references.bib

@article{axtell2013a,
	title = {ShortStack: Comprehensive annotation and quantification of small RNA genes},
	author = {Axtell, Michael J.},
	year = {2013},
	month = {04},
	journal = {RNA},
	pages = {740--751},
	volume = {19},
	number = {6},
	doi = {10.1261/rna.035279.112},
	url = {http://dx.doi.org/10.1261/rna.035279.112},
	langid = {en}
}

@article{shahid2014,
	title = {Identification and annotation of small RNA genes using ShortStack},
	author = {Shahid, Saima and Axtell, Michael J.},
	year = {2014},
	month = {05},
	journal = {Methods},
	pages = {20--27},
	volume = {67},
	number = {1},
	doi = {10.1016/j.ymeth.2013.10.004},
	url = {http://dx.doi.org/10.1016/j.ymeth.2013.10.004}
}
	
@article{johnson2016a,
	title = {Improved Placement of Multi-mapping Small RNAs},
	author = {Johnson, Nathan R and Yeoh, Jonathan M and Coruh, Ceyda and Axtell, Michael J},
	year = {2016},
	month = {07},
	journal = {G3 Genes|Genomes|Genetics},
	pages = {2103--2111},
	volume = {6},
	number = {7},
	doi = {10.1534/g3.116.030452},
	url = {http://dx.doi.org/10.1534/g3.116.030452},
	langid = {en}
}

@article{moran_cnidarian_2014,
	title = {Cnidarian {microRNAs} frequently regulate targets by cleavage},
	volume = {24},
	doi = {10.1101/gr.162503.113},
	abstract = {In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA "seed") to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.},
	journal = {Genome research},
	author = {Moran, Yehu and Fredman, David and Praher, Daniela and Li, Xin and Wee, Liang and Rentzsch, Fabian and Zamore, Phillip and Technau, Ulrich and Seitz, Hervé},
	month = mar,
	year = {2014},
	keywords = {Cnidaria, corals, miRNA},
	file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\GWQLI4VR\\Moran et al. - 2014 - Cnidarian microRNAs frequently regulate targets by.pdf:application/pdf;PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\4R2KVIMR\\Moran et al. - 2014 - Cnidarian microRNAs frequently regulate targets by.pdf:application/pdf},
}

@misc{admoni_target_2023,
	title = {Target complementarity in cnidarians supports a common origin for animal and plant {microRNAs}},
	copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2023.01.08.523153v2},
	doi = {10.1101/2023.01.08.523153},
	abstract = {microRNAs (miRNAs) are important post-transcriptional regulators that activate silencing mechanisms by annealing to mRNA transcripts. While plant miRNAs match their targets with nearly-full complementarity leading to mRNA cleavage, miRNAs in most animals require only a short sequence called ‘seed’ to inhibit target translation. Recent findings showed that miRNAs in cnidarians, early-branching metazoans, act similarly to plant miRNAs, by exhibiting full complementarity and target cleavage; however, it remained unknown if seed- based regulation was possible in cnidarians. Here, we investigate the miRNA-target complementarity requirements for miRNA activity in the cnidarian Nematostella vectensis. We show that bilaterian-like complementarity of seed-only or seed and supplementary 3’ matches are insufficient for miRNA-mediated knockdown. Furthermore, miRNA-target mismatches in the cleavage site decrease knockdown efficiency. Finally, miRNA silencing of a target with three seed binding sites in the 3’ untranslated region that mimics typical miRNA targeting was repressed in zebrafish but not in Nematostella and Hydractinia symbiolongicarpus. Altogether, these results unravel striking similarities between plant and cnidarian miRNAs consolidating the evidence for common evolutionary origin of miRNAs in plants and animals.},
	language = {en},
	urldate = {2023-12-15},
	publisher = {bioRxiv},
	author = {Admoni, Yael and Fridrich, Arie and Razin, Talya and Salinas-Saavedra, Miguel and Rabani, Michal and Frank, Uri and Moran, Yehu},
	month = oct,
	year = {2023},
	note = {Pages: 2023.01.08.523153
Section: New Results},
	keywords = {unread},
	file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\KPFCPXGE\\Admoni et al. - 2023 - Target complementarity in cnidarians supports a co.pdf:application/pdf},
}

