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19 publications mentioning dme-mir-10

Open access articles that are associated with the species Drosophila melanogaster and mention the gene name mir-10. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 266
Other miRNAs from this paper: dme-mir-993
Evidence has indicated that many miRNAs and their most strongly predicted targets are often expressed in mutually exclusive patterns [10], which is consistent with what we observed for miR-10-5p: Scr and miR-10-3p: Abd-B, limiting the potential for regulation of Hox protein expression during embryonic development. [score:9]
During late blastoderm development and the beginning of gastrulation the expression of pri-mir-10 becomes downregulated in a subset of cells, taking on a striped appearance, which is similar to, but not as refined as that of the pair rule genes (data not shown). [score:7]
In order to test whether Scr expression is altered in embryos that ectopically express mir-10, transgenic flies were constructed that allow expression of pri-mir-10 under the control of a variety of spatially and temporally specific GAL4 drivers. [score:7]
0031365.g004 Figure 4Overexpression or lack of pri-miR-10 has no observable effect on putative target protein expression. [score:7]
Overexpression or lack of pri-miR-10 has no observable effect on putative target protein expression. [score:7]
Due to the conserved location of the mir-10 gene in animal Hox complexes (Figure S4), and the potential for miRNAs to be spawned from, as well as to target nearby genes [42], we were interested in the possibility that miR-10-5p and miR-10-3p might be regulators of Hox gene expression. [score:6]
In order to determine the expression pattern of the mir-10 gene during embryogenesis, we performed in situ hybridizations using probes antisense to pri-mir-10 sequence and analyzed expression throughout embryogenesis. [score:5]
At this point pri-mir-10 is expressed in a broad band which corresponds to the trunk primordia of the embryo and is reminiscent of gap gene or Hox gene expression patterns (Figure 2A). [score:5]
pri-mir-10 is expressed in a pattern complementary to predicted targets. [score:5]
During this stage, pri-miR-10 is not actively transcribed in all of these cells, but it seemed possible that miR-10-5p produced from early transcripts might still be present in these cells to inhibit translation. [score:5]
pri-mir-10 is expressed in the endodermal cells, while Abd-B is expressed in the visceral mesoderm surrounding the gut. [score:5]
The anteroposterior extent of pri-mir-10 expression in the CNS is reminiscent of its blastoderm expression pattern. [score:5]
Although miRNA target prediction algorithms have had varying success at prediction of true positive miRNA-mRNA interactions [54], its status as the top hit in our predictions, along with the conservation in arthropods, suggests that Scr is one of the best putative targets of miR-10-5p in Drosophila. [score:5]
0031365.g003 Figure 3 pri-mir-10 is expressed in a pattern complementary to predicted targets. [score:5]
While Abd-B is expressed in the majority of the posterior ectoderm, it is completely excluded from the developing anal pads, where pri-miR-10 and miR-10-3p are strongly expressed (Figure 2G–H; Figure 3D–F and H–J). [score:5]
The longer Abd-B 3′UTR contains the putative miR-10-3p target site, while the shorter 3′UTR lacks the target site. [score:5]
Embryos expressing UAS- pri-miR-10 under the control of engrailed-GAL4 (en> pri-miR-10) (C,D,G,H) exhibit no consistent detectable decrease in either SCR protein (A–D) or ABD-B protein (E–H) in cells expressing ectopic miRNA [marked with anti- en antibodies (green), or circled with dotted lines] versus control cells in wild type embryos (A,B,E,F). [score:5]
Abd-B is also expressed throughout later embryogenesis in the visceral mesoderm surrounding the large intestine of the hindgut, whereas miR-10-3p is expressed only in the endodermal cells of this region (Figure 3G). [score:5]
Conversely, embryos which are deleted for the mir-10 gene (Df(3R)CP1), and thus lacking miR-10-3p [46], do not exhibit ectopic expression of Abd-B mRNA or protein in either the large intestine endoderm or in the anal pads, suggesting that miR-10-3p does not regulate Abd-B in these tissues (data not shown). [score:4]
