword(s):  
Cell Fate ◽  
Cellular Differentiation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cell Types ◽  
Cell Fates ◽  
C Elegans ◽  
L1 And L2 ◽  
Proliferative Cell

ABSTRACTHuman Lin28 is a conserved RNA-binding protein that promotes proliferation and pluripotency and can be oncogenic. Lin28 and C. elegans LIN-28 bind to precursor RNAs of the conserved, cellular differentiation-promoting, microRNA let-7 and inhibits production of mature let-7 microRNA. Lin28/LIN-28 also binds to and regulates many mRNAs in various cell types. However, the determinants and consequences of these LIN-28-mRNA interactions are not well understood. Here, we report that LIN-28 in C. elegans represses the expression of LIN-46, a downstream protein in the heterochronic pathway, via the 5’ UTR of the lin-46 mRNA. We show that both LIN-28 and the 5’UTR of lin-46 are required to prevent LIN-46 expression in the L1 and L2 stages, and that precocious LIN-46 expression is sufficient to skip L2 stage proliferative cell-fates, resulting in heterochronic defects similar to the ones observed in lin-28(0) animals. We propose that the lin-46 5’UTR mediates LIN-28 binding to and repression of the lin-46 mRNA. Our results demonstrate that precocious LIN-46 expression alone can account for lin-28(0) phenotypes, demonstrating the biological importance of regulation of individual target mRNAs by LIN-28.

scholarly journals Tethered NOS-3, a nematode Nanos RNA-binding protein, enhances reporter expression and mRNA stability

2021 ◽  
Author(s):  
Jonathan Doenier ◽  
Tina R Lynch ◽  
Judith Kimble ◽  
Scott T Aoki
Keyword(s):  
Cell Fate ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Reporter Expression ◽  
Reporter Protein ◽  
C Elegans ◽  
Intrinsically Disordered ◽  
Dual Reporter

AbstractRobust methods are critical for testing the in vivo regulatory mechanism of RNA binding proteins. Here we report improvement of a protein-mRNA tethering assay to probe the function of an RNA binding protein in its natural context within the C. elegans adult germline. The assay relies on a dual reporter expressing two mRNAs from a single promoter and resolved by trans-splicing. The gfp reporter 3’UTR harbors functional binding elements for λN22 peptide, while the mCherry reporter 3’UTR carries mutated nonfunctional elements. This strategy enables internally controlled quantitation of reporter protein by immunofluorescence and mRNA by smFISH. To test the new system, we analyzed a C. elegans Nanos protein, NOS-3, which serves as a post-transcriptional regulator of germ cell fate. Unexpectedly, tethered NOS-3 enhanced reporter expression. We confirmed this enhancement activity with a second reporter engineered at an endogenous germline gene. NOS-3 enhancement of reporter expression was associated with its N-terminal intrinsically disordered region, not its C-terminal zinc fingers. RNA quantitation revealed that tethered NOS-3 enhances stability of the reporter mRNA. We suggest that this direct NOS-3 enhancement activity may explain a paradox: classically Nanos proteins are expected to repress RNA, but nos-3 had been found to promote gld-1 expression, an effect that could be direct. Regardless, the new dual reporter dramatically improves in situ quantitation of reporter expression after RBP tethering to determine its molecular mechanism in a multicellular tissue.

scholarly journals Investigating the Roles of RNA Binding Protein Combinations in Neuronal Function and Organismal Behavior

2019 ◽  
Vol 4 (Spring 2019) ◽  
Author(s):  
Alexa Vandenburg
Keyword(s):  
Binding Sites ◽  
Neuronal Development ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Wild Type ◽  
C Elegans ◽  
Neuronal Gene ◽  
Touch Response

The Norris lab recently identified two RNA binding proteins required for proper neuron-specific splicing. The lab conducted touch- response behavioral assays to assess the function of these proteins in touch-sensing neurons. After isolating C. elegans worms with specific phenotypes, the lab used automated computer tracking and video analysis to record the worms’ behavior. The behavior of mutant worms differed from that of wild-type worms. The Norris lab also discovered two possible RNA binding protein sites in SAD-1, a neuronal gene implicated in the neuronal development of C. elegans1. These two binding sites may control the splicing of SAD-1. The lab transferred mutated DNA into the genome of wild-type worms by injecting a mutated plasmid. The newly transformed worms fluoresced green, indicating that the two binding sites control SAD-1 splicing.

FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline

Development ◽  
2000 ◽  
Vol 127 (24) ◽  
pp. 5265-5276 ◽  
Author(s):  
R. Clifford ◽  
M.H. Lee ◽  
S. Nayak ◽  
M. Ohmachi ◽  
F. Giorgini ◽  
...  
Keyword(s):  
Sex Determination ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Translational Repression ◽  
Specific Substrate ◽  
Interaction Domain ◽  
C Elegans ◽  
Male Sex ◽  
F Box Protein

Male sex determination in the Caenorhabditis elegans hermaphrodite germline requires translational repression of tra-2 mRNA by the GLD-1 RNA binding protein. We cloned fog-2 by finding that its gene product physically interacts with GLD-1, forming a FOG-2/GLD-1/tra-2 3′untranslated region ternary complex. FOG-2 has an N-terminal F-box and a novel C-terminal domain called FTH. Canonical F-box proteins act as bridging components of the SCF ubiquitin ligase complex; the N-terminal F-box binds a Skp1 homolog, recruiting ubiquination machinery, while a C-terminal protein-protein interaction domain binds a specific substrate for degradation. However, since both fog-2 and gld-1 are necessary for spermatogenesis, FOG-2 cannot target GLD-1 for ubiquitin-mediated degradation. We propose that FOG-2 also acts as a bridge, bringing GLD-1 bound to tra-2 mRNA into a multiprotein translational repression complex, thus representing a novel function for an F-box protein. fog-2 is a member of a large, apparently rapidly evolving, C. elegans gene family that has expanded, in part, by local duplications; fog-2 related genes have not been found outside nematodes. fog-2 may have arisen during evolution of self-fertile hermaphroditism from an ancestral female/male species.

scholarly journals A Novel Double-stranded RNA-binding Protein, Disco Interacting Protein 1 (DIP1), Contributes to Cell Fate Decisions duringDrosophilaDevelopment

2003 ◽  
Vol 278 (39) ◽  
pp. 38040-38050 ◽  
Author(s):  
Dorothy DeSousa ◽  
Mahua Mukhopadhyay ◽  
Peter Pelka ◽  
Xiaoli Zhao ◽  
Bijan K. Dey ◽  
...  
Keyword(s):  
Cell Fate ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Interacting Protein ◽  
Double Stranded Rna ◽  
Cell Fate Decisions

scholarly journals Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast

Genetics ◽  
2010 ◽  
Vol 185 (2) ◽  
pp. 513-522 ◽  
Author(s):  
Joshua J. Wolf ◽  
Robin D. Dowell ◽  
Shaun Mahony ◽  
Michal Rabani ◽  
David K. Gifford ◽  
...  
Keyword(s):  
Cell Fate ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Feed Forward ◽  
Cell Fate Determinant ◽  
A Cell

scholarly journals Cbk1 Regulation of the RNA-Binding Protein Ssd1 Integrates Cell Fate with Translational Control

2009 ◽  
Vol 19 (24) ◽  
pp. 2114-2120 ◽  
Author(s):  
Jaclyn M. Jansen ◽  
Antony G. Wanless ◽  
Christopher W. Seidel ◽  
Eric L. Weiss
Keyword(s):  
Cell Fate ◽  
Translational Control ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals Nucleocytoplasmic transport of the RNA-binding protein CELF2 regulates neural stem cell fates

