Analysis of tomato (Solanum lycopersicum) small RNA data sets revealed the presence of a regulatory cascade affecting disease resistance. The initiators of the cascade are microRNA members of an unusually diverse superfamily in which miR482 and miR2118 are prominent members. Members of this superfamily are variable in sequence and abundance in different species, but all variants target the coding sequence for the P-loop motif in the mRNA sequences for disease resistance proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) motifs. We confirm, using transient expression in Nicotiana benthamiana, that miR482 targets mRNAs for NBS-LRR disease resistance proteins with coiled-coil domains at their N terminus. The targeting causes mRNA decay and production of secondary siRNAs in a manner that depends on RNA-dependent RNA polymerase 6. At least one of these secondary siRNAs targets other mRNAs of a defenserelated protein. The miR482-mediated silencing cascade is suppressed in plants infected with viruses or bacteria so that expression of mRNAs with miR482 or secondary siRNA target sequences is increased. We propose that this process allows pathogen-inducible expression of NBS-LRR proteins and that it contributes to a novel layer of defense against pathogen attack.

The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2-is an iconic species that is endemic to New Zealand 2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes 2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.

Current molecular biology laboratories rely heavily on the purification and manipulation of nucleic acids. Yet, commonly used centrifuge- and column-based protocols require specialised equipment, often use toxic reagents, and are not economically scalable or practical to use in a high-throughput manner. Although it has been known for some time that magnetic beads can provide an elegant answer to these issues, the development of open-source protocols based on beads has been limited. In this article, we provide step-by-step instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols for their use in the high-throughput purification of plasmids, genomic DNA, RNA and total nucleic acid (TNA) from a range of bacterial, animal, plant, environmental and synthetic sources. We also provide a bead-based protocol for bisulfite conversion and size selection of DNA and RNA fragments. Comparison to other methods highlights the capability, versatility, and extreme cost-effectiveness of using magnetic beads. These open-source protocols and the associated webpage (https://bomb.bio) can serve as a platform for further protocol customisation and community engagement.

In plants, RNA-directed DNA methylation (RdDM), a mechanism where epigenetic modifiers are guided to target loci by small RNAs, plays a major role in silencing of transposable elements (TEs) to maintain genome integrity. So far, two RdDM pathways have been identified: RNA Polymerase IV (PolIV)-RdDM and RNA-dependent RNA Polymerase 6 (RDR6)-RdDM. PolIV-RdDM involves a selfreinforcing feedback mechanism that maintains TE silencing, but cannot explain how epigenetic silencing is first initiated. A function of RDR6-RdDM is to reestablish epigenetic silencing of active TEs, but it is unknown if this pathway can induce DNA methylation at naïve, non-TE loci. To investigate de novo establishment of RdDM, we have used virus-induced gene silencing (VIGS) of an active FLOWERING WAGENINGEN epiallele. Using genetic mutants we show that unlike PolIV-RdDM, but like RDR6-RdDM, establishment of VIGS-mediated RdDM requires PolV and DRM2 but not Dicer like-3 and other PolIV pathway components. DNA methylation in VIGS is likely initiated by a process guided by virus-derived small (s) RNAs that are 21/22-nt in length and reinforced or maintained by 24-nt sRNAs. We demonstrate that VIGS-RdDM as a tool for gene silencing can be enhanced by use of mutant plants with increased production of 24-nt sRNAs to reinforce the level of RdDM.RNA-directed DNA methylation | virus-induced gene silencing | epigenetics | Arabidopsis thaliana M ethylation of cytosine (C) residues of DNA is a stable and heritable modification that mediates epigenetic control in eukaryotic genomes. In plants this modification occurs at CG, CHG, and CHH sequences (where H can be C, A, or T) and involves RNA-directed DNA methylation (RdDM) pathways. The DNA methyltransferases in these pathways are guided to target loci by ribonucleoproteins in which a small (s)RNA is the specificity determinant (1, 2).There are two mechanisms to maintain DNA methylation. In RdDM pathways acting at predominantly transposable elements (TEs), SAWADEE HOMEODOMAIN HOMOLOG (SHH)1 binds and recruits RNA Polymerase IV (PolIV) to transcribe methylated DNA (3, 4). The PolIV transcripts are then made double-stranded by RNA-dependent RNA polymerase (RDR)2 and cleaved by Dicer-like 3 (DCL3) into 24-nt sRNAs that are loaded into and guide AGONAUTE (AGO)4 to complementary scaffold RNAs transcribed from the same locus by RNA polymerase V (PolV). The sRNA-bound AGO and the PolV transcript interact and recruit the de novo methyltransferase DRM2 that modifies C residues of the DNA strand acting as the template for PolV (5).Maintenance of CG and CHG methylation during DNA replication occurs via MET1, the plant homolog of the mammalian DNA methyltransferase DNMT1, and the plant-specific CHROMOMETHYLASE 3 (CMT3) that works in concert with the SU(VAR)3-9 HOMOLOG (SUVH) SET domain histone methyltransferse KRYPTONITE. Both MET1 and CMT3 act independently of sRNAs but maintenance of CHH methylation within euchromatin is dependent on the continuous operation of the sRNA establishment mechanism, resulting in a self-...

