David Ichikawa,Marcus Noyes
David Ichikawa
The discovery of regulatory domains has been limited to the investigation of transcription factors and homologous protein sequences. In this issue of Cell Genomics, motivated by an oncogenic protein fusion, Tak et al.1 direct the regulatory...
Katie Teng,Hartland Warren Jackson
Katie Teng
Tissue-tumor interactivity is the culmination of cell intrinsic features and their extrinsic interactions with the environment. Recently in Cell, Dhainaut and Rose et al. established a strategy to track pooled CRISPR-modified cells in vivo ...
Unscrambling cancer genomes via integrated analysis of structural variation and copy number [0.03%]
通过结构变异和拷贝数的综合分析解开癌症基因组
Charles Shale,Daniel L Cameron,Jonathan Baber et al.
Charles Shale et al.
Complex somatic genomic rearrangements and copy number alterations are hallmarks of nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural variant and copy number data derived from short-read, whole-ge...
Open for connections: HiCAR reveals the interactions of accessible DNA [0.03%]
开放的连接：HiCAR揭示易接近DNA的互作关系
Benoit Moindrot,Daan Noordermeer
Benoit Moindrot
Hi-C is a powerful technology for exploring 3D genome organization on a genome-wide scale, yet it can be financially and computationally challenging. In a recent issue of Molecular Cell, Wei et al.1 introduce HiCAR, which simplifies Hi-C by...
Eva Gracia Villacampa,Ludvig Larsson,Reza Mirzazadeh et al.
Eva Gracia Villacampa et al.
Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, comme...
A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation [0.03%]
介导细胞类型特异性基因调控的DNA基元组合的顺式调控词典
Laura K H Donohue,Margaret G Guo,Yang Zhao et al.
Laura K H Donohue et al.
Gene expression is controlled by transcription factors (TFs) that bind cognate DNA motif sequences in cis-regulatory elements (CREs). The combinations of DNA motifs acting within homeostasis and disease, however, are unclear. Gene expressio...
Meta-analysis fine-mapping is often miscalibrated at single-variant resolution [0.03%]
元分析精细定位在单变异分辨率下经常校准错误
Masahiro Kanai,Roy Elzur,Wei Zhou;Global Biobank Meta-analysis Initiative;Mark J Daly et al.
Masahiro Kanai et al.
Meta-analysis is pervasively used to combine multiple genome-wide association studies (GWASs). Fine-mapping of meta-analysis studies is typically performed as in a single-cohort study. Here, we first demonstrate that heterogeneity (e.g., of...
Heather R Keys,Kristin A Knouse
Heather R Keys
A complete understanding of the genetic determinants underlying mammalian physiology and disease is limited by the capacity for high-throughput genetic dissection in the living organism. Genome-wide CRISPR screening is a powerful method for...
Damaging missense variants in IGF1R implicate a role for IGF-1 resistance in the etiology of type 2 diabetes [0.03%]
IGF1R中的有害错义变异表明IGF-1耐药性在2型糖尿病的病因中起作用
Eugene J Gardner,Katherine A Kentistou,Stasa Stankovic et al.
Eugene J Gardner et al.
Type 2 diabetes (T2D) is a heritable metabolic disorder. While population studies have identified hundreds of common genetic variants associated with T2D, the role of rare (frequency < 0.1%) protein-coding variation is less clear. We perfor...
Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19 [0.03%]
改变和等位基因特异性开放染色质景观揭示了COVID-19中先天免疫的表观遗传和遗传调节因子
Bowen Zhang,Zhenhua Zhang,Valerie A C M Koeken et al.
Bowen Zhang et al.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes severe COVID-19 in some patients and mild COVID-19 in others. Dysfunctional innate immune responses have been identified to contribute to COVID-19 severity, but t...