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15 publications mentioning cel-mir-35

Open access articles that are associated with the species Caenorhabditis elegans and mention the gene name mir-35. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 146
Using miRNA target prediction logarithms (mirSOM, TargetScan) we extracted a list of potential direct targets of the mir-35 family. [score:8]
However, since reduced SUP-26 levels resulted in embryonic lethality under low oxygen conditions, we hypothesize that the mir-35 family negatively regulates sup-26 in order to keep its expression to a physiological level, but not to eliminate its expression, for optimal survival of the embryos in hypoxia. [score:6]
mir-35 downregulates GFP expression (sup-26 3’UTR) and not the RFP sensor (control 3’UTR). [score:6]
We found that mir-35 robustly downregulates GFP expression (sup-26 3’UTR) and not the RFP sensor (control 3’UTR) (Fig. 5B–D). [score:6]
We detected ubiquitous expression of YFP throughout embryogenesis indicating that sup-26 is expressed in a common temporal and spatial window to that of the mir-35 family (Fig. 4). [score:5]
As a potential target of the mir-35 family one would expect sup-26 to be expressed during embryogenesis, the period at which the mir-35 family predominates. [score:5]
Although the involvement of mir-35 family in embryonic development has been observed in the past 24 37, there is a lack of information as to the downstream regulatory targets of these miRNAs during embryogenesis. [score:5]
These data suggests that post-transcriptional mechanisms within the mother regulate the differential expression of the mir-35 family under hypoxic stress. [score:4]
To test the possibility that sup-26 is a direct mir-35 target we conducted sensor experiments in a heterologous tissue, the pharynx, after failing to do so in embryos due to specific transgene toxicity (data not shown). [score:4]
Expression of the mir-35 family is regulated by chronic hypoxia. [score:4]
Taken together, these results show that embryonic expression of the mir-35 family is induced by hypoxia in a hif-1-independent manner and that mir-38 and mir-41 are differentially regulated by hypoxia in utero. [score:4]
Hypoxic induction of the mir-35 family is independent of HIF-1. sup-26 is a potential mir-35–41 direct target. [score:4]
mir-35 was expressed in the pharynx together with a RFP reporter controlled by the unregulated unc-54 3’UTR and a GFP reporter controlled by the sup-26 3’UTR (wild type or mir-35 binding site mutated). [score:4]
A mir-35–41 [prom] ::2xNLS::yfp transcriptional reporter drives expression throughout the embryo from the 20 cell stage. [score:3]
Finally, we asked whether sup-26 plays a role in the hypoxic response of embryos as one may expect as a potential mir-35 family target. [score:3]
We drove expression of mir-35 in the pharynx in combination with a RFP reporter under the control of the unrelated unc-54 3’UTR and a GFP reporter under the control of the sup-26 3’UTR (wild type or mir-35 binding site mutated) (Fig. 5B–D). [score:3]
Using qRT-PCR analysis we observed an approximate 4-fold induction in expression of all mir-35 family members except for mir-38 and mir-41 (Figure S4B). [score:3]
sup-26 is a mir-35–41 target and is required for hypoxic survival. [score:3]
Further, regulation via the sup-26 3’UTR is dependent on the predicted mir-35 binding site (Fig. 5B–D) strongly suggesting a direct interaction between mir-35 and the sup-26 3’UTR. [score:3]
The mir-35–41 promoter drives ubiquitous expression in the embryo. [score:3]
Thus, the rescuing mir-35 intronic promoter drives expression throughout embryogenesis in most, if not all cells. [score:3]
The mir-35 family is predominantly expressed during embryogenesis 24. [score:3]
Other mir-35 target genes are also very likely to be involved in this process since the embryonic lethality of the sup-26 mutants is not significantly increased by the milder oxygen conditions (0.5% for 24 hrs). [score:3]
Hypoxic induction of the mir-35 family is independent of HIF-1The mir-35 family is predominantly expressed during embryogenesis 24. [score:3]
