Hi-Tag:a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin immunoprecipitation.However,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science research.Here,we develop a novel method,Hi-Tag,that identifies high-resolution,long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation(with a phosphorothioate-modified linker).Hi-Tag can be implemented using as few as 100,000 cells,involving simple experimental procedures that can be completed within 1.5 days.Meanwhile,Hi-Tag is capable of using its own data to identify the binding sites of specific proteins,based on which,it can acquire accurate interaction information.Our results suggest that Hi-Tag has great potential for advancing chromatin interaction studies,particularly in the context of limited cell availability.

3C-based methods to detect long-range chromatin interactions

Transcriptional regulatory regions are often located several thousand bases from the gene that they control.To function, the chromatin strand forms loops to juxtapose distal regions with the promoter. These long-rangechromatin interactions have profound influences on the regulation of gene expression and mapping these interactions iscurrently a subject of intensive investigation. Chromosome conformation capture (3C) technology and its derivativeshave been widely used to detect chromatin interactions and greatly contributed to understanding of the relationshipbetween genome organization and genome function. Here we review these 3C-based methods for the study of long-rangechromatin interactions and recent exciting findings obtained by using these technologies.

THE VLASOV-POISSON-BOLTZMANN SYSTEM NEAR MAXWELLIANS FOR LONG-RANGE INTERACTIONS

In this article, we are concerned with the construction of global smooth small-amplitude solutions to the Cauchy problem of the one species Vlasov-Poisson-Boltzmann system near Maxwellians for long-range interactions. Compared with the former result obtained by Duan and Liu in [12] for the two species model, we do not ask the initial perturbation to satisfy the neutral condition and our result covers all physical collision kernels for the full range of intermolecular repulsive potentials.

Dynamics of the Random Ising Model with Long-Range Interaction

Critical dynamics of the random Ising model with long-range interaction decaying as r-(d+σ) where d is the dimensionality) is studied by the theoretic renormalization-group approach. The system is released to an evolution within a model A dynamics. Asymptotic scaling laws are studied in a frame of the expansion in = 2σ - d. In dimensions d ＜ 2σ. the dynamic exponent z is calculated to the second order in at the random fixed point.

Lagrangian formulation of continuum with internal long-range interactions

Based on a new definition of nonlocal variable,this paper establishes the Lagrangian formulation for continuum with internal long-range interactions.Distinguished from the existing theories,the nonlocal term in the Lagrangian formulation automatically satisfies the zero mean condition determined by the action and reaction law.By this formulation,elastic wave in a rod with the internal long-range interactions is investigated.The dispersion of the elastic wave is predicted.

Some Thoughts upon Long-Range Interaction and Entangled States

The problems of long-range interaction and associated questions on entangled states are reconsidered in terms of a recently developed revised quantum electrodynamic theory by the author, as being applied to subatomic systems. There are indications that the theories of relativity and quantum mechanics do not necessarily have to be in conflict. But more investigations are required for a full understanding to be obtained on these problems.

Screening and functional analysis of the long-range interaction elements ofβ-globin genes

Objective:Studies have shown thatβ-globin gene presents a selective expression transformation mechanism during development,and its upstream locus control region(LCR)regulates the expression pattern ofβ-globin gene family.To further explore the molecular network ofβ-globin gene expression regulation,other long-range regulatory elements that may be involved in the regulation ofβ-globin gene expression were screened and the dynamic regulation and transformation mechanism ofβ-globin gene was deeply studied.Methods:Promyelocytic cells were induced to differentiate by all-trans retinoic acid.β-globin gene promoter region and LCR were used as the target sites for circular chromosome conformational capture(4C)analysis.Through sequencing and regulatory element analysis,the sites interacting withβ-globin family loci were screened in the whole genome.Results:According to the results of 4C sequencing,the sites that interact with HBD promoter region and LCR were screened.Verified by chromosome conformational capture(3C),the results were consistent with those of sequencing.The functional analysis of regulatory elements by formaldehyde-assisted separation regulatory elements and Epiregio online website showed that the screening sites AC105129.4,AL354707.17,AC078785.22 and AC021646.35 were all potential regulatory elements involved inβ-globin gene.Conclusion:The interaction between 4C screening site and anchor site showed the complex spatial organization ofβ-globin family loci in the nucleus.