This correlation is consistent with the hypothesis that miR-10-5p is negatively regulating Scr mRNA levels, but ectopic expression of pri-mir-10 did not provide any support for this hypothesis. [score:4]
To test the possibility that miR-10-3p is regulating Abd-B expression in the CNS more generally, transheterozygote Df(3R)CP1: Df(3R)LIN embryos deficient for mir-10 were analyzed for alterations in Abd-B transcript and protein levels in segments A5–A8/9 of the CNS. [score:4]
Ectopic expression of pri-mir-10 in the CNS either through ubiquitous overexpression (Figure 4J) or in a subset of cells (Figure 4G, H) did not result in obviously reduced levels of ABD-B protein compared to wildtype (Compare to Figure 4E, F, and I). [score:4]
Ectopic expression of pri-mir-10 by GAL4 drivers that persistently produce pri-mir-10 in all embryonic cells results in death during early larval development and minor cuticle phenotypes in the anterior of the early larvae. [score:4]
While not a top hit in most computational predictions due to the shortened seed match, Scr has been previously suggested as a target for miR-10-5p [30]. [score:3]
Additionally, embryos ectopically expressing pri-mir-10 from a variety of other GAL4 drivers did not exhibit detectable changes in either pattern or levels of Scr transcript or protein accumulation (data not shown). [score:3]
Similar to the putative target site for miR-10-5p in the Scr 3′UTR, this sequence appears as one of our top hits among all Drosophila 3′UTRs using RNAHybrid, contains potential long continuous helix pairings with the miRNA, and is well conserved in the putative 3′UTR sequences of most insect Abd-B orthologs (Figure 1E and data not shown). [score:3]
Expression of Drosophila pri-mir-10 transcripts. [score:3]
mir-10 primary transcripts are first expressed during the blastoderm stage of embryogenesis [46]. [score:3]
However, expression of pri-mir-10 was unaltered when examined in embryos mutant for the hunchback gene (data not shown). [score:3]
When expressed from a prd-GAL4 driver (prd> pri-mir-10), cytoplasmic miR-10-5p is detectable in the prd pattern at high levels in a germband extended embryo (A). [score:3]
mir-10 expression during embryogenesis. [score:3]
Figure S5 Putative miR-10-5p target sites in the 3′UTRs of insect Sex combs reduced (Scr ) orthologs are conserved in regions of relatively poor conservation. [score:3]
Both miR-10-5p (Figure 2D) and miR-10-3p (Figure 2G) can be detected in late embryonic stages utilizing this technique, and the expression pattern of each is equivalent to pri-mir-10 (compare Figure 2D to 2C and Figure 2G to 2E). [score:3]
Expression of mature miRNAs from pri-mir-10. [score:3]
Unfortunately, available chromosomal deletions which lack mir-10 sequences also delete Scr, precluding the possibility of ascertaining the change in Scr expression in these mutant embryos. [score:3]
We also used the RNAHybrid program [53], and our analysis identified this Scr sequence as one of the strongest putative targets for miR-10-5p within all Drosophila 3′UTRs (data not shown). [score:3]
The other possibility was that miR-10-5p might be acting through Scr mRNA degradation as has been shown for a number of miRNA targets [57], [58]. [score:3]
The best putative target site for miR-10-5p was found in the 3′UTR of the Hox gene Sex combs reduced (Scr). [score:3]
Figure S6 Putative miR-10-3p target sites in the 3′UTRs of Brachyceran Abdominal-B (Abd-B ) orthologs are conserved in regions of relatively poor conservation. [score:3]
As germband elongation proceeds, pri-mir-10 transcription is initiated in the anal pad and large intestine primordia and in ventral neurectoderm of the trunk segments where it is expressed in the developing neuroblasts (Figure 2B). [score:3]
If this were the case, then transcript pattern and/or levels would be altered in embryos ectopically expressing or lacking the mir-10 gene. [score:3]
Expression of mature miRNAs from pri-mir-10 After a pre-miRNA is cleaved by Dicer, one strand of the resulting ∼22 nt dsRNA is packaged into an RNA Induced Silencing Complex (RISC). [score:3]
0031365.g002 Figure 2 mir-10 expression during embryogenesis. [score:3]