We therefore performed rescue experiments by expressing either mir-35 alone or the entire mir-35–41 cluster under the control of mir-35-locus upstream sequence located within the intron of its host gene (Fig. 1 and Figure S2B–C). [score:3]
We observed that the expression levels of the mature miRNAs differ between members of the mir-35 family. [score:3]
We have shown that the mir-35 family is required for hypoxic survival of embryos and is expressed throughout embryogenesis. [score:3]
We found that the expression of the mature sequence of all eight members of the mir-35 family was induced by approximately 2-fold after 4 hrs but not after 20 mins (Fig. 3A–B). [score:3]
The mir-35–41 family regulates the embryonic response to hypoxia. [score:2]
The mir-35–41 family regulates the embryonic response to hypoxiaWe focused our studies on the mir-35–41(nDf50) mutant strain due to its high sensitivity to hypoxia (Fig. 1 and Table S1). [score:2]
Regulation via the sup-26 3’UTR is dependent on the mir-35 binding site. [score:2]
During our qRT-PCR analysis, we observed additional evidence that the mir-35 cluster is potentially post-transcriptionally regulated. [score:2]
Thus, defective regulation of sup-26 levels may be one of the causes of hypoxic lethality exhibited by loss of the mir-35 family. [score:2]
Next, we asked whether the level of each mir-35 family member is regulated by hypoxia. [score:2]
At 0.5% O [2], both mir-35–41 mutants approach 100% embryonic lethality (n = 176–242), whereas wild type and hif-1(ia4) mutant embryos exhibit 10% (n = 974) and 40% (n = 1132) lethality respectively. [score:1]
The genomic rescue fragment used in (D) is marked in green, which includes a 602 bp upstream region and the mir-35 hairpin. [score:1]
nDf50 (blue) and gk262 (red) alleles remove the entire mir-35–41 locus and part of the Y62F5A. [score:1]
This prompted us to ask whether hypoxia -induced mir-35–42 induction may differ in utero. [score:1]
However, when we subjected both mir-35–41 deletion mutant strains to 2 g/l sodium sulfite, which mimics hypoxic stress 26, we also observed a significant increase in embryonic lethality (Figure S3A) indicating that mir-35 family has a specific role in survival of embryos in hypoxia. [score:1]
We focused our studies on the mir-35–41(nDf50) mutant strain due to its high sensitivity to hypoxia (Fig. 1 and Table S1). [score:1]
We next asked whether hypoxic induction of the mir-35 family is due to enhanced transcription of the mir-35–41 locus. [score:1]
Loss of certain miRNAs or miRNA families led to hypoxia sensitivity (mir-2, mir-35, mir-44, mir-49, mir-51, mir-60, mir-63 and mir-67) and others to hypoxia resistance (let-7, mir-58, mir-67, mir-79, mir-237, mir-246, mir-359). [score:1]
We subjected embryos of this strain to 0.5% O [2] for 4 hrs and found that the intensity of mir-35–41-promoter driven GFP was similar to that of embryos cultivated in normoxia (Fig. 3D). [score:1]
The mutant strain carrying the nDf50 deficiency lacks 7 (mir-35–41) of the 8 members of mir-35 family (Fig. 1A). [score:1]
Hypoxia sensitivity was also phenocopied in the independently isolated mir-35–41(gk262) mutant strain (Fig. 1A–B). [score:1]
However, we wished to exclude the possibility that the hypoxia -induced embryonic lethality of mir-35–41 mutant embryos is due to general sensitivity of strains that exhibit a high embryonic lethality in ambient O [2] conditions. [score:1]
The mir-35 family is required for embryonic hypoxic survival. [score:1]
To answer this question, we used a strain carrying an integrated gfp transgene driven by genomic region upstream of the mir-35 locus 34. [score:1]
We still detected induction of mir-35–42 indicating that this is independent of HIF-1 (Figure S4A). [score:1]
Taken together, these results suggest that the induction of the mir-35 family in hypoxia is controlled by a post-transcriptional mechanism such as increased protection by RNA binding proteins 35 36. [score:1]
These data point to a specific role for the mir-35 family in the embryonic hypoxic response. [score:1]
The mir-35 seed sequence is shown in blue and the predicted sup-26 3’UTR is shown in red. [score:1]
This promoter region was sufficient to rescue the nDf50 hypoxic phenotype when driving the mir-35–41 cluster (Figure S2). [score:1]
The 3’UTR of sup-26 contains a sequence complementary to the seed sequence of all the mir-35 family members. [score:1]
