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Article
Open AccessRNase κ promotes robust piRNA production by generating 2′,3′-cyclic phosphate-containing precursors
In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations betwe...
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Article
Open AccessUnraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis
Malignant cutaneous melanoma (CM) is a potentially lethal form of skin cancer whose worldwide incidence has been constantly increasing over the past decades. During their lifetime, about 8% of CM patients will...
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Article
Open AccessThe transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content
Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation sta...
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Article
Open AccessLong-term exposure of human endothelial cells to metformin modulates miRNAs and isomiRs
Increasing evidence suggest that the glucose-lowering drug metformin exerts a valuable anti-senescence role. The ability of metformin to affect the biogenesis of selected microRNAs (miRNAs) was recently sugges...
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Article
Open AccessRibosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner
The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple c...
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Article
Open AccessProfiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer
MicroRNA (miRNA) isoforms (“isomiRs”) and tRNA-derived fragments (“tRFs”) are powerful regulatory non-coding RNAs (ncRNAs). In human tissues, both types of molecules are abundant, with expression patterns that...
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Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap
There is an increasing interest within the scientific community in identifying tRNA-derived fragments (tRFs) and elucidating the roles they play in the cell. Such endeavors can be greatly facilitated by mining...
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Article
Open AccessIncreasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells
Piwi proteins and their bound Piwi-interacting RNAs (piRNAs) are predominantly expressed in the germline and play crucial roles in germline development by silencing transposons and other targets. Bombyx mori BmN4...
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Article
Open AccessN-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration
Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...
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Article
Open AccessMINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data
Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. ...
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Article
Open AccessConsequential considerations when map** tRNA fragments
We examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of current...
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Article
Open Access“Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs
CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated nucleases) is a powerful component of the prokaryotic immune system that has been adapted for targeted genetic engineerin...
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Article
Open AccessArgonaute CLIP-Seq reveals miRNA targetome diversity across tissue types
To date, analyses of individual targets have provided evidence of a miRNA targetome that extends beyond the boundaries of messenger RNAs (mRNAs) and can involve non-Watson-Crick base pairing in the miRNA seed ...
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Article
Open AccessThe human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome
For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes’ relationship is with t...
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Article
The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis
The mammalian genome is transcribed in a developmentally regulated manner, generating RNA strands ranging from long to short non-coding RNA (ncRNAs). NcRNAs generated by intergenic sequences and protein-coding...
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Article
Open AccessThe complex transcriptional landscape of the anucleate human platelet
Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provi...
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Article
Erratum: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets
To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) ‘seed’ region and pe...
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Article
Open AccessMolecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets
To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) ‘seed’ region and pe...
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Article
Decoy for microRNAs
Pseudogenes are considered to be defunct relatives of known genes. But there is some surprising news: pseudogenes are functional and could have a role in the control of cancer1. Two experts discuss the significan...
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Article
Insights into the Regulation of a Common Variant of HMGA2 Associated with Human Height During Embryonic Development
Early genetic studies in the mouse and chicken identified the HMGA oncogene as a candidate that regulates body height. Subsequent genome-wide SNP studies revealed a significant association of rs1042725 genotyp...