@article{karimzadeh_regulation_2021,
	title = {Regulation of {DNA} methylation machinery by epi-{miRNAs} in human cancer: emerging new targets in cancer therapy},
	volume = {28},
	copyright = {2020 The Author(s), under exclusive licence to Springer Nature America, Inc.},
	issn = {1476-5500},
	shorttitle = {Regulation of {DNA} methylation machinery by epi-{miRNAs} in human cancer},
	url = {https://www.nature.com/articles/s41417-020-00210-7},
	doi = {10.1038/s41417-020-00210-7},
	abstract = {Disruption in DNA methylation processes can lead to alteration in gene expression and function that would ultimately result in malignant transformation. In this way, studies have shown that, in cancers, methylation-associated silencing inactivates tumor suppressor genes, as effectively as mutations. DNA methylation machinery is composed of several genes, including those with DNA methyltransferases activity, proteins that bind to methylated cytosine in the promoter region, and enzymes with demethylase activity. Based on a prominent body of evidence, DNA methylation machinery could be regulated by microRNAs (miRNAs) called epi-miRNAs. Numerous studies demonstrated that dysregulation in DNA methylation regulators like upstream epi-miRNAs is indispensable for carcinogenesis; consequently, the malignant capacity of these cells could be reversed by restoring of this regulatory system in cancer. Conceivably, recognition of these epi-miRNAs in cancer cells could not only reveal novel molecular entities in carcinogenesis, but also render promising targets for cancer therapy. In this review, at first, we have an overview of the methylation alteration in cancers, and the effect of this phenomenon in miRNAs expression and after that, we conduct an in-depth discussion about the regulation of DNA methylation regulators by epi-miRNAs in cancer cells.},
	language = {en},
	number = {3},
	urldate = {2025-01-28},
	journal = {Cancer Gene Therapy},
	author = {Karimzadeh, Mohammad Reza and Pourdavoud, Peyman and Ehtesham, Naeim and Qadbeigi, Mohaddese and Asl, Masood Movahedi and Alani, Behrang and Mosallaei, Meysam and Pakzad, Bahram},
	month = apr,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cancer, Cancer genetics},
	pages = {157--174},
	file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\99ZJBPIN\\Karimzadeh et al. - 2021 - Regulation of DNA methylation machinery by epi-miR.pdf:application/pdf},
}

@article{admoni_mirna-target_2025,
	title = {{miRNA}-target complementarity in cnidarians resembles its counterpart in plants},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-024-00350-z},
	doi = {10.1038/s44319-024-00350-z},
	abstract = {microRNAs (miRNAs) are important post-transcriptional regulators that activate silencing mechanisms by annealing to mRNA transcripts. While plant miRNAs match their targets with nearly-full complementarity leading to mRNA cleavage, miRNAs in most animals require only a short sequence called ‘seed’ to inhibit target translation. Recent findings showed that miRNAs in cnidarians, early-branching metazoans, act similarly to plant miRNAs, by exhibiting full complementarity and target cleavage; however, it remained unknown if seed-based regulation was possible in cnidarians. Here, we investigate the miRNA-target complementarity requirements for miRNA activity in the cnidarian Nematostella vectensis. We show that bilaterian-like complementarity of seed-only or seed and supplementary 3’ matches are insufficient for miRNA-mediated knockdown. Furthermore, miRNA-target mismatches in the cleavage site decrease knockdown efficiency. Finally, miRNA silencing of a target with three seed binding sites in the 3’ untranslated region that mimics typical miRNA targeting was repressed in zebrafish but not in Nematostella and another cnidarian, Hydractinia symbiolongicarpus. Altogether, these results unravel striking similarities between plant and cnidarian miRNAs supporting a possible common evolutionary origin of miRNAs in plants and animals.},
	urldate = {2025-02-07},
	journal = {EMBO reports},
	author = {Admoni, Yael and Fridrich, Arie and Weavers, Paris K and Aharoni, Reuven and Razin, Talya and Salinas-Saavedra, Miguel and Rabani, Michal and Frank, Uri and Moran, Yehu},
	month = jan,
	year = {2025},
	note = {Num Pages: 24
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Cnidaria, MicroRNA, Nematostella},
	pages = {1--24},
	file = {Admoni et al. - 2025 - miRNA-target complementarity in cnidarians resembl.pdf:C\:\\Users\\Owner\\Zotero\\storage\\YRPRRKCF\\Admoni et al. - 2025 - miRNA-target complementarity in cnidarians resembl.pdf:application/pdf},
}