The mir-35 binding site in the sup-26 3’UTR was mutated from CCCGGUG to CCatGgG to prevent binding of mir-35 family miRNAs. [score:1]
Therefore we subjected hif-1(ia4) mutant embryos to 4 hrs of 0.5% O [2] and quantified induction of the mir-35 family. [score:1]
The mir-35–41 cluster is located within an intron of a worm specific gene (Y62F5A. [score:1]
The sequence used to rescue mir-35 is shown as a green line in (A). [score:1]
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2
[+] score: 91
In contrast, we found that whereas miR-35-3p expression was upregulated in 12-hr starved larvae, gld-1 mRNA was downregulated (Fig 7B), a result that is consistent with the idea that an increase of miR-35-3p would lead to the degradation of its target gld-1 mRNA. [score:11]
Also, we confirmed that the expression of three members of the miR-35-41 family (miR-35-3p, miR-36-3p, and miR-39-3p) was upregulated in 12-hr starved worms, consistent with the RNA-seq results in which the expression of all of the-3p forms of the miRNAs that constitute the mir-35-41 cluster were upregulated from 6 to 20 times under starvation conditions in early L4 larvae (Fig 7B). [score:11]
Differential (upregulated or downregulated) expression of miR-35-3p and target mRNAs gld-1 and lin-23 (qRT-PCR) was also analyzed using Wilcoxon Signed Rank Test. [score:11]
This is the case of mir-35, which was upregulated, and mir-79 and mir-85, both downregulated upon starvation. [score:7]
It is important to experimentally elucidate if mRNA destabilization is the mechanism used by miRNAs to regulate gene expression in C. elegans in general, and, in particular, if the down regulation of gld-1 mRNA observed under a 12-hr fasting is mediated by a direct binding of miR-35-3p. [score:6]
Changes in the abundance of gld-1 and lin-23 mRNAs during starvation, known targets of miR-35-3pThe gld-1 and lin-23 mRNAs have been reported to be direct targets of miR-35-3p [93]. [score:6]
In the 12-hr starvation condition, up-regulation of miR-35-3p will negatively regulate G1/S transition in intestinal cells and will negatively regulate oogenesis [93]. [score:6]
As can be seen in Table 1, seven members of the miR-35 family (from miR-35-3p to miR-41-3p; [80]) were upregulated from ~6- to 20-fold under starvation conditions. [score:4]
Given the functions ascribed to the members of the mir-35 family, their up-regulation can have effects on RNAi sensitivity and reproduction. [score:4]
The gld-1 and lin-23 mRNAs have been reported to be direct targets of miR-35-3p [93]. [score:4]
This could be explained if the binding of miR-35-3p to lin-23 mRNA leads to translational repression [111, 112]. [score:3]
Most embryo cells express mir-35 members, first at the onset of gastrulation, with a peak at the onset of elongation [11, 57, 60]. [score:3]
Since the individual expression of each of the members of the mir-35 family (but not the unrelated mir-43 and mir-44) rescued the defects caused by deletion of all family members, it appears that miRNAs of the mir-35 family act redundantly [60]. [score:3]
Changes in the abundance of gld-1 and lin-23 mRNAs during starvation, known targets of miR-35-3p. [score:3]
For miR-240-5p, miR-246-3p, miR-35-3p, miR-36-3p, miR-39-3p quantification, miR-58-3p was used as a control. [score:1]
The mir-35 family is conserved in worms and planaria [80, 91]. [score:1]
Relative quantification of (A) miR-240-5p, miR-246-3p, and (B) miR-35-3p, miR-36-3p, miR-39-3p, and gld-1 and lin-23 mRNA abundance in well-fed and 12-hr starved early L4 larvae by. [score:1]
For Reverse Transcription of miRNAs (miR-35-3p, miR-36-3p, miR-39-3p, miR-240-5p, miR-246-3p, and miR-58-3p) and mRNAs (gld-1, lin-23 and β-actin), a total of 2000 ng and 300 ng were used, respectively. [score:1]
In addition to its participation in germ cell proliferation, a key role has been ascribed to mir-35 family members in the G1/S transition in intestinal cells, as loss of mir-35 shows a significant decrease of nuclei numbers in both the intestine and the distal mitotic gonad [93]. [score:1]
A mutant with a deletion of all eight members of the mir-35 family resulted in temperature-sensitive embryonic or L1 larval lethality [60]. [score:1]