Cell Reports ◽  
2021 ◽  
Vol 35 (10) ◽  
pp. 109226
Author(s):  
Melissa J. MacPherson ◽  
Sarah L. Erickson ◽  
Drayden Kopp ◽  
Pengqiang Wen ◽  
Mohamad-Reza Aghanoori ◽  
...  
Keyword(s):  
Stem Cell ◽  
Neural Stem Cell ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Nucleocytoplasmic Transport ◽  
Cell Fates

scholarly journals CRISPR-TRAPSeq identifies the QKI RNA binding protein as important for astrocytic maturation and control of thalamocortical synapses

2020 ◽  
Author(s):  
Kristina Sakers ◽  
Yating Liu ◽  
Lorida Llaci ◽  
Michael J. Vasek ◽  
Michael A. Rieger ◽  
...  
Keyword(s):  
Rna Binding ◽  
Gene Knockout ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cell Types ◽  
Specific Gene ◽  
Specific Cell ◽  
Normal Brain ◽  
Oligodendrocyte Development

AbstractQuaking RNA binding protein(QKI) is essential for oligodendrocyte development as myelination requires MBP mRNA regulation and localization by the cytoplasmic isoforms(e.g. QKI-6). QKI-6 is also highly expressed in astrocytes, which were recently demonstrated to have regulated mRNA localization. Here, we show via CLIPseq that QKI-6 binds 3’ UTRs of a subset of astrocytic mRNAs, including many enriched in peripheral processes. Binding is enriched near stop codons, which is mediated partially by QKI binding motifs(QBMs) yet spreads to adjacent sequences. We developed CRISPR TRAPseq: a viral approach for mosaic, cell-type specific gene mutation with simultaneous translational profiling. This enabled study of QKI-deleted astrocytes in an otherwise normal brain. Astrocyte-targeted QKI deletion altered translation and maturation, while also increasing synaptic density within the astrocyte’s territory. Overall, our data indicate QKI is required for astrocyte maturation and demonstrate an approach for a highly targeted translational assessment of gene knockout in specific cell-types in vivo.

scholarly journals Regulation of nuclear-cytoplasmic partitioning by the lin-28-lin-46 pathway reinforces microRNA repression of HBL-1 to confer robust cell-fate progression in C. elegans

2019 ◽  
Author(s):  
Orkan Ilbay ◽  
Victor Ambros
Keyword(s):  
Cell Fate ◽  
Translational Regulation ◽  
Rna Binding ◽  
Nuclear Accumulation ◽  
Synthesis Rate ◽  
Microrna Target ◽  
Cell Fates ◽  
Down Regulation ◽  
C Elegans ◽  
Necessary And Sufficient

AbstractMicroRNAs target complementary mRNAs for degradation or translational repression, reducing or preventing protein synthesis. In C. elegans, the transcription factor HBL-1 (Hunchback-like 1) promotes early larval (L2) stage cell-fate, and the let-7-family microRNAs temporally down-regulate HBL-1 to enable the L2-to-L3 cell-fate progression. In parallel to let-7-family microRNAs, the conserved RNA binding protein LIN-28 and its downstream gene lin-46, also act upstream of HBL-1 in regulating the L2-to-L3 cell-fate progression. The molecular function of LIN-46, and how the lin-28-lin-46 pathway regulates HBL-1, are not understood. Here, we report that the regulation of HBL-1 by the lin-28-lin-46 pathway is independent of the let-7/lin-4 microRNA complementary sites (LCSs) in the hbl-1 3’UTR, and involves a stage-specific post-translational regulation of HBL-1 nuclear accumulation. We find that LIN-46 is necessary and sufficient to prevent nuclear accumulation of HBL-1. Our results illuminate that the robust progression from L2 to L3 cell-fates depends on the combination of two distinct modes of HBL-1 down-regulation: decreased synthesis of HBL-1 via let-7-family microRNA activity, and decreased nuclear accumulation of HBL-1 via action of the lin-28-lin-46 pathway. Like HBL-1, many microRNA targets are transcription factors (TFs); and cooperation between regulation of nuclear accumulation and microRNA-mediated control of synthesis rate may be required to increase the precision of or confer robustness to down-regulation of these microRNA target TFs, which can be critical to achieve the optimal phenotypes.

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