Questions tagged [microrna]

Micro RNA (miRNA) are a class of small (22 nucleotide in the mature form) non-coding RNA. They are present in plants and animals and function as transcriptional and post-transcriptional regulators of genes. They bind to a complementary region in the transcribed gene to form doublestanded RNA molecules. These are silenced since they cannot be translated and often subsequently degraded by the cell.

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If downstream genomic loci of a microRNA were detected as miR cis-eQTL, what regulatory mechanism is possible?

I found several miR cis-eQTLs in the downstream genomic loci of a certain microRNA (around 334kb away from the transcription start site of the primary microRNA), what can be possible implications as a ...
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How to confirm secondary structure formation of Precursor miRNA on gel?

I want to fold precursor-miRNA into its secondary structure and then confirm it on gel. At first, I heat it in annealing buffer at 95°C for 5 minutes and cool down slowly. Then I run it on gel but the ...
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Are microRNAs transcribed from the same DNA strand as their parent messenger RNAs?

I am new to micro RNAs. I have been trying to find the answer to the question if microRNAs are transcribed from the same DNA strand as the messenger RNAs encoded by the encompassing gene? From the ...
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Which mRNAs enter P-bodies?

Processing bodies (P-bodies) are distinct foci within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover (ref). They play a fundamental role in RNA silencing/...
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What is the difference between “dysregulation” and “deregulation” of miRNA?

I've started to study the role of miRNA in cancer. Wikipedia says: Just as miRNA is involved in the normal functioning of eukaryotic cells, so has dysregulation of miRNA been associated with ...
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What is cognate miRNA?

I understand what miRNA are, but I'm unsure of what cognate means. Looking at this post, it seems that a cognate miRNA is a known miRNA vs. a recently discovered/possible miRNA. Is this thinking on ...
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Why are there two mature sequences of microRNAs in miRBase entries?

In the miRBase database entries generally show a stem loop sequence and two mature sequences. For example the entry for hsa-mir-15a gives three sequences: (1) the Stem-loop sequence hsa-mir-15a, (2) ...
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Do all microRNA isoforms need to be known and sequenced to obtain microRNA expression?

From what I understand, microRNA are short "hairpin" shaped nc structures. When sequencing and counting miRNA, isoform miRNA are "found" which are subsections of varying length and possibly with some ...
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Can a miRNA be upregulated and downregulated in the same disease

I am computational guy and hence apologies if the question is silly. Can the same miRNA show upregulation and downregulation in the same disease? (Not in the same experiment, though). For e.g. can ...
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What is the difference between hsa-miR-33a and hsa-miR-33b?

Does anyone know what is the difference between two miRNAs like hsa-miR-33a and hsa-miR-33b? The last letter in them shows what? Also, if we know that hsa-miR-33a targets gene A, can we say that hsa-...
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Small non-coding RNA (sRNA) vs. micro RNA (miRNA)?

What are the differences between micro RNAs (miRNA) and small non-coding RNAs (sRNA)? Are these two terms used interchangeably?
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Converting miRNA names

I need to convert all of my microRNA names e.g. hsa-miR-30e-5p to e.g. entrez gene IDs, ensemble IDs or another ID. Does anyone know a good ID conversion tool for microRNAs? (I managed to convert it ...
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miRNA targets mRNAs

If we observe that a miRNA, say hsa-mir-233, targets a mRNA, say XXX, in a given tissue in disease condition, can we say that always hsa-mir-233 targets mRNA XXX regardless of type of tissue and ...
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Difference between micro RNA and short-interfering RNA and CRISPR Cas 9 system?

I read this article https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/ and am slightly puzzled as to why the CRISPR/Cas 9 system is seen as being so revolutionary. It seems like the ...
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Are non-coding RNAs introns?

I am slightly confused as to what part of the genome codes for non-coding RNAs. Is it the introns? This would make sense to me as to why they are not transcribed as the introns are not transcribed. Or ...
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What is the silencing mechanism of AGO1,AGO3 and AGO4?

I read that this proteins lack of slicer activity, so what mechanism do they use to perform gene regulation?
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What is the meaning of conservation site in miRNA-mRNA pairing context?

I am not biologist and just work in Bioinformatics field. Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs? Example: Each of these duplexes ...
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Naming convention of miRNAs

I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it nomenclature Based on it, I try to figure out what is hsa-let-7a. As far as I understood, hsa refers to ...
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Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
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what the best E-value cutoff in the miRNA homology search

I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop ...
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How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
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Periods of Heavy Speciation

I have a set of microRNA ages with corresponding labels suggesting which clade they first emerged from. For instance, for hsa-mir-1, let's say, it would have an age of Eutheria. I have several peaks ...
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Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an ...
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Steps to confirm if predicted miRNA is good or bad

I aligned all miRNAs available to the supercontigs of a particular genome with certain parameters (e value of 0.01 and a word match of atleast 7 as suggested in this paper). I have also isolated the ...
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mFOLD prediction result interpretation

I am trying to predict the secondary structure of certain predicted pre-miRNAs through mFOLD which is the generally accepted technique for structure prediction in most studies. I am finding it hard to ...
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Known MicroRNA - Gene Systems?

Have there been any experimentally-verified systems of microRNAs targeting a gene set (e.g., in cancer, perhaps)?
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circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...