Transcription's bubble under the influence of long-range interactions and helicoidal coupling

The influence of power-low long-range interactions （LRI） and helicoidal coupling （HC） on the properties of localized solitons in a DNA molecule when a ribonucleic acid polymerase （RNAP） binds to it at the physiological temperature is analytically and numerically investigated in this paper. We have made an analogy with the Heisenberg model Hamiltonian of an anisotropic spin ladder with ferromagnetic legs and anti-ferromagnetic rung coupling. When we limit ourselves to the second-order terms in the Taylor expansion, the DNA dynamics is found to be governed by a completely integrable nonlinear Schr？dinger （NLS） equation. In this case, results show that increasing the value of HC force or LRI parameter enhances the bubble height and reduces the number of base pairs which form the bubble. For the fourth-order terms in a Taylor expansion, results are closely resembling those of second-order terms, and are confirmed by numerical investigation. These results match with some experimental data and thus provide a better representation of the base pairs opening in DNA which is essential for the transcription process.

Dynamical Stability of Gap Soliton of One-Dimensional Condensate in Optical Lattices with Strong Interatomic Interaction

By developing the multiple scales method, we analytically study the dynamics properties of gap soliton of Bose- Einstein condensate in optical lattices. It is shown that the gap soliton will appear at Brillouin zone edge of linear band spectrum of the condensates when the interatomic interaction strength is larger than the lattice depth. Moreover, the density of gap soliton starts to be relatively small, while it increases with time and becomes stable.

Short—Time Critical Behavior Affected by Weakly Long—Range Interactions

The theoretic renormalization group approach is applied to the study of short-time critical behavior of the Ginzburg–Landau model with weakly long-range interactions . The system initially at a high temperature is firstly quenched to the critical temperature and then released to an evolution with a model A dynamics. A double expansion in and with of order is employed, where is the spatial dimension. The asymptotic scaling laws and the initial slip exponents and for the order parameter and the response function respectively are calculated to the second order in for close to 2.

Spin waves and phase transition on a magnetically frustrated square lattice with long-range interactions

We investigate the effects of long-range interactions on the spin wave spectra and the competition between magnetic phases on a frustrated square lattice with large spin S.Applying the spin wave theory and assisted with symmetry analysis,we obtain analytical expressions for spin wave spectra of competing Neel and(π,0)stripe states of systems containing anyorder long-range interactions.In the specific case of long-range interactions with power-law decay,we find surprisingly that the staggered long-range interaction suppresses quantum fluctuation and enlarges the ordered moment,especially in the Neel state,and thus extends its phase boundary to the stripe state.Our findings illustrate the rich possibilities of the roles of long-range interactions,and advocate future investigations in other magnetic systems with different structures of interactions.

Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants

Higher-order chromatin organization is essential for transcriptional regulation,genome stability maintenance,and other genome functions.Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals.However,the extent,pattern,and rules of chromatin organization in plants are still unclear.In this study,we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome.We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications.Furthermore,we demonstrated that these chromatin loops are dependent on Polycomb group(PcG)proteins,suggesting that the Polycomb repressive complex2(PRC2)complex is essential for establishing and maintaining these novel loops.Although most of these PcG-medicated chromatin loops are stable,many of these loops are tissue-specific or dynamically regulated by different treatments.Interestingly,tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions.Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters.Finally,we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max,indicating that these long-range chromatin loops are conserved in plants.Our results provide novel insights into genome evolution and transcriptional coregulation in plants.

Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes

Studies on the lung cancer genome are indispensable for developing a cure for lung cancer.Whole-genome resequencing,genome-wide association studies,and transcriptome sequencing have greatly improved our understanding of the cancer genome.However,dysregulation of longrange chromatin interactions in lung cancer remains poorly described.To better understand the three-dimensional(3D)genomic interaction features of the lung cancer genome,we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II(RNAPII),CCCTC-binding factor(CTCF),enhancer of zeste homolog 2(EZH2),and histone 3 lysine 27 trimethylation(H3K27me3)using long-read chromatin interaction analysis by paired-end tag sequencing(ChIA-PET).Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes,either through loops or domains,and their distributions along the genome were distinct from and complementary to those associated with RNAPII.Cancer-related genes were highly enriched with chromatin interactions,and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes,such as additional repressive interactions on FOXO4 and promoter–promoter interactions between NF1 and RNF135.Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes,suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes.These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.

A Classification of Long-Range Interactions between Two Stacks of p＆ p＇-Branes

We generalize the computations of the long-range interactions between two parallel stacks of branes to various cases when two stacks of branes are not placed parallel to each other. We classify the nature of interaction(repulsive or attractive) for each special case and this classification can be used to justify the nature of long-range interaction between two complicated brane systems such as brane bound states. We will provide explicit examples in this paper to demonstrate this.