No pri-mir-10 transcription is detected in the brain, with the anterior border of expression in the posterior region of the sub-esophageal ganglion, extending posteriorly to near the terminal end of the CNS (Figure 2E–F). [score:3]
Expression of Drosophila pri-mir-10 transcriptsmiRNAs are initially transcribed as RNA polymerase II primary transcripts which are serially processed to produce mature miRNAs [44]. [score:3]
This target site for miR-10-3p in the Abd-B mRNA was also predicted in a previous study [55]. [score:3]
Although the conservation of this sequence is not as strong as the predicted miR-10-5p target in Scr orthologs (Figure S5), the Antp sequences that would pair with miR-iab-4-5p are completely conserved amongst Drosophila species (Figure S9). [score:3]
During embryogenesis pri-miR-10 and Abd-B are expressed in mostly non-overlapping regions. [score:3]
However, embryos which are mutant for Abd-B gene products do not show altered expression of pri-mir-10 (data not shown). [score:3]
Scr and pri-mir-10 are expressed in largely complementary patterns in both early embryonic ectoderm (Figure 3A–C) and in late stage CNS (Figure 3H–J). [score:3]
We also identified a putative target site for miR-10-3p in the 3′UTR of the Hox gene Abdominal-B (Abd-B) (Figure 1E). [score:3]
Additionally, among our top predicted miR-10-3p targets, this is the only site with significant evolutionary conservation (data not shown). [score:3]
In order to test the abundance and timing of expression of the products of the mir-10 duplex, Northern blot analysis was performed on RNA from multiple embryonic stages using antisense probes complementary to each arm of the hairpin. [score:3]
In addition to being conserved in both sequence and genomic position, mir-10 appears to have a conserved expression pattern in the CNS of Drosophila and zebrafish [47], [48]. [score:3]
No consistent detectable change in ABD-B protein levels is seen in the CNS of embryos ubiquitously expressing UAS- pri-miR-10 under the control of da-GAL4 (da> pri-miR-10) (J) or in embryos deficient for the mir-10 locus ((Df3R) CP1) (K) compared to wild type embryos (I). [score:2]
Images of in situ hybridizations of pri-mir-10, Scr, and Abd-B at various stages of development. [score:2]
When pri-mir-10 is expressed under the control of engrailed-GAL4, these cells have no obvious decrease in SCR protein levels when compared to wildtype controls (compare Figure 4C–D with Figure 4A–B). [score:2]
Taken together these data suggest that, although Scr appears to be post-transcriptionally regulated in these cells, it is not through the activity of miR-10-5p. [score:2]
When expressed from an Actin-GAL4 (Act5C> pri-mir-10) (C) or da-GAL4 driver (da> pri-mir-10) (D) malformations are noticeable in the head cuticle (arrows) when compared to wild type (B). [score:2]
Alignment of conserved sequences found in the 3′UTRs (or 3′ of the stop codon in putative UTR sequence) of Abd-B genes in Brachycerans and complementarity to mature miR-10-3p sequence. [score:1]
Starting around stage 13 both mir-10-5p (D) and miR-10-3p (G) mature miRNAs are detected by LNA in situ in the same patterns as for pri-mir-10 (compare to C and F respectively). [score:1]
Due to the presence of miR-10-5p sequences in most other animals the possibility of a second miRNA from this locus was largely ignored. [score:1]
This strain produces embryos which are deficient for both miR-10-3p and ABD-B m-type protein. [score:1]
Time course shows both miR-10-5p and miR-10-3p are produced at very low levels in blastoderm embryos and during early germ band extension (0–4 hrs) and progressively increase in abundance throughout embryogenesis. [score:1]
However, while the 3′ hairpin sequence is not well conserved in deuterostomes (Figure S3B), if only arthropods are examined, both miR-10-5p and miR-10-3p sequences are found to be well conserved (Figure S3A). [score:1]
Both miR-10-5p [50], [51] and miR-10-3p [50] were cloned in early efforts to determine the miRNA complement of the Drosophila genome. [score:1]
However, LNA antisense oligo staining did not detect any mature miR-10-5p in these cells at this stage (data not shown). [score:1]
After germband retraction pri-mir-10 is transcribed in the anal pads and large intestine endoderm as well as a subsection of the central midgut endoderm (Figure 2C). [score:1]
The mir-10 primary transcript was also detected in yolk cells of blastoderm stage embryos (data not shown). [score:1]
