Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain.

Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.

Family-Wide Characterization of Histone Binding Abilities of PHD Domains of AL Proteins in Arabidopsis thaliana.

Alfin1-like (AL) is a family of proteins homologous to the alfalfa Alfin1 in plant and bears an Alfin domain and a PHD domain at their N- and C-terminus, respectively. There are 7 AL proteins in Arabidopsis, and the PHD domains of most AL proteins are reported to bind to histone H3K4me3. Here we reported gene cloning, protein expression and purification of the PHD domains of all the AL family proteins in Arabidopsis. We then systematically characterized their histone binding abilities by quantitative isothermal titration calorimetry and fluorescence polarization binding assays. Our binding results indicate that all the PHD domains of the AL proteins bind to the histone H3K4me3 peptide with varying methylation state preference and binding affinities. Our study presented here provides the foundation for further studies of the peptide state-specific recognition by PHD domains of AL proteins.

Dynamics of major air pollutants from crop residue burning in mainland China, 2000-2014.

Based on satellite image data and China's Statistical Yearbooks (2000 to 2014), we estimated the total mass of crop residue burned, and the proportion of residue burned in the field vs. indoors as domestic fuel. The total emissions of various pollutants from the burning of crop residue were estimated for 2000-2014 using the emission factor method. The results indicate that the total amount of crop residue and average burned mass were 8690.9Tg and 4914.6Tg, respectively. The total amount of emitted pollutants including CO2, CO, NOx, VOCs, PM2.5, OC (organic carbon), EC (element carbon) and TC (total carbon) were 4212.4-8440.9Tg, 192.8-579.4Tg, 4.8-19.4Tg, 18.6-61.3Tg, 18.8-49.7Tg, 6.7-31.3Tg, 2.3-4.7Tg, and 8.5-34.1Tg, respectively. The emissions of pollutants released from crop residue burning were found to be spatially variable, with the burning of crop residue mainly occurring in Northeast, North and South China. In addition, pollutant emissions per unit area (10 km × 10 km) were mostly concentrated in the central and eastern regions of China. Emissions of CO2, NOx, VOCs, OC and TC were mainly from rice straw burning, while burning of corn and wheat residues contributed most to emissions of CO, PM2.5 and EC. The increased ratio of PM2.5 emissions from crop residue burning to the total emitted from industry during the study period is attributed to the implementation of strict emissions management policies in Chinese industry. This study also provides baseline data for assessment of the regional atmospheric environment.

Structural and histone binding studies of the chromo barrel domain of TIP60.

Tat-interactive protein 60 consists of an N-terminal chromo barrel domain (TIP60-CB) and a C-terminal acetyltransferase domain and acetylates histone and nonhistone proteins in diverse cellular processes. While TIP60-CB is thought to recognize histone tails, molecular details of this interaction remain unclear. Here, we attempted a quantitative analysis of the interaction between the human TIP60-CB and histone peptides, but did not observe any detectable binding by either fluorescence polarization or isothermal titration calorimetry assays. We also determined the crystal structure of the TIP60-CB alone. Analysis of the apo-structure reveals a putative peptide-binding site that might be occluded by the basic side chain of a residue in a unique ß hairpin between the two N-terminal strands of the ß barrel, leading to the inability of TIP60-CB to bind histones.

Understanding fire drivers and relative impacts in different Chinese forest ecosystems.

In this study, spatial patterns and driving factors of fires were identified from 2000 to 2010 using Ripley's K (d) function and logistic regression (LR) model in two different forest ecosystems of China: the boreal forest (Daxing'an Mountains) and sub-tropical forest (Fujian province). Relative effects of each driving factor on fire occurrence were identified based on standardized coefficients in the LR model. Results revealed that fires were spatially clustered and that fire drivers vary amongst differing forest ecosystems in China. Fires in the Daxing'an Mountains respond primarily to human factors, of which infrastructure is recognized as the most influential. In contrast, climate factors played a critical role in fire occurrence in Fujian, of which the temperature of fire season was found to be of greater importance than other climate factors. Selected factors can predict nearly 80% of the total fire occurrence in the Daxing'an Mountains and 66% in Fujian, wherein human and climate factors contributed the greatest impact in the two study areas, respectively. This study suggests that different fire prevention and management strategies are required in the areas of study, as significant variations of the main fire-driving exist. Rapid socio-economic development has produced similar effects in different forest ecosystems within China, implying a strong correlation between socio-economic development and fire regimes. It can be concluded that the influence of human factors will increase in the future as China's economy continues to grow - an issue of concern that should be further addressed in future national fire management.