SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells [0.03%]
活细胞中染色质环和活跃转录的同步成像技术SI-CLAT
Xin Wan,Jie Kong,Xiaodi Hu et al.
Xin Wan et al.
We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA acro...
Wei Ge,Yi-Lin Niu,Yu-Kang Li et al.
Wei Ge et al.
Background: In humans and other mammals, the process of oogenesis initiates asynchronously in specific ovarian regions, leading to the localization of dormant and growing follicles in the cortex and medulla, respectively;...
Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis [0.03%]
利用启动子捕获Hi-C技术在拟南芥中鉴定出与启动子相关的拓扑关联结构及其喷泉模式
Dingyue Wang,Suxin Xiao,Jiayue Shu et al.
Dingyue Wang et al.
Background: Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However...
Molecular dependencies and genomic consequences of a global DNA damage tolerance defect [0.03%]
全球DNA损伤耐受缺陷的分子依赖关系和基因组后果
Daniel de Groot,Aldo Spanjaard,Ronak Shah et al.
Daniel de Groot et al.
Background: DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiq...
Charles C Bell,Geoffrey J Faulkner,Omer Gilan
Charles C Bell
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states. Through pervasive, local, feedback loo...
Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations [0.03%]
Descart：一种检测具有细胞间相关性的空间染色质可及性模式的方法
Xiaoyang Chen,Keyi Li,Xiaoqing Wu et al.
Xiaoyang Chen et al.
Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within tissue slices. Identifying peaks that display spatial variation and cellular heterogeneity is the key analytic task ...
vmrseq: probabilistic modeling of single-cell methylation heterogeneity [0.03%]
VMRSeq：单细胞甲基化异质性的概率建模
Ning Shen,Keegan Korthauer
Ning Shen
Single-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated regions (VMRs) have relied on ...
Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy [0.03%]
多组学方法揭示弥漫性中线胶质瘤存在DNA复制改变并易受到DNA复制压力治疗的影响
Anastasia E Hains,Kashish Chetal,Tsunetoshi Nakatani et al.
Anastasia E Hains et al.
Background: The fatal diffuse midline gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling differentiation. The identification of targetable pathwa...
Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA [0.03%]
基于甲基化的血浆游离DNA细胞类型去卷积方法的系统评估
Tongyue Sun,Jinqi Yuan,Yacheng Zhu et al.
Tongyue Sun et al.
Background: Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the tissue origin of cfDNA through cell type deconvolution, we can detect changes in tissue homeostasis that occur ...
SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine [0.03%]
SQUiD：用于精准医学发展的超安全的遗传数据存储和分析方法
Jacob Blindenbach,Jiayi Kang,Seungwan Hong et al.
Jacob Blindenbach et al.
Cloud computing allows storing the ever-growing genotype-phenotype datasets crucial for precision medicine. Due to the sensitive nature of this data and varied laws and regulations, additional security measures are needed to ensure data pri...