Furthermore, in situ analysis using a probe flanking the 3′ of the miR-10 hairpin region suggests that pri-miR-10 transcripts that include a polyadenylation signal are not made in the ectoderm of early blastoderm embryos (data not shown). [score:1]
Figure S3 Conservation of mature miRNA sequences in mir-10 hairpins. [score:1]
html, and the Lottia gigantea Hox complexes with locations of mir-10, mir-993, and a mir-10-related genes indicated as hairpins. [score:1]
Boxed regions indicate miR-10-5p (red) and miR-10-3p (green) sequences. [score:1]
In late embryogenesis pri-mir-10 staining can be seen in the anal pads, large intestine endoderm, midgut endoderm, and in the ventral nerve cord of the central nervous system (CNS) (Figure 2E–F). [score:1]
Both miR-10-5p and miR-10-3p were found to be present in embryos, with levels increasing throughout embryogenesis, and with miR-10-3p present at significantly higher levels at all stages (Figure 2I). [score:1]
In order to determine the primary transcript that produces miR-10 (pri-mir-10), 5′ and 3′ RACE (rapid amplification of cDNA ends) were performed on a cDNA library created from polyadenylated (polyA) RNA from a 0–24 hour embryo collection. [score:1]
Alignment of conserved sequences found in the 3′UTRs (or 3′ of the stop codon in putative UTR sequence) of Scr genes in insects and complementarity to mature miR-10-5p sequence. [score:1]
The sequence just upstream of the 5′ end of the RACE products contains properly spaced INR, DPE, and MTE elements [45], and is also well conserved amongst Drosophilids (Figure S1), which point to this region as a likely pri-mir-10 promoter. [score:1]
Since the domain of pri-mir-10 transcription extends into the posterior of the CNS, but appears to decrease toward the extreme posterior (Figure 3H, J), we hypothesized that miR-10-3p might be repressing r-type ABD-B protein in more anterior segments of the CNS. [score:1]
Outlined in red are nucleotides that can pair with miR-10-5p. [score:1]
This type of analysis predicts that there is no biochemical reason why Drosophila miR-10-5p (previously called miR-10) should be preferentially packaged into RISC more often than miR-10-3p (previously called miR-10*), and in fact suggests that miR-10-3p should be packaged into RISC preferentially over miR-10-5p ([49] and data not shown). [score:1]
Figure S1 Alignment of basal promoter regions of pri-miR-10 from 12 Drosophila species. [score:1]
On the other hand, miR-10 is a highly conserved miRNA, not only in sequence, but also in its genomic position in the complex between the Hox4 and Hox5 orthologs of most bilaterian animals [43]. [score:1]
To detect pri-mir-10 in Figure 2 the detection scheme was as follows: mir-10-DIG>sheep anti-DIG-HRP>Cy3 Tyramide amplification; To detect pri-mir-10, Scr, and Abd-B, the detection scheme was as follows: pri-mir-10-DIG>sheep anti-DIG-HRP>Cy3 Tyramide amplification; Scr-cDNA-BIO>mouse anti-BIO>donkey anti-mouse Alexa488; Abd-B-cDNA-DNP>rabbit anti-DNP>donkey anti-rabbit Alexa647. [score:1]
Shortly after the beginning of gastrulation, transcription of pri-mir-10 appears to shut off and then re-initiates during the early stages of germband elongation in a different pattern. [score:1]
Figure S2 Alignment of mir-10 hairpins from bilaterians. [score:1]
The pri-mir-10 transgene can produce significant amounts of mature miRNA, as visualized by antisense LNA oligo staining in embryos containing both the UAS- mir-10 transgene as well as a prd-GAL4 driver (Figure S8A). [score:1]
Functional analysis of miR-10-3p. [score:1]
Although the sequence from the 5′ arm of the mir-10 hairpin is well conserved in bilaterians, the sequence from the 3′ arm is not particularly well conserved. [score:1]
Although their transcription is largely complementary in most tissues, in the ventral nerve cord of later stage embryos, pri-mir-10 and Abd-B overlap from the posterior compartment of segment A5 through A8/9 (parasegments 10–14) (Figure 3D–F and H–J). [score:1]
In C. elegans, the study of mir-57, which is likely to be a derived ortholog of mir-10, indicates that loss-of-function mutants have partially penetrant posterior patterning defects that may in part be due to the derepression of nob-1b, a C. elegans ortholog of Abd-B [41]. [score:1]
