ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3′ Ends of ZNF Genes

Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that genes for the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. One current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 both in vivo and in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3′ ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNF that is involved in recruitment of the KAP1 and SETDB1 to specific regions of the human genome

Assessment of carbon in woody plants and soil across a vineyard-woodland landscape

<p>Abstract</p> <p>Background</p> <p>Quantification of ecosystem services, such as carbon (C) storage, can demonstrate the benefits of managing for both production and habitat conservation in agricultural landscapes. In this study, we evaluated C stocks and woody plant diversity across vineyard blocks and adjoining woodland ecosystems (wildlands) for an organic vineyard in northern California. Carbon was measured in soil from 44 one m deep pits, and in aboveground woody biomass from 93 vegetation plots. These data were combined with physical landscape variables to model C stocks using a geographic information system and multivariate linear regression.</p> <p>Results</p> <p>Field data showed wildlands to be heterogeneous in both C stocks and woody tree diversity, reflecting the mosaic of several different vegetation types, and storing on average 36.8 Mg C/ha in aboveground woody biomass and 89.3 Mg C/ha in soil. Not surprisingly, vineyard blocks showed less variation in above- and belowground C, with an average of 3.0 and 84.1 Mg C/ha, respectively.</p> <p>Conclusions</p> <p>This research demonstrates that vineyards managed with practices that conserve some fraction of adjoining wildlands yield benefits for increasing overall C stocks and species and habitat diversity in integrated agricultural landscapes. For such complex landscapes, high resolution spatial modeling is challenging and requires accurate characterization of the landscape by vegetation type, physical structure, sufficient sampling, and allometric equations that relate tree species to each landscape. Geographic information systems and remote sensing techniques are useful for integrating the above variables into an analysis platform to estimate C stocks in these working landscapes, thereby helping land managers qualify for greenhouse gas mitigation credits. Carbon policy in California, however, shows a lack of focus on C stocks compared to emissions, and on agriculture compared to other sectors. Correcting these policy shortcomings could create incentives for ecosystem service provision, including C storage, as well as encourage better farm stewardship and habitat conservation.</p

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1

Genomic Targets of Brachyury (T) in Differentiating Mouse Embryonic Stem Cells

The T-box transcription factor Brachyury (T) is essential for formation of the posterior mesoderm and the notochord in vertebrate embryos. Work in the frog and the zebrafish has identified some direct genomic targets of Brachyury, but little is known about Brachyury targets in the mouse.Here we use chromatin immunoprecipitation and mouse promoter microarrays to identify targets of Brachyury in embryoid bodies formed from differentiating mouse ES cells. The targets we identify are enriched for sequence-specific DNA binding proteins and include components of signal transduction pathways that direct cell fate in the primitive streak and tailbud of the early embryo. Expression of some of these targets, such as Axin2, Fgf8 and Wnt3a, is down regulated in Brachyury mutant embryos and we demonstrate that they are also Brachyury targets in the human. Surprisingly, we do not observe enrichment of the canonical T-domain DNA binding sequence 5'-TCACACCT-3' in the vicinity of most Brachyury target genes. Rather, we have identified an (AC)(n) repeat sequence, which is conserved in the rat but not in human, zebrafish or Xenopus. We do not understand the significance of this sequence, but speculate that it enhances transcription factor binding in the regulatory regions of Brachyury target genes in rodents.Our work identifies the genomic targets of a key regulator of mesoderm formation in the early mouse embryo, thereby providing insights into the Brachyury-driven genetic regulatory network and allowing us to compare the function of Brachyury in different species

Heterochromatin and the molecular mechanisms of 'parent-of-origin' effects in animals.

Twenty five years ago it was proposed that conserved components of constitutive heterochromatin assemble heterochromatinlike complexes in euchromatin and this could provide a general mechanism for regulating heritable (cell-to-cell) changes in gene expressibility. As a special case, differences in the assembly of heterochromatin-like complexes on homologous chromosomes might also regulate the parent-of-origin-dependent gene expression observed in placental mammals. Here, the progress made in the intervening period with emphasis on the role of heterochromatin and heterochromatin-like complexes in parent-of-origin effects in animals is reviewed

Considering Soil Potassium Pools with Dissimilar Plant Availability

Soil potassium (K) has traditionally been portrayed as residing in four functional pools: solution K, exchangeable K, interlayer (sometimes referred to as “fixed” or “nonexchangeable”) K, and structural K in primary minerals. However, this four-pool model and associated terminology have created confusion in understanding the dynamics of K supply to plants and the fate of K returned to the soil in fertilizers, residues, or waste products. This chapter presents an alternative framework to depict soil K pools. The framework distinguishes between micas and feldspars as K-bearing primary minerals, based on the presence of K in interlayer positions or three-dimensional framework structures, respectively; identifies a pool of K in neoformed secondary minerals that can include fertilizer reaction products; and replaces the “exchangeable” K pool with a pool defined as “surface-adsorbed” K, identifying where the K is located and the mechanism by which it is held rather than identification based on particular soil testing procedures. In this chapter, we discuss these K pools and their behavior in relation to plant K acquisition and soil K dynamics