One cluster contains mir-35 through mir-41 (mir-35-41), while the other contains mir-42, mir-43 and mir-44, although the last two do not belong to the mir-35 family [80]. [score:1]
The quantification of miR-35-3p, miR-36-3p, miR-39-3p, miR-240-5p, and miR-246-3p expression relative to miR-58-3p was calculated as in Pfaffl, 2001[47]. [score:1]
The mir-35 family is composed of eight miRNAs, mir-35 to mir-42, all of them located on chromosome II. [score:1]
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3
[+] score: 66
Other miRNAs from this paper: cel-mir-42
However, the previously described somatic role of SUP-26 in controlling tra-2 translation makes sup-26 an interesting candidate mir-35 family target gene in the context of hermaphrodite fecundity. [score:5]
If sup-26 is a mir-35 family target gene whose de-repression in mir-35-41(nDf50) contributes to loss of fecundity, then sup-26(lf) might suppress one or more aspects of the mir-35-41(nDf50) fecundity phenotype. [score:5]
Thus, future studies of mir-35 family function may have broad implications for our understanding of the reversibility of microRNA target repression and the full complement of microRNA functions during development. [score:4]
For sup-26 to be a direct mir-35 family target, the longest 1146-bp 3′ UTR must be used. [score:4]
Therefore, the predicted mir-35 family target gene sup-26 functions downstream of mir-35-41 in regulating spermatogenesis at restrictive temperature. [score:4]
Our interpretation of these results is that the sperm defect is due to germline loss of mir-35, and thus cannot be rescued by nEx1187 because expression from high-copy extrachromosomal arrays is silenced in the germline (Kelly et al. 1997); however, other interpretations for the failure of nEx1187 to rescue the sperm defect are also possible. [score:3]
First, zygotic mir-35 expression does not fully rescue this phenotype, indicating a maternal effect of mir-35-41 on fecundity of the adult. [score:3]
Although the basis of temperature sensitivity of these phenotypes is not fully understood, we hypothesize that microRNA target repression (at least by mir-35 family microRNAs) is less efficient at 25° than at 20°. [score:3]
Thus, endogenous sup-26 mRNA contains a highly conserved mir-35 family target site and associates with miRISC. [score:3]
The fact that adult fecundity is affected by loss of mir-35-41 is intriguing in light of the expression pattern of the mir-35 family: primarily in oocytes and early embryos. [score:3]
Next, we looked for predicted mir-35 family target genes that might play a role in hermaphrodite fecundity downstream of mir-35-41. [score:3]
The mir-35 microRNA family may provide a fascinating setting in which to explore the effects of natural in vivo temperature changes on microRNA target recognition and/or repression. [score:3]
Expression of mir-35 from a transgenic extrachromosomal array (nEx1187) (Alvarez-Saavedra and Horvitz 2010) rescued both the Egl phenotype and the ability to produce large numbers of cross-progeny when mated (Figure 3, D and E). [score:3]
This is consistent with the temporal expression pattern of the mir-35 family, primarily in oocytes and early embryos. [score:3]
Multiple 3′ UTRs have been annotated for the sup-26 mRNA (Mangone et al. 2010; Jan et al. 2011), only one of which contains the mir-35 family target site (Figure S2A). [score:3]
SUP-26 contributes to the temperature-sensitive sperm defect in mir-35-41(nDf50)Next, we looked for predicted mir-35 family target genes that might play a role in hermaphrodite fecundity downstream of mir-35-41. [score:3]
Previous work demonstrated that mir-35 family function in embryonic viability can be rescued by either maternal or zygotic mir-35 family expression (Alvarez-Saavedra and Horvitz 2010). [score:3]
One possibility is that the maternal load of sup-26 is at a sufficiently low concentration to be subject to mir-35 family regulation, while strong zygotic transcription increases sup-26 mRNA abundance beyond the threshold of repression. [score:2]
This suggests that that the spermatogenesis defect of mir-35-41(nDf50) hermaphrodites could be caused (at least in part) by reduction of mir-35 family function early in development. [score:2]
