113 research outputs found
Cross-Mapping Events in miRNAs Reveal Potential miRNA-Mimics and Evolutionary Implications
MicroRNAs (miRNAs) have important roles in various biological processes. miRNA cross-mapping is a prevalent phenomenon where miRNA sequence originating from one genomic region is mapped to another location. To have a better understanding of this phenomenon in the human genome, we performed a detailed analysis in this paper using public miRNA high-throughput sequencing data and all known human miRNAs. We observed widespread cross-mapping events between miRNA precursors (pre-miRNAs), other non-coding RNAs (ncRNAs) and the opposite strands of pre-miRNAs by analyzing the high-throughput sequencing data. Computational analysis on all known human miRNAs also confirmed that many of them could be involved in cross-mapping events. The processing or decay of both ncRNAs and pre-miRNA opposite strand transcripts may contribute to miRNA enrichment, although some might be miRNA-mimics due to miRNA mis-annotation. Comparing to canonical miRNAs, miRNAs involved in cross-mapping events between pre-miRNAs and other ncRNAs normally had shorter lengths (17–19 nt), lower prediction scores and were classified as pseudo miRNA precursors. Notably, 4.9% of all human miRNAs could be accurately mapped to the opposite strands of pre-miRNAs, which showed that both strands of the same genomic region had the potential to produce mature miRNAs and simultaneously implied some potential miRNA precursors. We proposed that the cross-mapping events are more complex than we previously thought. Sequence similarity between other ncRNAs and pre-miRNAs and the specific stem-loop structures of pre-miRNAs may provide evolutionary implications
Evolution of the human-specific microRNA miR-941
MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding sites, presumably to escape regulation. We further show that miR-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage
A multilevel dataset of microplastic abundance in the world’s upper ocean and the Laurentian Great Lakes
A total of 8218 pelagic microplastic samples from the world’s oceans were synthesized to create a dataset composed of raw, calibrated, processed, and gridded data which are made available to the public. The raw microplastic abundance data were obtained by different research projects using surface net tows or continuous seawater intake. Fibrous microplastics were removed from the calibrated dataset. Microplastic abundance which fluctuates due to vertical mixing under different oceanic conditions was standardized. An optimum interpolation method was used to create the gridded data; in total, there were 24.4 trillion pieces (8.2 × 104 ~ 57.8 × 104 tons) of microplastics in the world’s upper oceans
Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter
Double-stranded RNAs that are complementary to non-coding transcripts at gene promoters can activate or inhibit gene expression in mammalian cells. Understanding the mechanism for modulating gene expression by promoter-targeted antigene RNAs (agRNAs) will require identification of the proteins involved in recognition. Previous reports have implicated argonaute (AGO) proteins, but identifications have differed with involvement of AGO1, AGO2, or both AGO1 and AGO2 being reported by different studies. The roles of AGO3 and AGO4 have not been investigated. Here, we examine the role of AGO 1–4 in gene silencing and activation of the progesterone receptor (PR) gene. Expression of AGO2 is necessary for efficient gene silencing or activation and AGO2 is recruited to the non-coding transcript that overlaps the promoter during both gene silencing and activation. Expression of AGO1, AGO3 and AGO4 are not necessary for gene silencing or activation nor are AGO1, AGO3, or AGO4 recruited to the target non-coding transcript during gene activation. These data indicate that AGO2 is the primary AGO variant involved in modulating expression of PR by agRNAs
Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers
MicroRNAs (miRNAs) are ∼22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus.To determine the number of miRNAs localized to the nucleus, we systematically investigated the subcellular distribution of small RNAs (sRNAs) by independent deep sequencing sequenced of the nuclear and cytoplasmic pools of 18- to 30-nucleotide sRNAs from human cells. We identified 339 nuclear and 324 cytoplasmic known miRNAs, 300 of which overlap, suggesting that the majority of miRNAs are imported into the nucleus. With the exception of a few miRNAs evidently enriched in the nuclear pool, such as the mir-29b, the ratio of miRNA abundances in the nuclear fraction versus in the cytoplasmic fraction vary to some extent. Moreover, our results revealed that a large number of tRNA 3′trailers are exported from the nucleus and accumulate in the cytoplasm. These tRNA 3′ trailers accumulate in a variety of cell types, implying that the biogenesis of tRNA 3′ trailers is conserved and that they have a potential functional role in vertebrate cells.Our results provide the first comprehensive view of the subcellular distribution of diverse sRNAs and new insights into the roles of miRNAs and tRNA 3′ trailers in the cell
A NORTHERN SKY SURVEY FOR POINT-LIKE SOURCES OF EeV NEUTRAL PARTICLES WITH THE TELESCOPE ARRAY EXPERIMENT
We report on the search for steady point-like sources of neutral particles around 10(18) eV between 2008 and 2013 May with the scintillator SD of the Telescope Array experiment. We found overall no significant point-like excess above 0.5 EeV in the northern sky. Subsequently, we also searched for coincidence with the Fermi bright Galactic sources. No significant coincidence was found within the statistical uncertainty. Hence, we set an upper limit on the neutron flux that corresponds to an averaged flux of 0.07 km(-2) yr(-1) for E > 1 EeV in the northern sky at the 95% confidence level. This is the most stringent flux upper limit in a northern sky survey assuming point-like sources. The upper limit at the 95% confidence level on the neutron flux from Cygnus X-3 is also set to 0.2 km(-2) yr(-1) for E > 0.5 EeV. This is an order of magnitude lower than previous flux measurementsopen0
Measurement of the proton-air cross section with Telescope Array's Middle Drum detector and surface array in hybrid mode
In this work we are reporting on the measurement of the proton-air inelastic cross section sigma(inel)(p-air) using the Telescope Array detector. Based on the measurement of the sigma(inel)(p-air), the proton-proton cross section sigma(p-p) value is also determined at root s = 95(-8)(+5) TeV. Detecting cosmic ray events at ultrahigh energies with the Telescope Array enables us to study this fundamental parameter that we are otherwise unable to access with particle accelerators. The data used in this report are the hybrid events observed by the Middle Drum fluorescence detector together with the surface array detector collected over five years. The value of the sigma(inel)(p-air) is found to be equal to 567.0 +/- 70.5[Stat](-25)(+29)[Sys] mb. The total proton-proton cross section is subsequently inferred from Glauber formalism and the Block, Halzen and Stanev QCD inspired fit and is found to be equal to 170(-44)(+48)[Stat](-17)(+19)[Sys] mb.open20
Indications of intermediate-scale anisotropy of cosmic rays with energy greater than 57 EeV in the northern sky measured with the surface detector of the Telescope Array experiment
We have searched for intermediate-scale anisotropy in the arrival directions of ultrahigh-energy cosmic rays with energies above 57 EeV in the northern sky using data collected over a 5 yr period by the surface detector of the Telescope Array experiment. We report on a cluster of events that we call the hotspot, found by oversampling using 20?? radius circles. The hotspot has a Li-Ma statistical significance of 5.1??, and is centered at R.A. = 146.??7, decl. = 43.??2. The position of the hotspot is about 19?? off of the supergalactic plane. The probability of a cluster of events of 5.1?? significance, appearing by chance in an isotropic cosmic-ray sky, is estimated to be 3.7 ?? 10-4 (3.4??).open2
Pierre Auger Observatory and Telescope Array:Joint Contributions to the 34th International Cosmic Ray Conference (ICRC 2015)
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