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Cohesin-mediated physical interactions between distal regulatory DNA elements are critical for transcriptional regulation. Here, the authors suggest that the vast majority of these loops on individual DNA molecules exist in a dynamic, extruding state.

Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth.

Here the authors developed ‘Lamina-Inducible Methylation and Hi-C’ (LIMe-Hi-C) to simultaneously measure chromosome conformation, DNA methylation, and nuclear lamina positioning. Application of the method revealed dynamic changes upon PRC2 inhibition and an essential function of H3K27me3 in regulating sub-compartments and lamina association.

Liu et al. use mediation analysis to find changes in DNA methylation that mediate the genetic risk for rheumatoid arthritis.

In-depth characterization of adeno-associated virus (AAV)-mediated CRISPR delivery is still lacking. Here, the authors show high levels of integration into Cas9-induced double-strand breaks (DSBs) in therapeutically relevant genes in vivo.

Srinivasan Yegnasubramanian and colleagues show that androgen signaling promotes recruitment of androgen receptor and TOP2B to sites of TMPRSS2-ERG genomic breakpoints, triggering TOP2B-mediated double-strand breaks. These findings provide insights into the mechanism underlying this common prostate cancer gene fusion event.

The spatial organization of cells in solid tumors is considered to be important for immune response and response to therapy. Here the authors use multiomics including spatial transcriptomics of human lung tumors prior to patients being treated and show among other things an association of stem-immunity hubs rich in stem-like CD8⁺ T cells with positive response to anti-PD-1 therapy.

A statistical approach using a linear mixed model and principal-component analysis discovers phenotype-specific changes in epigenomes without requiring information on cell type composition.

Mouse induced pluripotent stem (iPS) cells have been shown to retain an epigenetic 'memory' of their cell type of origin. Kim et al. study this question in human cells and document both incomplete erasure of methylation and aberrant de novo methylation during reprogramming.

Andrew Feinberg and colleagues show that differential methylation of CpG island shores distinguish human induced pluripotent stem cells from the fibroblasts from which they were derived. These differentially methylated regions of the genome can also distinguish normal colon tissue from colorectal cancer.

This paper reports that there are substantial differences in DNA methylation patterns between nurses and forager caste phenotypes in honeybees, and that reverting foragers back to nurses reestablishes methylation levels for a majority of genes.

The relationship between cellular histogenesis and molecular phenotypes for the EWSR1- ATF1 fusion in clear cell sarcoma (CCS) requires further characterization. Here, the authors investigate the EWSR1-ATF1 gene regulation networks in CCS cell lines, primary tumors, and mesenchymal stem cells.

Long-range CRISPR activation can be enhanced by concurrent recruitment of artificial TFs to the enhancer and promoter of a target gene. This CRISPR activation system can be employed to achieve allele-selective gene upregulation by differentially targeting single-nucleotide polymorphisms embedded in enhancers or other distally located sequences.

This is a protocol for profiling the methylome and transcriptome of a single cell by using Smart-seq2 and reduced representation bisulfite sequencing.

Combining droplet-based ATAC-seq and mitochondrial DNA sequencing reveals clonal variation in human cells and tissues.

Combining microfluidics with combinatorial indexing enables rapid mapping of genome accessibility in hundreds of thousands of single cells.

Single-nucleus and spatial, whole-transcriptome profiling of 43 pancreatic adenocarcinomas provides a refined molecular and cellular classification, highlighting a new neoadjuvant treatment-associated neural-like progenitor tumor cell state.

DNA methylation is efficiently profiled in non-coding regulatory sequences in single cells.

Fine-mapping of blood cell traits in the UK Biobank identifies putative causal variants and enrichment of fine-mapped variants in accessible chromatin of hematopoietic progenitor cells. The study provides an analytical framework for single-variant and single-cell analyses of genetic associations.

A fusion of the FokI nuclease and a catalytically inactive Cas9 is a highly specific genome editing tool.

CIRCLE-seq is an in vitro assay for selectively sequencing off-target sites cleaved by Cas9–sgRNA in genomic DNA. It sensitively profiles genome-wide off-target cut sites and characterizes the contribution of SNPs to these cleavage events.

The increasing accessibility of single cell omics technologies beyond transcriptomics demands parallel advances in analysis. Here, the authors introduce STREAM, a pipeline for reconstruction and visualization of differentiation trajectories from both single-cell RNA-seq and ATAC-seq data.

Disease risk variants can exert their influence on phenotypes by altering epigenome function. Here, Pelikan et al. show that variants inducing allelic imbalance in histone marks in lymphoblastoid cell lines from lupus patients are enriched in autoimmune disease haplotypes and influence gene expression.

An unbiased approach for the genome-wide detection of off-target cleavage by CRISPR-Cas9 RNA–guided nucleases reveals wide variability in the off-target activity of different guide RNAs.

A single-cell approach is used to follow the heritable stochastic changes to DNA methylation that occur in primary chronic lymphocytic leukaemia and healthy B cells, allowing the tracing of cell lineage histories and evolution during treatment with ibrutinib.

A strategy developed to define off-target effects of gene-editing nucleases in whole organisms is validated and leveraged to show that CRISPR–Cas9 nucleases can be used effectively in vivo without inducing detectable off-target mutations.

Structure-guided protein engineering of Cas12a yields variants that have increased activity and that can edit sites with previously inaccessible PAMs.

A base editor that concurrently modifies both adenine and cytosine broadens the potential applications of base editing.

CRISPR DNA base editors induce transcriptome-wide off-target RNA editing, which can be reduced by using engineered variants that retain on-target DNA editing activities.

Engineered variants of DNA base editors have reduced RNA off-target editing while retaining DNA on-target efficiency.

During haematopoiesis, multipotent progenitors differentiate into progressively restricted myeloid or lymphoid progenitors. A comprehensive genome-wide DNA methylation analysis of haematopoietic cell populations with well-characterized differentiation potentials reveals remarkable epigenetic plasticity during lymphoid and myeloid restriction.

CRISPR-Cas9 nucleases are widely used for genome editing, but the range of sequences that Cas9 can recognize is constrained by the need for a specific protospacer adjacent motif (PAM); here the commonly used Streptococcus pyogenes Cas9 (SpCas9) is modified to recognize alternative PAM sequences, enabling robust editing of endogenous gene sites in zebrafish and human cells not currently targetable by wild-type SpCas9.

On-target activities and genome-wide specificities of Cpf1 nucleases in human cells.

GUIDE-seq (genome-wide unbiased identification of double-stranded breaks enabled by sequencing) is a sensitive, unbiased, genome-wide method for defining the specificity of genome-editing nucleases in living cells.

This protocol describes CIRCLE-seq (circularization for in vitro reporting of cleavage effects by sequencing), a sensitive and unbiased method for defining the on-target and off-target activity of CRISPR–Cas9 nucleases genome-wide.

Christopher Lietz et al. examined genome-wide methylation in patient cohorts of primary osteosarcoma. Their results suggest that genomic hypomethylation is predictive of response to standard chemotherapy, and provide further insight into clinical implications of methylation patterns.