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The quantitative induction of VIN3 by low temperatures is required for PRC2 repression of FLC and promotion of flowering (vernalization) in Arabidopsis. Histone acetylation, a chromatin modification commonly associated with gene transcription, increased on VIN3 chromatin in two spatially and temporally distinct phases in response to low temperatures. During short-term cold exposure, histone H3 acetylation at the transcription start site rapidly increased, implying that it is required for VIN3 induction. Subsequent changes in histone H3 and H4 acetylation occurred following continued VIN3 transcription during prolonged cold exposure. Members of the SAGA-like transcriptional adaptor complex, including the histone acetyltransferase GCN5, which induces expression of the cold acclimation pathway genes, do not regulate VIN3 induction during cold exposure, indicating that the cold acclimation pathway and the cold-induction of VIN3 are regulated by different transcriptional mechanisms. Mutations in the other 11 histone acetyltransferase genes did not affect VIN3 induction. However, nicotinamide, a histone deacetylase inhibitor, induced VIN3 and altered histone acetylation at the VIN3 locus. VIN3 induction was proportional to the length of nicotinamide treatment, which was associated with an early-flowering phenotype and repression of FLC. However, unlike vernalization, the repression of FLC was independent of VIN3 activity. Nicotinamide treatment did not cause a change in the expression of any genes in the autonomous pathway or members of the PRC2 complex, the well characterized repressors of FLC. Our data suggest that FLC is repressed via a novel pathway involving the SIR2 class of histone deacetylases.

19Current molecular biology laboratories rely heavily on the purification and manipulation of 20 nucleic acids. Yet, commonly used centrifuge-and column-based protocols require 21 specialised equipment, often use toxic reagents and are not economically scalable or practical 22 to use in a high-throughput manner. Although it has been known for some time that magnetic 23 beads can provide an elegant answer to these issues, the development of open-source 24 protocols based on beads has been limited. In this article, we provide step-by-step 25 instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols 26 for their use in the high-throughput purification of plasmids, genomic DNA and total RNA from 27 different sources, as well as environmental TNA and PCR amplicons. We also provide a bead-28 based protocol for bisulfite conversion, and size selection of DNA and RNA fragments. 29Comparison to other methods highlights the capability, versatility and extreme cost-30 effectiveness of using magnetic beads. These open source protocols and the associated 31 webpage (https://bomb.bio) can serve as a platform for further protocol customisation and 32 community engagement. 33 3 Abbreviations 34 BOMB: Bio-On-Magnetic-Beads 35 SPRI: Solid-Phase Reversible Immobilisation 36 MNP: magnetic nanoparticle 37 38The authors would like to thank all members of the Jurkowski and Hore laboratories for 456helping to optimise and test the BOMB protocols. We are also indebted to Ken Wyber (Otago 457Polytechnic) for help with laser cutting magnetic plates. We are grateful to Dr. Renata 458Jurkowska for critical reading of the manuscript. We would like to thank the wider research 459 community for offering unpublished information and resources concerning magnetic bead 460 22 preparation and utility, in particular, Dr Ethan Ford, Dr James Hadfield, Dr Brant Faircloth, Dr 461 Nadin Rohland and associated authors. 462 Author's contribution 463 The idea was conceived by TPJ and TH. Protocol setup and optimisation was led by PO, PS, 464 DB, TPJ and TH, with contributions from SH, JF, VM, LS, VJS, G-JJ and FvM. Laser cutting 465 designs were contributed by SRH. The electron microscope analysis was done by KH. The 466 website and its content were created by TM, PS, PO, TPJ and TH. The manuscript was written 467 by TPJ, TH, PS and PO. All authors contributed to the editing of the manuscript and approved 468 its final version. 469

SUMMARYVERNALIZATION INSENSITIVE 3 (VIN3), which is required for the vernalization-mediated epigenetic repression of FLOWERING LOCUS C (FLC) in Arabidopsis thaliana, is quantitatively induced in response to low temperatures. We found that hypoxic conditions also induce VIN3 in a quantitative manner but high salt, high temperatures and osmotic stress do not. Inhibition of mitochondrial respiration did not induce VIN3 expression, consistent with the lack of VIN3 induction in response to other stresses that affect the rate of mitochondrial respiration. De novo protein synthesis is required for VIN3 induction during hypoxic conditions; this situation is not the case for VIN3 induction by low temperatures, indicating that different mechanisms act to induce VIN3 expression in response to cold and hypoxic conditions. Without VIN3 activity, fewer seedlings survived following a 72-h period of hypoxic treatment, indicating that VIN3 is required for the survival of Arabidopsis thaliana in response to hypoxic stress. Complementation of the vin3 mutant with a VIN3 transgene restored the wild-type response to low oxygen and confirmed the role of VIN3 in protecting both shoots and roots during low oxygen conditions. Loss of VIN3 protein did not affect the transcriptional regulation of genes known to be important in the response to low oxygen stress, which suggests that there is a novel mechanism to combat hypoxia that involves VIN3. This mechanism is likely to involve chromatin remodelling and may be similar to the role of VIN3 in the epigenetic repression of FLC during the vernalization response.