We therefore conclude that at least one pri-mir-10 transcript in Drosophila melanogaster spans an approximately 7.5 kb region of the chromosome between Scr and Dfd with a single approximately 5.5 kb intron (Figure 1A and B), although the existence of secondary transcripts remains a possibility. [score:1]
Embryos mutant for the Abd-B-m specific transcripts (Abd-B [D14]) and deficient for mir-10 do not exhibit ectopic r-type ABD-B protein (L). [score:1]
In this study we investigated three strongly predicted miRNA:Hox-target interactions: miR-10-5p: Scr, miR-10-3p: Abd-B, and miR-iab-4-5p: Antp. [score:1]
Outlined in red are nucleotides which can pair with miR-10-3p. [score:1]
In order to characterize a possible interaction between miR-10-3p and Abd-B, we used in situ hybridization to determine their relative patterns of expression. [score:1]
To detect pri-mir-10 in Figure 2 the detection scheme was as follows: mir-10-DIG>sheep anti-DIG-HRP>Cy3 Tyramide amplification;To detect pri-mir-10, Scr, and Abd-B, the detection scheme was as follows: pri-mir-10-DIG>sheep anti-DIG-HRP>Cy3 Tyramide amplification; Scr-cDNA-BIO>mouse anti-BIO>donkey anti-mouse Alexa488; Abd-B-cDNA-DNP>rabbit anti-DNP>donkey anti-rabbit Alexa647. [score:1]
Functional analysis of miR-10-5p. [score:1]
Although the 5′ seed sequence pairing of miR-10-5p with this Scr site is not as extensive as the ‘prototypical’ mRNA pairing—a continuous helix of base pairs 3–7, as opposed to the ‘ideal’ seed sequence of miRNA nucleotides 2–8—there is potential for a long continuous helix formed between Scr and the 3′ end of the miR-10-5p (bases 11–22) (Figure 1D and Figure S5), suggesting formation of an energetically stable duplex with miR-10-5p primed RISC. [score:1]
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2
[+] score: 34
Early embryonic expression of mir 10 differed between Drosophila and Apis, but later expression was similar and is consistent with regulation by separate cis-regulatory elements (one controlling early expression, one controlling later expression) as suggested previously for Drosophila mir-10 [8]. [score:11]
However ectopic expression of Dme mir 10 had no significant effect on the expression of predicted Hox targets (Scr and Abd-B) [25], suggesting that they may not be biologically relevant targets for mir-10 in a laboratory setting. [score:9]
It is located within the Hox complex in Drosophila between the deformed (dfd) and sex combs reduced (Scr) Hox genes and has been predicted to directly regulate mRNA translation of nearby Hox genes that contain mir-10 binding sites in their 3 [′]UTRs [26]. [score:5]
Previous deep sequencing of Drosophila embryonic RNA revealed that most of the reads correspond to the 3 [′] arm of the mir-10 precursor [27], although RNA expression patterns of both mir-10-5p and mir-10-3p is similar in Drosophila embryos [25]. [score:3]
However, while only 10% of the total reads for pre-mir-10 were from the 3p arm in honeybee embryos (Figure 1), it was still a significant number (425) and more abundant that some of the other miRNAs detected (Table 2), indicating that the mature miRNA from this arm of the mir-10 hairpin (mir-10-3p) may have a distinct role during honeybee development. [score:2]
Mir-10 is a wi dely conserved miRNA in both sequence and genomic location in both invertebrates and vertebrate Hox gene clusters. [score:1]
Our results and those from Tribolium[18] would indicate that the ancestral dominant arm was the mir-10-5p (producing the mature miRNA) and that this has switched during Drosophila evolution to the mir-10-3p arm. [score:1]
This has also been found for mir-10 in Tribolium[18]. [score:1]
We found that the 90% of sequence reads are from the 5 [′] arm of the pre-miRNA in honeybee embryos, indicating that mir-10-5p is responsible for the majority of mir-10 function (Figure 1). [score:1]
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3
[+] score: 24
This spatial expression pattern is proximal to the anterior limit of miR-10 expression [14, 64]. [score:5]
The homeotic gene Scr is a predicted target of miR-10 [63] and is also expressed in the blastoderm at stage 5 [64]. [score:5]
The genomic locations of the miRNAs iab-4 and miR-10 are proximal to their targets, which is certainly consistent with the possibility of coordinated regulation [65]. [score:4]