@article{gresova_small_2022,
	title = {Small {RNA} {Targets}: {Advances} in {Prediction} {Tools} and {High}-{Throughput} {Profiling}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-7737},
	shorttitle = {Small {RNA} {Targets}},
	url = {https://www.mdpi.com/2079-7737/11/12/1798},
	doi = {10.3390/biology11121798},
	abstract = {MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. They are suggested to be involved in most biological processes of the cell primarily by targeting messenger RNAs (mRNAs) for cleavage or translational repression. Their binding to their target sites is mediated by the Argonaute (AGO) family of proteins. Thus, miRNA target prediction is pivotal for research and clinical applications. Moreover, transfer-RNA-derived fragments (tRFs) and other types of small RNAs have been found to be potent regulators of Ago-mediated gene expression. Their role in mRNA regulation is still to be fully elucidated, and advancements in the computational prediction of their targets are in their infancy. To shed light on these complex RNA–RNA interactions, the availability of good quality high-throughput data and reliable computational methods is of utmost importance. Even though the arsenal of computational approaches in the field has been enriched in the last decade, there is still a degree of discrepancy between the results they yield. This review offers an overview of the relevant advancements in the field of bioinformatics and machine learning and summarizes the key strategies utilized for small RNA target prediction. Furthermore, we report the recent development of high-throughput sequencing technologies, and explore the role of non-miRNA AGO driver sequences.},
	language = {en},
	number = {12},
	urldate = {2025-02-11},
	journal = {Biology},
	author = {Grešová, Katarína and Alexiou, Panagiotis and Giassa, Ilektra-Chara},
	month = dec,
	year = {2022},
	note = {Number: 12
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {machine learning, computational biology, high-throughput sequencing, miRNA target prediction, small RNA target prediction},
	pages = {1798},
	file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\6LENU3ZD\\Grešová et al. - 2022 - Small RNA Targets Advances in Prediction Tools an.pdf:application/pdf},
}

@article{luck_sirna-finder_2019,
	title = {{siRNA}-{Finder} (si-{Fi}) {Software} for {RNAi}-{Target} {Design} and {Off}-{Target} {Prediction}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.01023/full},
	doi = {10.3389/fpls.2019.01023},
	abstract = {{\textless}p{\textgreater}RNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS also mediates genomic stability by silencing of retroelements. RNAi has become an important research tool for studying gene function by strong and selective suppression of target genes. Here, we present {\textless}bold{\textgreater}si-Fi{\textless}/bold{\textgreater}, a software tool for design optimization of RNAi constructs necessary for specific target gene knock-down. It offers efficiency prediction of RNAi sequences and off-target search, required for the practical application of RNAi. {\textless}bold{\textgreater}si-Fi{\textless}/bold{\textgreater} is an open-source (CC BY-SA license) desktop software that works in Microsoft Windows environment and can use custom sequence databases in standard FASTA format.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2025-02-27},
	journal = {Frontiers in Plant Science},
	author = {Lück, Stefanie and Kreszies, Tino and Strickert, Marc and Schweizer, Patrick and Kuhlmann, Markus and Douchkov, Dimitar},
	month = aug,
	year = {2019},
	note = {Publisher: Frontiers},
	keywords = {Barley ( Hordeum vulgare L.), Blumeria graminis, MLO gene family, Off-target prediction, Post-transcriptional gene silencing (PTGS), Python (programming language), RNAi, RNAi design, RNAi efficiency},
	file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\IU698X4Y\\Lück et al. - 2019 - siRNA-Finder (si-Fi) Software for RNAi-Target Desi.pdf:application/pdf},
}