| 1. |
- Derkacheva, Maria, et al.
(författare)
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H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system
- 2016
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Ingår i: Nature plants. - 2055-026X .- 2055-0278. ; 2:9
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Tidskriftsartikel (refereegranskat)abstract
- Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.
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| 2. |
- Derkacheva, Maria, et al.
(författare)
-
H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system
- 2016
-
Ingår i: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 2
-
Tidskriftsartikel (refereegranskat)abstract
- Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.
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| 3. |
- Gentry, Matthew, et al.
(författare)
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A Structural Bisulfite Assay to Identify DNA Cruciforms
- 2016
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Ingår i: Molecular Plant. - : Elsevier BV. - 1674-2052 .- 1752-9867. ; 9, s. 1328-1336
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Tidskriftsartikel (refereegranskat)abstract
- In the half century since the discovery of the double-helix structure of DNA, it has become increasingly clear that DNA functionality is based on much more than its sequence in a double-helical structure. Further advances have highlighted the importance of additional aspects of DNA structure: its packaging in the higher order chromatin structure, positioning of nucleosomes along the DNA, and the occurrence of non-helical DNA structures. Of these, the latter has been problematic to prove empirically. Here, we describe a method that uses non-denaturing bisulfite sequencing on isolated Arabidopsis thaliana nuclei to determine the location of cytosines positioned outside the double helix as a result of non-B-form DNA structures. We couple this with computational methods and S1 nuclease digest to reliably identify stable, non-B-form, cruciform structures. This enables us to identify a palindrome in the promoter of FLOWERING LOCUS T that forms a stable non-B-form structure. The stronger conservation of the ability to form a non-helical secondary structure than of the sequence suggests that this structure is biologically relevant.
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| 4. |
- Gentry, Matthew
(författare)
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Local heat, local food: Integrating vertical hydroponic farming with district heating in Sweden
- 2019
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Ingår i: Energy. - : Elsevier BV. - 0360-5442 .- 1873-6785. ; 174, s. 191-197
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Forskningsöversikt (refereegranskat)abstract
- By 2050, it is estimated that 70% of the world's population will live in urban areas. This growth in cities creates a demand for fresh produce to ensure a healthy population, produce that often has to travel a long way to reach the consumer, not only losing quality and nutrition along the way, but also requiring a significant fossil fuel cost for transportation and storage. The average plate of food will travel over 2400 km before it reaches your plate. There is potential within District heating (DH) areas to move farming indoors and into the heart of the urban environment. Vertical hydroponic farming (VHF) offers many advantages over conventional farming including more efficient water and land use, and vastly reduced transport costs if it is performed in the urban area. For this model to become economically sustainable however, it must be intelligently integrated into existing urban infrastructure. A mutually beneficial relationship with DH is possible whereby VHFs are integrated to feed back into the DH system, lower the return temperature in line with 4th Generation District Heating guidelines, and reduce CO2 emissions in food and energy production. Crown Copyright (C) 2019 Published by Elsevier Ltd. All rights reserved.
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| 5. |
- Gentry, Matthew, et al.
(författare)
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Remodelling chromatin to shape development of plants
- 2014
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Ingår i: Experimental Cell Research. - : Elsevier BV. - 0014-4827 .- 1090-2422. ; 321, s. 40-46
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Forskningsöversikt (refereegranskat)abstract
- Establishment and dynamic regulation of a higher order chromatin structure is an essential component of development. Chromatin remodelling complexes such as the SWI2/SNF2 family of ATP-dependent chromatin remodellers can alter chromatin architecture by changing nucleosome positioning or substituting histones with histone variants. These remodellers often act in concert with chromatin modifiers such as the polycomb group proteins which confer repressive states through modification of histone tails. These mechanisms are highly conserved across the eukaryotic kingdom although in plants, owing to the maintenance of dedifferentiated cell states that allow for post-embytonic changes in development, strict control of chromatin remodelling is even more paramount. Recent and ongoing studies in the model plant Arabidopsis thaliana have found that while the major families of the SWI2/SNF2 ATPase chromatin remodellers are represented, a number of redundancies and divergent functions have emerged that show a break from the roles of their metazoan counterparts. This review focusses on the SNF2 and CHD families of ATP-dependent remodellers and their roles in plant development. (C) 2013 Elsevier Inc. All rights reserved.
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| 6. |
- Lawrenson, Kate, et al.
(författare)
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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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