By examining the phenotype of mir-35-41(nDf50) at multiple temperatures and the effects of a somatic mir-35 rescue, we have delineated at least four ways in which mir-35-41 promotes fecundity. [score:1]
Thus, the mir-35 family may represent a novel paradigm for microRNA control of embryogenesis. [score:1]
We have demonstrated that the mir-35 family acts at multiple levels to promote hermaphrodite fecundity. [score:1]
The mir-35 family is unique among microRNAs across diverse species for its strong maternal effect. [score:1]
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4
[+] score: 52
Other miRNAs from this paper: cel-let-7, cel-mir-1, cel-mir-52, cel-mir-58a, dme-mir-1, mmu-let-7g, mmu-let-7i, mmu-mir-1a-1, dme-bantam, mmu-let-7d, dme-let-7, mmu-let-7a-1, mmu-let-7a-2, mmu-let-7b, mmu-let-7c-1, mmu-let-7c-2, mmu-let-7e, mmu-let-7f-1, mmu-let-7f-2, mmu-mir-16-1, mmu-mir-16-2, mmu-mir-1a-2, cel-lsy-6, dre-mir-430a-1, dre-mir-430b-1, dre-mir-430c-1, dre-let-7a-1, dre-let-7a-2, dre-let-7a-3, dre-let-7a-4, dre-let-7a-5, dre-let-7a-6, dre-let-7b, dre-let-7c-1, dre-let-7c-2, dre-let-7d-1, dre-let-7d-2, dre-let-7e, dre-let-7f, dre-let-7g-1, dre-let-7g-2, dre-let-7h, dre-let-7i, dre-mir-1-2, dre-mir-1-1, dre-mir-16a, dre-mir-16b, dre-mir-16c, dre-mir-430c-2, dre-mir-430c-3, dre-mir-430c-4, dre-mir-430c-5, dre-mir-430c-6, dre-mir-430c-7, dre-mir-430c-8, dre-mir-430c-9, dre-mir-430c-10, dre-mir-430c-11, dre-mir-430c-12, dre-mir-430c-13, dre-mir-430c-14, dre-mir-430c-15, dre-mir-430c-16, dre-mir-430c-17, dre-mir-430c-18, dre-mir-430a-2, dre-mir-430a-3, dre-mir-430a-4, dre-mir-430a-5, dre-mir-430a-6, dre-mir-430a-7, dre-mir-430a-8, dre-mir-430a-9, dre-mir-430a-10, dre-mir-430a-11, dre-mir-430a-12, dre-mir-430a-13, dre-mir-430a-14, dre-mir-430a-15, dre-mir-430a-16, dre-mir-430a-17, dre-mir-430a-18, dre-mir-430i-1, dre-mir-430i-2, dre-mir-430i-3, dre-mir-430b-2, dre-mir-430b-3, dre-mir-430b-4, dre-mir-430b-6, dre-mir-430b-7, dre-mir-430b-8, dre-mir-430b-9, dre-mir-430b-10, dre-mir-430b-11, dre-mir-430b-12, dre-mir-430b-13, dre-mir-430b-14, dre-mir-430b-15, dre-mir-430b-16, dre-mir-430b-17, dre-mir-430b-18, dre-mir-430b-5, dre-mir-430b-19, dre-mir-430b-20, dre-let-7j, mmu-mir-1b, cel-mir-58b, mmu-let-7j, mmu-let-7k, cel-mir-58c
Translational activity was monitored through measurement of RL activity in the presence of miR-35 2′- O-Me inhibitor or a non-cognate miR-1 2′- O-Me inhibitor. [score:5]
In untreated or mock -depleted extracts, a 2- to 4-fold increase in RL light counts was observed when a miR-35 2′- O-Me inhibitor was added prior to RL-6×-miR-35-pA [86] reporter translation, in comparison with a non-cognate miR-1 2′- O-Me control (Figure 4A, left panel). [score:5]
For this, we examined the translation of a RL-6×-miR-35 transcript lacking a poly(A) tail (RL-6×-miR-35-pA [0]) in the in vitro translation extract (Figure 5A). [score:5]
In a mock -depleted extract, as in an untreated extract, the reporter was significantly de-repressed when treated with miR-35 2′- O-Me inhibitor, but not when treated with a non-cognate miR-1 inhibitor (Figure 5C). [score:5]
RL-6×-miR-35-p(A) [0] reporter translation was specifically de-repressed when the extract was treated with a miR-35 2′- O-Me inhibitor, but not when supplemented with a non-cognate miR-1 control (Figure 5B). [score:5]
Translation counts were monitored over time in the presence of miR-35 or miR-1 2′- O-Me inhibitors. [score:5]
Furthermore, addition of 2.5 μM GST-PAIP-2 completely abolished miR-35 -dependent translation silencing of the RL-6×-miR-35-pA [86] reporter (right panel), whereas supplementation with 2.5 μM GST had no effect on miRNA -mediated repression (left panel). [score:3]
However, the same treatment did not de-repress the RL-6×-miR-35-pA [0] reporter when translated in a PAB-1/2 -depleted extract (Figure 5D). [score:3]
To address if PABPs are required for poly(A)-tail independent silencing, we performed reporter translation silencing assays on RL-6×-miR-35-pA [0] in the PAB-1/2 -depleted extract. [score:2]
In PAB-1/2 -depleted extracts, deadenylation of Renilla luciferase (RL) transcripts encoding six miR-35 -binding sites and a poly(A) tail (RL-6×-miR-35-pA [86]) was slowed, but not blocked (Figure 3B; 6× miR-35). [score:1]