雷帕霉素诱导β-珠蛋白家族基因座位重塑调控该基因的转换表达

β-珠蛋白基因编码异常导致的β-地中海贫血是许多亚洲国家最常见的血红蛋白病。深入研究珠蛋白基因表达的分子基础和表观遗传机制,是探索治疗地中海贫血新方案的关键。本研究利用FAIRE、3C及ChIP等主要技术方法,探讨雷帕霉素诱导CD4^(+)T细胞核内染色质重塑过程中,β-珠蛋白家族基因座位的三维相互作用网络及其重塑在功能上调控基因表达的分子机制。结果显示,雷帕霉素处理浓度从低到高的变化过程中,珠蛋白基因染色质的开放程度、基因启动子区与调控元件LCR之间的相互作用频率以及CTCF在基因启动子区的富集效率发生不同的改变,这种变化导致了基因表达模式也呈现相同的变化趋势。10 nmol/L浓度处理时,染色质可及性降低,基因表达下降(P<0.05);20 nmol/L和50 nmol/L浓度时,染色质可及性增加,基因表达上调(P<0.05)。本研究通过这种动态的变化过程阐述了β-珠蛋白家族基因表达转换调控的分子机制,为临床精准治疗提供了理论与临床实践基础。

The local density of H3K9me3 dictates the stability of HP1α condensates-mediated genomic interactions

The human genome can be demarcated into domains based on distinct epigenetic states.The trimethylation of histone H3 lysine 9(H3K9me3)is essential for the formation of constitutive heterochromatin nanodomains.However,the extent to which genomic regions require specific densities or degrees of H3K9me3 for stable interactions remains unclear.Here,we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions.We select three loci(IDR3,TCF3,and PR1)with distinct levels of H3K9me3 to examine the genomic interactions and association with endogenous Heterochromatin Protein 1(HP1α)condensates.Our results demonstrate a positive correlation between the levels of H3K9me3 at the loci and their association with HP1αcondensates.By dual-color labeling and long-term tracking of IDR3 and PR1 loci,we find a periodical association between the two ranging from one to three hours.Epigenetic perturbation-induced Genome organization(EpiGo)-KRAB introduces∼20 kilobases of H3K9me3 at the TCF3 locus,which is sufficient to establish a stable association between TCF3 and HP1αcondensates.In addition,EpiGo-mediated H3K9me3 also leads to stable genomic interaction between IDR3 and TCF3.Briefly,these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1αcondensates.

Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions

The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events.Studies in animals,plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses.In this review,we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription,mRNA splicing,and DNA damage response.Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis.Finally,the potentials in exploiting chromatin remodeling for management of crop disease are presented.

Tn5-FISH,a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution

There is an increasing interest in understanding how three-dimensional(3D)organization of the genome is regulated.Different strategies have been employed to identify genome-wide chromatin interactions.However,due to current limitations in resolving genomic contacts,visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date.Here,we describe Tn5 transposase-based Fluorescencein situhybridization(Tn5-FISH),a PCR-based,cost-effective imaging method,which can co-localize the genomic loci with sub-kilobase resolution,dissect genome architecture,and verify chromatin interactions detected by chromatin configuration capture(3C)-derived methods.To validate this method,short-range interactions in keratin-encoding gene(KRT)locus in topologically associated domain(TAD)were imaged by triple-color Tn5-FISH,indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD.Therefore,Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.

核酸-蛋白质互作的生物化学研究方法

研究核酸-蛋白质的互作是揭示生命活动机理的基础,文章简要综述了用于研究核酸-蛋白质互作的各种生物化学方法。从体内、体外两个研究角度,针对核酸、蛋白以及复合物3个研究水平,概述了硝化纤维膜过滤实验、足迹法、EMSA、Southwestern杂交等经典分析方法的原理、发展和运用。还着重介绍了最近在表观遗传学领域中广泛运用的nChIP、xChIP等基本染色质免疫沉淀(ChIP)技术及其衍生出的ChIP-on-chip等方法。

染色质免疫沉淀技术在研究DNA与蛋白质相互作用中的应用

在后基因组时代,DNA-蛋白质的相互作用是研究基因表达调控的一个重要领域。与其他方法相比,染色质免疫沉淀技术(chromatin immunoprecipitation assay,ChIP)是一种在体内研究DNA-蛋白质相互作用的理想的方法。近年来这种方法与DNA芯片和分子克隆技术相结合,可用于高通量的筛选已知蛋白因子的未知DNA靶点和研究反式作用因子在整个基因组上的分布情况,这将有助于深入理解DNA-蛋白质相互作用的调控网络。总结了染色质免疫沉淀技术的方法,特别介绍了使用这些方法取得的最新进展。