Topographic and geologic controls on soil variability in California's sierra Nevada foothill region

We evaluated the feasibility of quantitative soil mapping in two catenas established on different lithologies (metavolcanic and granitic) in the Sierra Foothill Region of California. Indices of landform and microclimate were extracted from a 1-m elevation model. Variation in soil "character" (clay content, pH, color, cation-exchange capacity [CEC], and Feo/Fed) was partitioned across variables associated with terrain shape and microclimate, lithologic variability, and sampling depth. The potential for using digital elevation models (DEM)-derived indices of terrain shape to predict spatial patterns in soil properties varied greatly between our two experimental catenas. Terrain shape accounted for 4% (metavolcanic site) to 30% (granitic site) of variance in soil properties, while lithology accounted for 14% (metavolcanic site) to 22% (granitic site) of variance in soil properties. Sample depth accounted for 3% (metavolcanic site) to 12% (granitic site) of variance in soil properties. At the metavolcanic site, variability in lithology contributed more to soil variation than terrain shape, which makes digital soil modeling efforts a challenge in these regions. Up to 66% of the variance in soil properties was explained at the granitic site when considering terrain, lithology, sample depth, and associated interactions of these variables. Variance proportions can provide insight into the relative importance of soil-forming factors and is a useful tool when evaluating the efficacy of digital soil mapping projects

Topographic and geologic controls on soil variability in California's sierra Nevada foothill region

We evaluated the feasibility of quantitative soil mapping in two catenas established on different lithologies (metavolcanic and granitic) in the Sierra Foothill Region of California. Indices of landform and microclimate were extracted from a 1-m elevation model. Variation in soil "character" (clay content, pH, color, cation-exchange capacity [CEC], and Feo/Fed) was partitioned across variables associated with terrain shape and microclimate, lithologic variability, and sampling depth. The potential for using digital elevation models (DEM)-derived indices of terrain shape to predict spatial patterns in soil properties varied greatly between our two experimental catenas. Terrain shape accounted for 4% (metavolcanic site) to 30% (granitic site) of variance in soil properties, while lithology accounted for 14% (metavolcanic site) to 22% (granitic site) of variance in soil properties. Sample depth accounted for 3% (metavolcanic site) to 12% (granitic site) of variance in soil properties. At the metavolcanic site, variability in lithology contributed more to soil variation than terrain shape, which makes digital soil modeling efforts a challenge in these regions. Up to 66% of the variance in soil properties was explained at the granitic site when considering terrain, lithology, sample depth, and associated interactions of these variables. Variance proportions can provide insight into the relative importance of soil-forming factors and is a useful tool when evaluating the efficacy of digital soil mapping projects

Mapping time-to-trafficability for California agricultural soils after dormant season deep wetting

Soil compaction is a threat to agricultural soil function due to constriction of macro- and meso-pores necessary for air and water movement and crop root elongation. Soils are most vulnerable to compaction when moist. Agricultural soils saturated from winter precipitation or from intentional flooding for groundwater recharge may limit growers’ operational access to fields. The objective of this research was to develop guidance for rain-free “time-to-trafficability” (including shallow workability—when a soil is conducive to both tillage and traffic) after deep wetting, using soil survey data, pedotransfer functions, and a hydroclimatological modeling approach. Trafficability is defined as a threshold of field capacity (θfc) at the soil surface (0–10 cm), ranging from 85% of θfc (clays and silty clays) to 95% of θfc (sands and loamy sands). The θfc threshold is guided by the soil texture plasticity index, an indicator of compaction risk. 2911 soil profiles from soil survey databases were subjected to a wetting simulation, followed by drainage and evaporation using HYDRUS-1D across 11 locations representing mean annual potential evapotranspiration (PET) quantiles from 5% to 95%, four months (January-April), and three different years, assuming no precipitation. Rain-free time-to-trafficability was greatest in fine and loamy soils during cold months (January and February). However, seasonal effects on time-to-trafficability were more pronounced in loamy soils. Non-linear predictive functions were developed for each 0–10 cm textural class to enable mapping the typical time-to-trafficability across PET gradients, revealing clear regional and temporal patterns. Model derived estimates can inform agricultural managed aquifer recharge timing decisions and subsequent risk of soil compaction. Additional research is needed for validation and to better constrain time-to-trafficability estimates for loamy and fine textured soils, which show a greater degree of uncertainty amid greater risk of compaction indicated by plasticity indices