When human PABC1 was added at 115 nM to the extract, it restored the deadenylation rate of the RL-6×-miR-35-pA [86] reporter in the GST-PAIP2 treated extract (Figure 3D). [score:1]
Akay A. Craig A. Lehrbach N. Larance M. Pourkarimi E. Wright J. E. Lamond A. Miska E. Gartner A. RNA -binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans Open Biol. [score:1]
A capped transcript containing a Renilla luciferase ORF and six miR-35 binding sites in its 3′UTR, but lacking a poly(A) tail. [score:1]
The constructs harboring 3 or 6× miR-35 sites or miR-52 sites and a 161 nt linker were previously generated in (9). [score:1]
As expected, RL-3×-miR-35-pA [86] reporters were deadenylated slower than 6× counterparts in the control extract (Figure 6B). [score:1]
Strikingly, no remaining miR-35-specific de-repression could be observed in PAB-1 and PAB-2 -depleted extracts (right panel). [score:1]
However, RL-3×-miR-35-pA [86] L262 was deadenylated much slower (>270 min) than its shorter linker version (L32; 112 min). [score:1]
Even though examined in different extract preparations, RL-6×-miR-35 reporters bearing an intermediate 161 nt linker exhibited an intermediate ∼2.5-fold delay under PAB-1/2 depletion (Figure 3B). [score:1]
5′ Biotinylated 2′- O-Me oligos containing miR-35, CeBantam or both sites were used to pull down the miRISC WT strain (N2) embryonic extract. [score:1]
Capped transcripts encode the Renilla luciferase ORF and either three or six miR-35 -binding sites in its 3′UTR, followed by a linker of 32 nt (L32) or 262 nt (L262). [score:1]
Surprisingly, pab-2 deletion left deadenylation of miR-35 reporter mRNAs unaffected (Supplementary Figure S4). [score:1]
To generate the pCI-RL-6×-miR-35-pA constructs with a short linker (L32), the pCI-RL-6×-miR35-pA plasmid was digested with XbaI/NotI (NEB) and the insert was cloned in the pCI-RL-L32-pA backbone. [score:1]
Six copies of miR-35 -binding sites exert a very potent drive toward reporter deadenylation in embryonic extracts. [score:1]
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5
[+] score: 24
Therefore, we tested whether the mir-51 family interacted with additional miRNA-regulated pathways by determining if loss of mir-51 family members could suppress other miRNA mutant phenotypes that are distinct from developmental timing, including regulation of neuronal asymmetry, let-7 family regulation of vulva cell fate specification, regulation of defecation, mir-35 family regulation of embryonic development and regulation of neuromuscular function. [score:11]
Additionally, we report that the mir-51 family interacts with multiple, diverse, miRNA regulated genetic pathways, including pathways regulated by the let-7 and mir-35 family miRNAs, as well as, miR-240/786, and miR-1. We provide evidence that is inconsistent with the mo del that the mir-51 family regulates miRNA biogenesis or miRNA activity. [score:4]
We found that loss of mir-54/55/56 did not suppress the embryonic lethal phenotype of mir-35/41 mutants, but rather significantly enhances this phenotype (Figure 3G). [score:3]
These family members are redundantly required for embryonic development and mutants lacking mir-35 through mir-41 exhibit temperature sensitive embryonic lethality [13]. [score:2]
mir-35 family. [score:1]
mir-35 familyThe mir-35 family comprises eight miRNAs, mir-35 through mir-42. [score:1]
The mir-35 family comprises eight miRNAs, mir-35 through mir-42. [score:1]
For some miRNA mutants, like let-7 or mir-35 family mutants, the lack of observed defects is a result of functional redundancy among miRNA family members, which share a six nucleotide 5′ seed sequence [12], [13]. [score:1]
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[+] score: 22
For example, the potential mir-35 targets, lin-23 and gld-1 [69], have also been identified as GLD-1 targets [55]. [score:5]
Given that both mir-35–41(nDf50) and gld-1(op236) ; mir-35–41(nDf50) mutants lay similar numbers of eggs (figure 2 a, right), the synthetic interaction between gld-1 and mir-35 family miRNAs must specifically affect early embryonic development. [score:2]
The mir-35 family of miRNAs comprises eight members (miR-35– 42), which are highly enriched in oocytes [20] and are required for embryonic development. [score:2]
