Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, ...histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants, especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable-element (TE) proliferation, but a substantial number of distal CREs also seem to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression.
•cis-regulatory elements are enriched within accessible chromatin regions (ACRs).•Sequence variation within ACRs disproportionately affects transcription.•Conservation in ACRs is primarily limited to ...transcription factor binding sites.•Many ACRs show dynamic responses to developmental and environmental cues.•Gene-distal ACRs and cis-regulatory elements are common in large plant genomes.
The systematic identification of cis-regulatory elements (CREs) in plant genomes is critically important in understanding transcriptional regulation during development and in response to environmental cues. Several genome-wide structure-based methods have been successfully applied to plant genomes in the past few years. Here, we review recent results on the identification and characterization of CREs in multiple plant species and in different biological processes and discuss future applications of chromatin accessibility data to understand the mechanism, function and evolution of transcriptional regulation networks.
Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a widely used method for mapping the genome-wide locations of chromatin-associated proteins. This protocol has been developed and ...utilized to perform ChIP on histone covalent modifications in various plant species including cereals. DNA and chromatin-associated proteins are crosslinked with formaldehyde. Chromatin is then isolated from nuclei and sheared via sonication. Antibodies targeting the histone modification of interest are incubated with the sheared chromatin and nonspecific interactions are washed away. DNA is purified via phenol-chloroform extraction, end-repaired, ligated to sequencing adapters, and PCR-amplified.
Members of the PIF/Harbinger superfamily share several characteristics: they have short terminal inverted repeats (TIRs), prefer to insert into 3-bp target sites embedded in longer palindromic ...sequences, and encode two proteins (a Myb-like DNA-binding protein and a TPase) that are both required for transposition 8,9. ...there are several important differences: (1) PIF- and Pong-like elements are present at moderate-to-high copy numbers in plant genomes (from dozens in Arabidopsis to ~1,000 in Brassica oleracea), whereas ALP1-like genes are present at single copy in land plants; (2) the DDE catalytic motif in PIF-like TPases is mutated in ALP1 and its homologues in angiosperms (but not in gymnosperms, ferns, bryophtyes, and green algae) and the Myb-like gene and TIRs are missing from ALP1 flanking sequences; and (3) the majority of PIF-like elements are transcriptionally silent and have accumulated missense or nonsense mutations, whereas ALP1 is broadly expressed in Arabidopsis leaves, stems, flowers, and roots, and its coding capacity is well preserved in land plants 1.
Changes in ambient temperature immensely affect developmental programs in many species. Plants adapt to high ambient growth temperature in part by vegetative and reproductive developmental ...reprogramming, known as thermo-morphogenesis. Thermo-morphogenesis is accompanied by massive changes in the transcriptome upon temperature change. Here, we show that transcriptome changes induced by warm ambient temperature require VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1), a facultative component of the Polycomb repressive complex PRC2, in Arabidopsis. Warm growth temperature elicits genome-wide accumulation of H3K27me3 and VIL1 is necessary for the warm temperature-mediated accumulation of H3K27me3. Consistent with its role as a mediator of thermo-morphogenesis, loss of function of VIL1 results in hypo-responsiveness to warm ambient temperature. Our results show that VIL1 is a major chromatin regulator in responses to high ambient temperature.
Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene-distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, ...they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic and functional molecular evidence to support the widespread existence of gene-distal (hereafter, distal) loci that act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate genetic interactions. Putative CREs also display elevated transcriptional enhancer activities, as measured by self-transcribing active regulatory region sequencing. These results provide functional support for the widespread existence of CREs that act over large genomic distances to control gene expression.
Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes ...including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.
Abstract
Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an ...organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations. Integration of epigenomic data into genome annotation is one such approach. In this study, we utilized sets of histone modification data, which are precisely distributed at either gene bodies or promoters to evaluate the annotation of the Zea mays genome. We leveraged these data genome wide, allowing for identification of annotations discordant with empirical data. In total, 13,159 annotation discrepancies were found in Z. mays upon integrating data across three different tissues, which were corroborated using RNA-based approaches. Upon correction, genes were extended by an average of 2128 base pairs, and we identified 2529 novel genes. Application of this method to five additional plant genomes identified a series of misannotations, as well as identified novel genes, including 13,836 in Asparagus officinalis, 2724 in Setaria viridis, 2446 in Sorghum bicolor, 8631 in Glycine max, and 2585 in Phaseolous vulgaris. This study demonstrates that histone modification data can be leveraged to rapidly improve current genome annotations across diverse plant lineages.