Like iab-4, the miRNA miR-10 is also expressed at stage 5 in a broad posterior region along the anterior–posterior axis [14]. [score:3]
The miRNAs miR-309clus, miR-10, and iab-4 (which all reside between annotated mRNA genes on the genome), and miR-11, miR-274, and miR-281clus (which all reside within introns of annotated genes) are all expressed in a graded fashion along the anterior–posterior axis of the blastoderm embryo [14, 60]. [score:3]
Hence the interaction of miR-10 with Scr at stage 5 of Drosophila development is also a candidate for the sharpening mechanism. [score:2]
The miR-10 site in the Scr 3′ UTR is likely to be functional because the pairing is well conserved in all drosophilid genomes and because the miRNA site is conserved in the Scr genes in mosquito, the flour beetle, and the silk moth [20]. [score:1]
gov/Genbank/) GeneIDs for the genes discussed in this paper are arf3 (817014), eve (36039), hb (41032), hoxb8 (15416), iab-4 (3772110), lbl1 (100037819), miR-10 (3772568), miR-11 (3771987), miR-196 (387191), miR-274 (3771876), miR-281–1 (3772402), miR-281–2 (3772497), miR-309 (3772613), scr (40833), tas3 (3768766), and ubx (42034). [score:1]
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4
[+] score: 15
It is impossible to determine from this analysis whether microRNAs have acquired more targets in one clade or lost targets in the other, but it is striking that both human homologs of the fly microRNAs miR-184 and miR-210 are expressed at low abundance across many human tissues, while the homologs of miR-10, miR-133, miR-125, let-7, and miR-285 are expressed overall at much higher levels [19]. [score:9]
We stress that the human homologs of miR-10 and miR-133 have average or below average numbers of predicted targets in human. [score:3]
However, certain microRNAs appear to have a significantly higher number of target genes in either humans (miR-10, miR-133, miR-125, let-7, and miR-285) or flies (miR-184 and miR-210). [score:3]
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5
[+] score: 10
Amongst motifs associated with decreased gene expression in mir-124 mutants, the top motif corresponds to the Pumilio site; others motifs include the seeds of K box family miRNAs, miR-10-5p, and an orphan motif (AUGCAAA) with several hundred conserved matches (defined by TargetScan). [score:5]
In addition to a global effect on neuroblast-to-neural transition, we observed that genes downregulated upon in vivo loss of miR-124 were enriched for seeds of K box miRNAs and miR-10-5p (Figure 8G). [score:4]
Two of these were seeds for K box miRNAs and for the Hox miRNA miR-10-5p (Figure 8G). [score:1]
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6
[+] score: 5
Other miRNAs from this paper: dme-mir-277, dme-mir-34, dme-mir-190
Further, we found that these target lists overlap (with up to 29 targets) with the well-studied miRNAs mir-34, mir-277, mir-190, and mir-10. [score:5]
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7
[+] score: 5
Likewise, although unstable PGC transcripts are enriched for miR-1, miR-2a-2 cluster, miR-8, miR-10, miR-11, miR-13b-1 cluster, miR-92a, miR-274, and miR-283 target sites, all of these miRs are expressed in the soma but not in the PGCs [73]. [score:5]
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8
[+] score: 5
Other miRNAs from this paper: hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7d, hsa-let-7e, hsa-let-7f-1, hsa-let-7f-2, hsa-mir-27a, hsa-mir-29a, hsa-mir-101-1, dme-mir-1, dme-mir-2a-1, dme-mir-2a-2, dme-mir-2b-1, dme-mir-2b-2, mmu-let-7g, mmu-let-7i, mmu-mir-1a-1, mmu-mir-101a, mmu-mir-124-3, mmu-mir-126a, mmu-mir-133a-1, mmu-mir-137, mmu-mir-140, mmu-mir-142a, mmu-mir-155, mmu-mir-10b, mmu-mir-183, mmu-mir-193a, mmu-mir-203, mmu-mir-143, hsa-mir-10a, hsa-mir-10b, hsa-mir-34a, hsa-mir-183, hsa-mir-199b, hsa-mir-203a, hsa-mir-210, hsa-mir-222, hsa-mir-223, dme-mir-133, dme-mir-34, dme-mir-124, dme-mir-79, dme-mir-210, dme-mir-87, mmu-mir-295, mmu-mir-34c, mmu-mir-34b, mmu-let-7d, dme-let-7, dme-mir-307a, dme-mir-2c, hsa-let-7g, hsa-let-7i, hsa-mir-1-2, hsa-mir-124-1, hsa-mir-124-2, hsa-mir-124-3, hsa-mir-133a-1, hsa-mir-133a-2, hsa-mir-137, hsa-mir-140, hsa-mir-142, hsa-mir-143, hsa-mir-126, hsa-mir-193a, 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-29a, mmu-mir-27a, mmu-mir-34a, mmu-mir-101b, hsa-mir-1-1, mmu-mir-1a-2, hsa-mir-155, mmu-mir-10a, mmu-mir-210, mmu-mir-223, mmu-mir-222, mmu-mir-199b, mmu-mir-124-1, mmu-mir-124-2, hsa-mir-101-2, hsa-mir-34b, hsa-mir-34c, hsa-mir-378a, mmu-mir-378a, mmu-mir-133a-2, mmu-mir-133b, hsa-mir-133b, mmu-mir-411, hsa-mir-193b, hsa-mir-411, mmu-mir-193b, hsa-mir-944, dme-mir-193, dme-mir-137, dme-mir-994, mmu-mir-1b, mmu-mir-101c, hsa-mir-203b, mmu-mir-133c, mmu-let-7j, mmu-let-7k, mmu-mir-126b, mmu-mir-142b, mmu-mir-124b
