A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana Researchers used high-throughput pyrosequencing to analyze 887,000 small RNA reads from Arabidopsis thaliana, revealing 340,000 unique sequences, a much greater diversity than previously observed in any species. Most of these small RNAs had the properties of heterochromatic small interfering RNAs (siRNAs), being 24 nucleotides long and mapping to intergenic regions. They were most densely found in the proximal and distal pericentromeric regions, with a slight preference for matching repetitive elements. Additionally, 38 new microRNAs (miRNAs) and dozens of other candidates were identified. One miRNA was found within an intron of DICER-LIKE 1 (DCL1), suggesting a second homeostatic autoregulatory mechanism for DCL1 expression. Another miRNA defined the phase for siRNAs derived from a newly identified trans-acting siRNA gene (TAS4). Two miRNAs depended on DCL4 rather than DCL1 for their accumulation, indicating a second pathway for miRNA biogenesis in plants. The study revealed a layer of miRNA-based control that is evolutionarily more fluid, employing many newly emergent and diverse miRNAs, each expressed in specialized tissues or at low levels under standard growth conditions. The study also identified a new tasiRNA gene (TAS4) in Arabidopsis, which produces siRNAs that target MYB transcripts. The TAS4 locus was found to be trans-acting, and its siRNAs were validated experimentally. The study further showed that the TAS4 siRNAs and miR828 have a close functional evolutionary relationship. The research also identified other endogenous siRNAs in Arabidopsis that mapped predominantly to intergenic regions. These siRNAs were mostly 24mers, associated with PolIV, heterochromatin formation, and DNA methylation. The study also found that some protein-coding genes had a high propensity for spawning small RNAs, with many of these genes being convergently transcribed with neighboring genes. Additionally, candidate siRNAs were found to be preferentially derived from pericentromeric regions, with a slight preference for repeats. The study highlights the diversity and evolutionary fluidity of miRNAs in Arabidopsis, suggesting that many miRNAs are expressed in specialized tissues or at low levels under standard growth conditions.A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana Researchers used high-throughput pyrosequencing to analyze 887,000 small RNA reads from Arabidopsis thaliana, revealing 340,000 unique sequences, a much greater diversity than previously observed in any species. Most of these small RNAs had the properties of heterochromatic small interfering RNAs (siRNAs), being 24 nucleotides long and mapping to intergenic regions. They were most densely found in the proximal and distal pericentromeric regions, with a slight preference for matching repetitive elements. Additionally, 38 new microRNAs (miRNAs) and dozens of other candidates were identified. One miRNA was found within an intron of DICER-LIKE 1 (DCL1), suggesting a second homeostatic autoregulatory mechanism for DCL1 expression. Another miRNA defined the phase for siRNAs derived from a newly identified trans-acting siRNA gene (TAS4). Two miRNAs depended on DCL4 rather than DCL1 for their accumulation, indicating a second pathway for miRNA biogenesis in plants. The study revealed a layer of miRNA-based control that is evolutionarily more fluid, employing many newly emergent and diverse miRNAs, each expressed in specialized tissues or at low levels under standard growth conditions. The study also identified a new tasiRNA gene (TAS4) in Arabidopsis, which produces siRNAs that target MYB transcripts. The TAS4 locus was found to be trans-acting, and its siRNAs were validated experimentally. The study further showed that the TAS4 siRNAs and miR828 have a close functional evolutionary relationship. The research also identified other endogenous siRNAs in Arabidopsis that mapped predominantly to intergenic regions. These siRNAs were mostly 24mers, associated with PolIV, heterochromatin formation, and DNA methylation. The study also found that some protein-coding genes had a high propensity for spawning small RNAs, with many of these genes being convergently transcribed with neighboring genes. Additionally, candidate siRNAs were found to be preferentially derived from pericentromeric regions, with a slight preference for repeats. The study highlights the diversity and evolutionary fluidity of miRNAs in Arabidopsis, suggesting that many miRNAs are expressed in specialized tissues or at low levels under standard growth conditions.