We indeed found that gld-1 enhances multiple let-7 and mir-35 family miRNA phenotypes affecting somatic development. [score:2]
While mir-35 family mutants do not individually exhibit an observable phenotype, combined mutation of either all or most mir-35 family members causes severe embryonic and larval lethal phenotypes [20], similar to those we observed in the gld-1(op236) ; vig-1(ok2536) double mutant. [score:2]
SQD-1 is the C. elegans orthologue of the Drosophila squid hnRNP protein, previously identified as an AIN-2 and mir-35 miRNA -associated protein [18, 65]. [score:1]
Figure 2. gld-1 genetically interacts with mir-35 and let-7 family miRNAs. [score:1]
The let-7 family (let-7, mir-48, mir-84, mir-241 and mir-795) miRNAs are much more studied compared with mir-35 family miRNAs during C. elegans development. [score:1]
gld-1 genetically interacts with mir-35 family miRNAs. [score:1]
The expression pattern and phenotypes of mir-35 family miRNAs make them suitable to investigate possible genetic interactions with gld-1. A deletion mutant, nDf50, which removes all mir-35 family miRNAs except for mir-42, causes a temperature-sensitive embryonic and early larval lethality [20]. [score:1]
In gld-1(op236) ; mir-35–41(nDf50) double-mutants embryonic and larval lethality increases to 67%, indicating a strong genetic interaction between gld-1 and the mir-35 miRNA family (figure 2 a, left). [score:1]
The expression pattern and phenotypes of mir-35 family miRNAs make them suitable to investigate possible genetic interactions with gld-1. A deletion mutant, nDf50, which removes all mir-35 family miRNAs except for mir-42, causes a temperature-sensitive embryonic and early larval lethality [20]. [score:1]
At 20°C, we observed that 33% of mir-35–41(nDf50) animals die either during embryogenesis or at the L1 larval stage. [score:1]
Enhancement of mir-35 family embryonic and larval lethal phenotypes may be explained by perturbation of maternal mRNA pools derived from gld-1(op236) germlines that may enhance mir-35 phenotypes. [score:1]
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Of the 550 up-regulated genes in mir-35-41(gk262), only a small fraction (4%) were predicted miR-35 targets based on a list of 606 genes from four different algorithms (Targetscan, PicTar, RNA22 and MiRWIP). [score:8]
Worm strains Phenotype % Unaffected Twitching Paralyzed wild-type (629) 10±1 88±3 2±2 rrf-3(pk1426) (594) 0 83±14 17±5 eri-1(mg366) (343) 0 73±3 27±3 ergo-1(tm1860) (452) 0 66±4 34±6 lin-35(n745) (248) 0 5±2 95±7 mir-35(gk262) (651) 0 17±5 83±14L4 staged worms of each strain were transferred to unc-22 RNAi and the percentage of unaffected, twitching or paralyzed adult worms was scored 28 hours later. [score:1]
In contrast, mir-35 miRNA levels were unaltered in lin-35(n745) mutant embryos (Figure 4C). [score:1]
Trizol reagent (Invitrogen) was used to extract total RNA from frozen embryo pellets of the wild type (N2) and mir-35(gk262) strains. [score:1]
Young GFP positive worms represented heterozygous mir-35−/+ F1 cross progeny. [score:1]
Strains used in this study include the following: wild type (WT) Bristol N2 strain, NL2098 rrf-1(pk1417)I, MT10430 lin-35(n745)I, VC514 mir-35-41(gk262)II, NL2099 rrf-3(pk1426)II, MT111 lin-8(n111)II, WM49 rde-4(ne301)III, GR1373 eri-1(mg366)IV, WM158 ergo-1(tm1860)V, WM27 rde-1(ne219)V, MT1806 lin-15A(n767)X, YY158 nrde-3(gg66)X. Double mutants: PQ300 [mir-35-41(gk262);rde-1(ne219)], PQ301 [mir-35-41(gk262);rde-4(ne301)], PQ302 [mir-35-41(gk262); eri-1(mg366)], PQ303 [mir-35-41(gk262);rrf-1(pk1417)], PQ304 [mir-35-41(gk262); ergo-1(tm1860)], PQ421 [mir-35(gk262);lin-8(n111)], PQ422 [mir-35-41(gk262);lin-15A(n767)], PQ423 [lin-35(n745);lin-8(n111)], PQ424 [lin-35(n745); lin-15A(n767)], PQ459 [mir-35-41(gk262);nrde-3(gg66)]. [score:1]
For paternal/zygotic rescue experiments, wild-type male worms containing a body muscle GFP marker (PD4251) were crossed to mir-35(gk262) (mir-35−/−) mutant hermaphrodites. [score:1]
Other GFP transgenes that lack lin-35 did not affect the RNAi hypersensitivity of mir-35 mutants, consistent with the idea that lin-35 is required for the rescue (Figure 4D). [score:1]
