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5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark that regulates gene expression. Charting the landscape of 5hmC in human tissues is fundamental to understanding its regulatory functions. Here, we systematically profiled the whole-genome 5hmC landscape at single-base resolution for 19 types of human tissues. We found that 5hmC preferentially decorates gene bodies and outperforms gene body 5mC in reflecting gene expression. Approximately one-third of 5hmC peaks are tissue-specific differentially-hydroxymethylated regions (tsDhMRs), which are deposited in regions that potentially regulate the expression of nearby tissue-specific functional genes. In addition, tsDhMRs are enriched with tissue-specific transcription factors and may rewire tissue-specific gene expression networks. Moreover, tsDhMRs are associated with single-nucleotide polymorphisms identified by genome-wide association studies and are linked to tissue-specific phenotypes and diseases. Collectively, our results show the tissue-specific 5hmC landscape of the human genome and demonstrate that 5hmC serves as a fundamental regulatory element affecting tissue-specific gene expression programs and functions. Charting the landscape of 5hmC in human tissues is fundamental to understanding its regulatory functions. Here, we systematically profiled the whole-genome 5hmC landscape at single-base resolution for 19 types of human tissues and found 5hmC shows tissue-specific patterns.

N 6 ,2′- O -dimethyladenosine (m 6 Am), a terminal modification adjacent to the mRNA cap, is a newly discovered reversible RNA modification. Yet, a specific and sensitive tool to directly map transcriptome-wide m 6 Am is lacking. Here, we report m 6 Am-seq, based on selective in vitro demethylation and RNA immunoprecipitation. m 6 Am-seq directly distinguishes m 6 Am and 5′-UTR N 6 -methyladenosine (m 6 A) and enables the identification of m 6 Am at single-base resolution and 5′-UTR m 6 A in the human transcriptome. Using m 6 Am-seq, we also find that m 6 Am and 5′-UTR m 6 A respond dynamically to stimuli, and identify key functional methylation sites that may facilitate cellular stress response. Collectively, m 6 Am-seq reveals the high-confidence m 6 Am and 5′-UTR m 6 A methylome and provides a robust tool for functional studies of the two epitranscriptomic marks. m 6 Am is a dynamic and reversible RNA modification found on the mRNA cap. Here the authors report m 6 Am-seq to directly distinguish m 6 Am from m 6 A and identify functional methylation sites.

The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality. The molecular mechanism of interaction between host and viral genomic RNA is yet unclear. We demonstrate herein that SARS-CoV-2 genomic RNA, as well as the negative-sense RNA, is dynamically N 6 -methyladenosine (m 6 A)-modified in human and monkey cells. Combined RIP-seq and miCLIP analyses identified a total of 8 m 6 A sites at single-base resolution in the genome. Especially, epidemic strains with mutations at these identified m 6 A sites have emerged worldwide, and formed a unique cluster in the US as indicated by phylogenetic analysis. Further functional experiments showed that m 6 A methylation negatively regulates SARS-CoV-2 infection. SARS-CoV-2 infection also triggered a global increase in host m 6 A methylome, exhibiting altered localization and motifs of m 6 A methylation in mRNAs. Altogether, our results identify m 6 A as a dynamic epitranscriptomic mark mediating the virus–host interaction.

The high-order three-dimensional (3D) organization of regulatory genomic elements provides a topological basis for gene regulation, but it remains unclear how multiple regulatory elements across the mammalian genome interact within an individual cell. To address this, herein, we developed scNanoHi-C, which applies Nanopore long-read sequencing to explore genome-wide proximal high-order chromatin contacts within individual cells. We show that scNanoHi-C can reliably and effectively profile 3D chromatin structures and distinguish structure subtypes among individual cells. This method could also be used to detect genomic variations, including copy-number variations and structural variations, as well as to scaffold the de novo assembly of single-cell genomes. Notably, our results suggest that extensive high-order chromatin structures exist in active chromatin regions across the genome, and multiway interactions between enhancers and their target promoters were systematically identified within individual cells. Altogether, scNanoHi-C offers new opportunities to investigate high-order 3D genome structures at the single-cell level. scNanoHi-C combines Nanopore long-read sequencing with a proximity-ligation-based Hi-C protocol to profile high-order genome structures in individual cells, enabling the capture of multiway interactions among enhancers and promoters.

