Evidence that miRNAs are different from other RNAs

Zhang, B. H.; Pan, Xiaoping; Cox, Stephen B.; Cobb, George P.; Anderson, Todd A.

doi:10.1007/s00018-005-5467-7

Cited by 511 publications

(502 citation statements)

References 42 publications

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“…However, a majority of the pre-miRNAs are 40 to 82 nt (26 out of 51, or 51%) in length (Table 1), then 83 to 125 = 12 (23%), 126 to 168 = 10 (20%), 169 to 211 = 1 (2%), and 212 to 254 = 2 (4%). Mature miRNA arm locations, length distribution of miRNAs, and their precursor sequences are similar to previous reports in other plant species (Zhang et al, 2006b(Zhang et al, , 2007bDin et al, 2014). MFE is very important for RNAs forming their secondary structures.…”

Section: Characterization Of Micrornas In the Genus Coffeasupporting

confidence: 86%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

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IntroductionMicroRNAs (miRNAs) are an extensive class of noncoding small endogenous RNAs of 18 to 26 nt in length that are derived from self-complementary fold-back structures of longer precursor sequences (pre-miRNAs) and are generated by Dicer-like 1 (DCL1) in plants (Bartel, 2004). Mature miRNAs inhibit gene expression at posttranscriptional levels by either targeting mRNAs for degradation or inhibiting protein translation. Both processes are accomplished by the complementary base pairing of miRNAs to their target mRNA sequences (Ambros, 2004). In plants, for a majority of cases, miRNAs interact with their targets through perfect or near-perfect base pairing and lead to target mRNA degradation (Jones-Rhoades et al., 2006). Increasing evidence has revealed that miRNAs play an important role in a wide range of development processes in plants, including cell proliferation, stress response, metabolism, inflammation, and signal transduction (Ambros, 2004;Jones-Rhoades et al., 2006;Zhang et al., 2007a;Ali et al., 2016) and crosskingdom gene regulation (Barozai and Din, 2017). To date, more than 28,645 miRNAs have been identified from 223 species of plants and animals and deposited in the publicly available database miRBase (Release 21) (Griffiths-Jones et al., 2008). The majority of plant miRNAs have been found in species with fully sequenced genomes including 713 from Oryza sativa, 401 from Populus trichocarpa, 384 from Arabidopsis thaliana, 343 from Solanum tuberosum, 321 from Zea mays, and 241 from Sorghum bicolor (Griffiths-Jones et al., 2008). miRNA-related research is continuously growing and miRNAs, along with their functions, are being identified and elucidated using a wide variety of computational tools and experimental methods including direct cloning, deep sequencing, and other approaches. Comparison of miRNAs across multiple plant species has demonstrated that some miRNAs are highly evolutionary conserved from species to species, such as from mosses to higher flowering eudicots in the plant kingdom (Floyd and Bowman, 2004;Zhang et al., 2006aZhang et al., , 2006b. Conservation of miRNA sequences has provided a powerful strategy for identifying miRNAs in other species. Currently, comparative genome-based homolog searches have been used to identify conserved miRNAs in many plant species, including cotton (

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Section: Characterization Of Micrornas In the Genus Coffeasupporting

confidence: 86%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

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“…Generally speaking, the lower the MFE value, the more stable the secondary structure of a RNA sequence (Zhang et al, 2006). In the present study, our results showed that the value of MFEs range from -18.1 kcal/mol to −74.7 kcal/mol with average value of −27.02 ± 8.19 kcal/mol (Fig.…”

Section: Characterization Of Mirnas In Rainbow Troutsupporting

confidence: 60%

A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

Yang

2014

Gene

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“…As well, some parameters describing the folded structure are common to other SVM approaches including minimum folding energy index (MFEI), adjusted minimum folding energy (AMFE) (Zhang et al 2006), normalized pairing propensity (Ng Kwang Loong and Mishra 2007), and loop length. The parameters that are unique to this type of sequencing data are descriptors of the seed itself and its positioning within the pre-miRNA structure.…”

Section: Novel Microrna Predictionmentioning

confidence: 99%

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

Morin¹,

O’Connor²,

Griffith³

et al. 2008

Genome Res.

1,008

922

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MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of their numbers and expression changes in different cell states. Here, we report a new method for surveying the expression of small RNAs, including microRNAs, using Illumina sequencing technology. We also present a set of methods for annotating sequences deriving from known miRNAs, identifying variability in mature miRNA sequences, and identifying sequences belonging to previously unidentified miRNA genes. Application of this approach to RNA from human embryonic stem cells obtained before and after their differentiation into embryoid bodies revealed the sequences and expression levels of 334 known plus 104 novel miRNA genes. One hundred seventy-one known and 23 novel microRNA sequences exhibited significant expression differences between these two developmental states. Owing to the increased number of sequence reads, these libraries represent the deepest miRNA sampling to date, spanning nearly six orders of magnitude of expression. The predicted targets of those miRNAs enriched in either sample shared common features. Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation.

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Evidence that miRNAs are different from other RNAs

Cited by 511 publications

References 42 publications

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

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