The clinical effect of a drug-eluting stent in the femoropopliteal segment has not been investigated in a randomised trial with a contemporary comparator. The IMPERIAL study sought to compare the ...safety and efficacy of the polymer-coated, paclitaxel-eluting Eluvia stent with the polymer-free, paclitaxel-coated Zilver PTX stent for treatment of femoropopliteal artery segment lesions.
In this randomised, single-blind, non-inferiority study, patients with symptomatic lower-limb ischaemia manifesting as claudication (Rutherford category 2, 3, or 4) with atherosclerotic lesions in the native superficial femoral artery or proximal popliteal artery were enrolled at 65 centres in Austria, Belgium, Canada, Germany, Japan, New Zealand, and the USA. Patients were randomly assigned (2:1) with a site-specific, web-based randomisation schedule to receive treatment with Eluvia or Zilver PTX. All patients, site personnel, and investigators were masked to treatment assignment until all patients had completed 12 months of follow-up. The primary efficacy endpoint was primary patency (defined as a peak systolic velocity ratio ≤2·4, without clinically driven target lesion revascularisation or bypass of the target lesion) and the primary safety endpoint was major adverse events (ie, all causes of death through 1 month, major amputation of target limb through 12 months, and target lesion revascularisation through 12 months). We set a non-inferiority margin of −10% at 12 months. Primary non-inferiority analyses were done when the minimum sample size required for adequate statistical power had completed 12 months of follow-up. The primary safety non-inferiority analysis included all patients who had completed 12 months of follow-up or had a major adverse event through 12 months. This trial is registered with ClinicalTrials.gov, number NCT02574481.
Between Dec 2, 2015, and Feb 15, 2017, 465 patients were randomly assigned to Eluvia (n=309) or to Zilver PTX (n=156). Non-inferiority was shown for both efficacy and safety endpoints at 12 months: primary patency was 86·8% (231/266) in the Eluvia group and 81·5% (106/130) in the Zilver PTX group (difference 5·3% one-sided lower bound of 95% CI −0·66; p<0·0001). 259 (94·9%) of 273 patients in the Eluvia group and 121 (91·0%) of 133 patients in the Zilver PTX group had not had a major adverse event at 12 months (difference 3·9% one-sided lower bound of 95% CI −0·46; p<0.0001). No deaths were reported in either group. One patient in the Eluvia group had a major amputation and 13 patients in each group required target lesion revascularisation.
The Eluvia stent was non-inferior to the Zilver PTX stent in terms of primary patency and major adverse events at 12 months after treatment of patients for femoropopliteal peripheral artery disease.
Boston Scientific.
In January 2012, on the basis of an initial report from a dermatologist, we began to investigate an outbreak of tattoo-associated Mycobacterium chelonae skin and soft-tissue infections in Rochester, ...New York. The main goals were to identify the extent, cause, and form of transmission of the outbreak and to prevent further cases of infection.
We analyzed data from structured interviews with the patients, histopathological testing of skin-biopsy specimens, acid-fast bacilli smears, and microbial cultures and antimicrobial susceptibility testing. We also performed DNA sequencing, pulsed-field gel electrophoresis (PFGE), cultures of the ink and ingredients used in the preparation and packaging of the ink, assessment of source water and faucets at tattoo parlors, and investigation of the ink manufacturer.
Between October and December 2011, a persistent, raised, erythematous rash in the tattoo area developed in 19 persons (13 men and 6 women) within 3 weeks after they received a tattoo from a single artist who used premixed gray ink; the highest occurrence of tattooing and rash onset was in November (accounting for 15 and 12 patients, respectively). The average age of the patients was 35 years (range, 18 to 48). Skin-biopsy specimens, obtained from 17 patients, showed abnormalities in all 17, with M. chelonae isolated from 14 and confirmed by means of DNA sequencing. PFGE analysis showed indistinguishable patterns in 11 clinical isolates and one of three unopened bottles of premixed ink. Eighteen of the 19 patients were treated with appropriate antibiotics, and their condition improved.
The premixed ink was the common source of infection in this outbreak. These findings led to a recall by the manufacturer.
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