Two conserved miRNA families with multiple members, i. e. miR-133 and miR-10, had individual members with large differential 5′-isomiR arm abundances. [score:1]
One such example is the miR-10 family where 5′-isomiRs of the same seed ‘CCCUGUA’ contributed to 21.8% and 28.6% of the miR-10a-5p abundances in human and mouse, respectively. [score:1]
We observed that miRNA orthologues (miR-10, miR-133, miR-137 and miR-79 in Table 3) swapped major miRNAs and 5′-isomiRs and had largely different 5′-isomiR arm abundances across human, mouse, fruitfly and worm. [score:1]
For example, miR-10-5p. [score:1]
iso1 in human and mouse had a high arm abundance, whereas miR-10-5p. [score:1]
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9
[+] score: 4
Other miRNAs from this paper: hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3, hsa-let-7b, hsa-let-7c, hsa-let-7d, hsa-let-7e, hsa-let-7f-1, hsa-let-7f-2, hsa-mir-17, hsa-mir-25, hsa-mir-92a-1, hsa-mir-92a-2, hsa-mir-105-1, hsa-mir-105-2, dme-mir-1, mmu-let-7g, mmu-let-7i, mmu-mir-1a-1, mmu-mir-124-3, mmu-mir-134, mmu-mir-10b, hsa-mir-10a, hsa-mir-10b, dme-mir-92a, dme-mir-124, dme-mir-92b, mmu-let-7d, dme-let-7, hsa-let-7g, hsa-let-7i, hsa-mir-1-2, hsa-mir-124-1, hsa-mir-124-2, hsa-mir-124-3, hsa-mir-134, 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-92a-2, hsa-mir-1-1, mmu-mir-1a-2, mmu-mir-10a, mmu-mir-17, mmu-mir-25, mmu-mir-124-1, mmu-mir-124-2, mmu-mir-92a-1, hsa-mir-379, mmu-mir-379, mmu-mir-412, gga-let-7i, gga-let-7a-3, gga-let-7b, gga-let-7c, gga-mir-92-1, gga-mir-17, gga-mir-1a-2, gga-mir-124a, gga-mir-10b, gga-let-7g, gga-let-7d, gga-let-7f, gga-let-7a-1, gga-mir-1a-1, gga-mir-124b, gga-mir-1b, gga-let-7a-2, gga-let-7j, gga-let-7k, dre-mir-10a, dre-mir-10b-1, dre-mir-430b-1, hsa-mir-449a, mmu-mir-449a, 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-10b-2, dre-mir-10c, dre-mir-10d, dre-mir-17a-1, dre-mir-17a-2, dre-mir-25, dre-mir-92a-1, dre-mir-92a-2, dre-mir-92b, dre-mir-124-1, dre-mir-124-2, dre-mir-124-3, dre-mir-124-4, dre-mir-124-5, dre-mir-124-6, 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, hsa-mir-412, hsa-mir-511, dre-let-7j, hsa-mir-92b, hsa-mir-449b, gga-mir-449a, hsa-mir-758, hsa-mir-767, hsa-mir-449c, hsa-mir-802, mmu-mir-758, mmu-mir-802, mmu-mir-449c, mmu-mir-105, mmu-mir-92b, mmu-mir-449b, mmu-mir-511, mmu-mir-1b, gga-mir-1c, gga-mir-449c, gga-mir-10a, gga-mir-449b, gga-mir-124a-2, mmu-mir-767, mmu-let-7j, mmu-let-7k, gga-mir-124c, gga-mir-92-2, gga-mir-449d, mmu-mir-124b, gga-mir-10c, gga-let-7l-1, gga-let-7l-2
Others, the mir-10, 99, 100, 125 family for example, diverge in the mature forms (See additional file 8: The mir-10, 99, 100, 125 family). [score:1]
Sequence alignment and selected secondary structure of the miRNAs in the mir-10, 99, 100, 125 family. [score:1]
Click here for file The mir-10, 99, 100, 125 family. [score:1]
The mir-10, 99, 100, 125 family. [score:1]
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10
[+] score: 3
Comparisons between P. tepidariorum and D. melanogaster shows that mir-10, mir-993a, mir-278b, mir-281, also display changes in arm use (fig. 4 B). [score:1]
These included mir-8 and mir-10, which were not duplicated in any of the other ecdysozoans that we surveyed (fig. 2). [score:1]
miR-10-5p is more abundant than miR-10-3p in both P. tepidariorum and T. castaneum, while miR-10-3p dominates in D. melanogaster (Griffiths-Jones et al. 2011). [score:1]
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11
[+] score: 3
For example, both stands of miR-10 are expressed in D. melanogaster and the beetle Tribolium castaneum, with the dominant mature microRNA switched between the two species [19], [20]. [score:3]
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12
[+] score: 2