N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m6A RNA methyltransferases in cotton. Here, a systematic analysis of the m6A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis thaliana, and Homo sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m6A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m6A in subsequent studies to improve the agronomic traits in cotton.

The variations in hydrodynamic parameters at different polysaccharides rates and the relationships between sheet erosion modulus and hydrodynamic parameters were analyzed to reveal the hydrodynamic mechanism of sheet erosion on loessial slopes. Artificially simulated rainfall experiments were carried out under three slope gradients (10°, 15°, and 20°), three rainfall intensities (1.0, 1.5, and 2.0 mm·min −1 ), and four dry-spreading rates of polysaccharides (0, 1, 3, and 5 g·m −2 ). The results showed that (1) four hydrodynamic parameters (flow velocity, shear stress, stream power, and unit stream power) all increased with both rainfall intensities and slope gradients at four rates of polysaccharides. (2) Polysaccharides could effectively reduce hydrodynamic parameters. In contrast to the bare slope, the average flow velocity, shear stress, stream power, and unit stream power diminished by 27.11~41.18%, 9.53~18.67%, 31.82~50.24%, and 27.11~41.18%, respectively. (3) Polysaccharides could effectively reduce the growth rate of the sheet erosion modulus with hydrodynamic parameters, and there were few differences among the different rates (1, 3, and 5 g·m −2 ). The increasing rates of the sheet erosion modulus with flow velocity, shear stress, stream power, and unit stream power were 14.0~65.7%, 14.8~33.9%, 7.8~23.7%, and 9.7~29.5%, respectively. (4) At different polysaccharides rates, the relationships between sheet erosion modulus and hydrodynamic parameters were all in logarithmic functions. Moreover, flow velocity ( R 2  ≥ 0.920) and stream power ( R 2  ≥ 0.876) were better hydrodynamic parameters than shear stress ( R 2  ≥ 0.598) or unit stream power ( R 2  ≥ 0.537). Polysaccharides decreased the hydrodynamic parameters and the response rates of sheet erosion to hydrodynamics.

Raindrops disperse large soil aggregates into smaller particles, which can clog soil pores, cause soil crusting, reduce rainfall infiltration and increase soil loss. It was found that natural polymer derivatives were effective in improving soil physical properties and decreasing soil erosion on an experimental loess hillslope. This study investigated the effect of new natural polymer derivatives (Jag S and Jag C162) on soil properties, rainfall infiltration and sediment yield at four rates of sprayed polymers (0, 1, 3 and 5 g/m2), three rainfall intensities (1, 1.5 and 2 mm/min) and a slope gradient of 15° with a silt loam soil through simulated rain. The results showed that both Jag S and Jag C162 significantly increased the shear strength and improved the aggregates composition of the soil surface. The water-stable soil aggregates >0.25 mm increased from 9% to 50% with increasing rates of Jag S and Jag C162. Jag S and Jag C162 also effectively increased rainfall infiltration and final infiltration rate, and reduced erosion compared to controls without natural polymer derivatives added. However, higher rates of Jag S produced lower infiltration rates. Although both Jag S and Jag C162 effectively influenced soil physical properties and erosion, the effect of Jag C162 was more significant than that of Jag S.