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Combining the alg-1(anti) mutation, but not the alg-1(0) deletion, with the mir-35–41 deletion enhances the mir-35–41 temperature sensitive embryonic lethality phenotype (Figure 6E), suggesting that the alg-1(anti) mutations affect the functions of the mir-35 family microRNAs in embryonic development. [score:4]
Enhancement of mir-35–41 embryonic lethality phenotype was assessed by determining the percentage of embryos capable of hatching for mir-35–41 embryos in combination with alg-1 mutations (the lin-31 mutation was present in the background of all strains to keep the alg-1 animals from bursting through the vulva). [score:3]
By contrast, the alg-1(anti) mutations we describe here cause severe developmental defects consistent with dramatic impairment of let-7-Family microRNA activity, impair functions of other microRNAs including lsy-6 and mir-35-Family, and result in lethality in combination with alg-2(0), consistent with broad defects in the activity of additional microRNAs. [score:3]
Deletion of all mir-35 family members (mir-34–42) results in early embryonic lethality, while deletion of mir-35–41 (leaving mir-42 functional) results in an incompletely penetrant temperature sensitive lethality [40], [41]. [score:1]
It should be noted that many animals with the mir-35–41 deletion arrested as larvae after hatching. [score:1]
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In order to confirm that this class of antisense reagents is also effective in inhibiting microRNAs during embryo development, we prepared [Rh]dextran-([as-2'OMe] mir-42) [1 ]against mir-42, a member of the mir-35 family which consists of eight microRNA genes of similar sequences. [score:4]
Deletion of the seven microRNAs (mir35 - 41, strain MT14119) leads to a temperature-sensitive late embryonic or L1 lethal phenotype. [score:1]
MT14119 contains a deletion of 1261 bases on chromosome II which removes mir-35 - mir-41 (ref. [score:1]
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While the loss of alg-1 in this sensitized background significantly increased the number of masculinized animals observed, the expression of ALG-1(TPmut) in her-1(gf)/alg-1(0) animals completely reestablished it to the level observed in her-1(gf) animals (Fig 6) demonstrating that the interaction with AINs is not required for the function of the mir-35 microRNA family in this embryonic decision. [score:3]
1006484.g006 Fig 6The embryonic sex determination controlled by the mir-35 microRNA family does not require an AIN-containing miRISC. [score:1]
The embryonic sex determination controlled by the mir-35 microRNA family does not require an AIN-containing miRISC. [score:1]
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Some sets of miRNA map to specific chromosomal clusters, as in the case of miR-35 to miR-41, which have redundant functions in embryonic development [42] and are abundantly expressed in the embryonic stage (Figures 3b and 7). [score:4]
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Exceptions are the early lethality phenotypes resulting from both the combined loss of mir-35- mir-42 [24] and of mir-51-mir-56, [24, 25], as well as the movement and body size defect resulting from combined mutation of mir-58, -80, -81 and -82 [24]. [score:2]
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Mutation of the mir-35–41 miRNA cluster resulted in temperature-sensitive embryonic and larval lethality; this lethality was rescued by the introduction of a transgene carrying the mir-35–41 genomic locus (unpublished data). [score:2]
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Other miRNAs from this paper: cel-let-7
Akay A. Craig A. Lehrbach N. Larance M. Pourkarimi E. Wright J. E. Lamond A. Miska E. Gartner A. RNA -binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegansOpen Biol. [score:1]
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Other miRNAs from this paper: cel-mir-1, cel-mir-58a, cel-mir-243, cel-mir-58b, cel-mir-58c
In henn-1 mutant L4 larvae, which are enriched for ALG-3/4 class 26G siRNAs, the levels of three miRNAs (miR-1, miR-35 and miR-58) and an ALG-3/4 class 26G siRNA (26G siR-S5) derived from ssp-16 were each indistinguishable from wild type (Figure 6D and 6E). [score:1]
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