Interestingly, mir-10, located between Dfd and Scr (top panel) also appears to be under direct control of Zld. [score:2]
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13
[+] score: 2
Most of the fly ≥70% full length homologs exhibit blocks of ≥7 nt identity at the 5′ end except the following 10: dme-miR-10, dme-miR-100, dme-miR-263a, dme-miR-263b, dme-miR-954, dme-miR-966, dme-miR-1009, dme-miR-1010, dme-miR-iab-4-3p and dme-miR-iab4as-3p. [score:1]
8 of the 40 Drosophila miRNAs with ≥70% homologous sequences in humans show extensive overall similarity with 5′ mismatches: dme-miR-8 with hsa-miR-141 and hsa-miR-200a, dme-miR-10 with hsa-miR-100 and hsa-miR-99a, dme-miR-100 with hsa-miR-10a and hsa-miR-10b, dme-miR-125 with hsa-miR-10a and hsa-miR-10b, dme-miR263a with hsa-miR-183, dme-miR-263b with hsa-miR-183, dme-miR-306 with hsa-miR-873, and dme-miR-993 with hsa-miR-100*. [score:1]
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14
[+] score: 2
These genes correspond to the fly genes abd-A and Abd-B. As in the case of miR10, a miRNA gene is found at a similar location in arthropods, though the primary sequence of the miRNA genes differ between the two lineages. [score:1]
The conserved miR-10 miRNA lies between the Drosophila Hox genes Deformed and Sex-comb-reduced. [score:1]
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15
[+] score: 1
Some of the miRNAs (miR-8, miR-9a, miR-10, miR-71, miR-252, miR-276, miR-281) are represented by both strands,-3p and-5p, as was also observed in the previous N6 library [14]. [score:1]
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16
[+] score: 1
Two pre-miRNAs only identified mature miRNAs on the star (*) arm (mir-10, mir-285). [score:1]
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17
[+] score: 1
These included the MIR-92 and MIR-10 families, which are also highly adenylated in early embryos of T. castaneum [17]. [score:1]
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18
[+] score: 1
Other miRNAs from this paper: dme-mir-2a-1, dme-mir-2a-2, dme-mir-2b-1, dme-mir-2b-2, dme-mir-9a, dme-mir-12, dme-mir-13a, dme-mir-13b-1, dme-mir-13b-2, dme-mir-276a, dme-mir-133, dme-mir-276b, dme-mir-210, dme-mir-31b, dme-mir-9c, dme-mir-306, dme-mir-9b, dme-mir-31a, dme-mir-309, dme-mir-316, dme-mir-317, dme-mir-2c, ame-mir-12, ame-mir-133, ame-mir-210, ame-mir-276, ame-mir-2-1, ame-mir-2-2, ame-mir-317, ame-mir-9a, ame-mir-9b, bmo-mir-9a, bmo-mir-10, bmo-mir-276, bmo-mir-31, bmo-mir-71, ame-mir-10, ame-mir-137, ame-mir-13a, ame-mir-2-3, ame-mir-29b, ame-mir-31a, ame-mir-375, ame-mir-71, ame-mir-932, dme-mir-193, dme-mir-375, dme-mir-932, dme-mir-970, dme-mir-971, dme-mir-989, dme-mir-137, dme-mir-1006, dme-mir-1007, bmo-mir-2a-1, bmo-mir-2a-2, bmo-mir-2b, bmo-mir-13a, bmo-mir-13b, bmo-mir-133, bmo-mir-210, bmo-mir-317, tca-mir-2-3, tca-mir-2-1, tca-mir-2-2, tca-mir-10, tca-mir-12, tca-mir-13a, tca-mir-13b, tca-mir-31, tca-mir-71, tca-mir-133, tca-mir-137, tca-mir-210, tca-mir-276, tca-mir-317, tca-mir-932, tca-mir-9b, bmo-mir-12, bmo-mir-137, bmo-mir-932, bmo-mir-9b, tca-mir-9a, tca-mir-970, ame-mir-13b, ame-mir-1006, ame-mir-316, bmo-mir-970, lmi-mir-276, lmi-mir-210, lmi-mir-10, lmi-mir-9a, bmo-mir-9c, bmo-mir-306a, bmo-mir-989a, bmo-mir-316, bmo-mir-1175, bmo-mir-9d, bmo-mir-750, bmo-mir-375, bmo-mir-306b, api-mir-137, api-mir-10, api-mir-276, api-mir-13a, api-mir-210, api-mir-29, api-mir-2a, api-mir-2b, api-mir-2c, api-mir-316, api-mir-317, api-mir-71, api-mir-971, api-mir-9a, api-mir-9b, api-mir-306, api-mir-3049, bmo-mir-989b, ame-mir-1175, ame-mir-193, ame-mir-989, ame-mir-3049, ame-mir-971, ame-mir-3770, ame-mir-9c, ame-mir-306, ame-mir-750, tca-mir-9c, tca-mir-316, tca-mir-9d, tca-mir-309a, tca-mir-3049, tca-mir-375, tca-mir-29, tca-mir-1175, tca-mir-750, tca-mir-989, tca-mir-309b, tca-mir-193, tca-mir-6012, tca-mir-9e, ame-mir-6037, ame-mir-6012, ame-mir-2b, tca-mir-309c, tca-mir-971b
Blast approaches on the genome assembly and on small RNA-seq reads led to find three of them: MIR-317, MIR-316 and MIR-971, as well as a new Mir-10 gene. [score:1]
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19
[+] score: 1
The miR-2 family was predicted to contain the most family members (n = 8), followed by miR-10 (n = 5), and miR-87, -184, -252, -263, -279, -9, -3015 (n = 4). [score:1]
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