Global warming is increasing the frequency and intensity of heat waves and droughts. One important phase in the life cycle of plants is seed germination. To date, the association of the temperature and water potential thresholds of germination with seed traits has not been explored in much detail. Therefore, we set up different temperature gradients (5–35 °C), water potential gradients (−1.2–0 MPa), and temperature × water potential combinations for nine native plants in the Loess Plateau region to clarify the temperature and water combinations suitable for their germination. Meanwhile, we elucidated the temperature and water potential thresholds of the plants and their correlations with the mean seed mass and flatness index by using the thermal time and hydrotime models. According to our findings, the germination rate was positively correlated with the germination percentage and water potential, with the former rising and the latter decreasing as the temperature increased. Using the thermal time and hydrotime models, the seed germination thresholds could be predicted accurately, and the germination thresholds of the studied species varied with an increase in germination percentage. Moreover, temperature altered the impact of water potential on the germination rate. Overall, the base water potential for germination, but not the temperature threshold, was negatively correlated with mean seed mass and was lower for rounder seeds than for longer seeds. This study contributes to improving our understanding of the seed germination characteristics of typical plants and has important implications for the management and vegetation restoration of degraded grasslands.

ObjectiveRoots can effectively reduce soil detachment. However, the dynamics of different root effects on soil detachment with root growth time are not clearly understood. Therefore, our objectives were to characterize the dynamics of soil detachment with root growth time and compare the effectiveness of roots of different types and planting densities on soil detachment.Materials and methodsA laboratory experiment was conducted to quantify and elucidate the effect of fibrous ryegrass (Lolium perenne L.) roots and alfalfa (Medicago sativa L.) taproots on soil detachment, with two planting densities at 4 different growth stages. Root parameters, soil properties, and the soil detachment rate (with a flow discharge of 3 L min−1 for 15 min on a 15° slope) were measured at days 28, 56, 84, and 112.Results and discussionRoot parameters increased with root growth time, and the fibrous roots varied more significantly than taproots. Soil bulk density decreased with root growth time, while the contents of soil organic matter and water-stable aggregates increased with root growth time. The effect of fibrous roots on soil properties was significantly greater than that of taproots. The absolute soil detachment rate and relative soil detachment rate from fibrous roots decreased by 53.35% and 51.98% from days 28 to 112 respectively, but those from taproots did not change significantly. Soil detachment under high-density cultivation was lower than that under low-density cultivation at the early growth stage but inversely later. Soil detachment decreased exponentially with root parameters, and the equation of root parameters and soil detachment in RL (ryegrass with a low planting density) best explained the soil detachment variation (91.3–96.1%).ConclusionsPlants with fibrous roots had greater effect on soil detachment reduction than those with taproots. Treatments with high planting density had a more significant influence on soil detachment reduction than did those with low planting density at the early growth stage, but the opposite was true later. This experiment helped to explain the mechanism and process of root growth affecting soil detachment and provided a fundamental basis for erosion management practices.

The successful accomplishment of the first telomere-to-telomere human genome assembly, T2T-CHM13, marked a milestone in achieving completeness of the human reference genome. The upcoming era of genome study will focus on fully phased diploid genome assembly, with an emphasis on genetic differences between individual haplotypes. Most existing sequencing approaches only achieved localized haplotype phasing and relied on additional pedigree information for further whole-chromosome scale phasing. The short-read-based Strand-seq method is able to directly phase single nucleotide polymorphisms (SNPs) at whole-chromosome scale but falls short when it comes to phasing structural variations (SVs). To shed light on this issue, we developed a Nanopore sequencing platform-based Strand-seq approach, which we named NanoStrand-seq. This method allowed for de novo SNP calling with high precision (99.52%) and acheived a superior phasing accuracy (0.02% Hamming error rate) at whole-chromosome scale, a level of performance comparable to Strand-seq for haplotype phasing of the GM12878 genome. Importantly, we demonstrated that NanoStrand-seq can efficiently resolve the MHC locus, a highly polymorphic genomic region. Moreover, NanoStrand-seq enabled independent direct calling and phasing of deletions and insertions at whole-chromosome level; when applied to long genomic regions of SNP homozygosity, it outperformed the strategy that combined Strand-seq with bulk long-read sequencing. Finally, we showed that, like Strand-seq, NanoStrand-seq was also applicable to primary cultured cells. Together, here we provided a novel methodology that enabled interrogation of a full spectrum of haplotype-resolved SNPs and SVs at whole-chromosome scale, with broad applications for species with diploid or even potentially polypoid genomes.