View article
An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites Open
We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for…
View article
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction Open
This study aims to understand through statistical learning the basic biophysical mechanisms behind three-dimensional folding of epigenomes. The 3DEpiLoop algorithm predicts three-dimensional chromatin looping interactions within topologica…
View article
Mediator and RNA polymerase II clusters associate in transcription-dependent condensates Open
Phase separation and gene control Many components of eukaryotic transcription machinery—such as transcription factors and cofactors including BRD4, subunits of the Mediator complex, and RNA polymerase II—contain intrinsically disordered lo…
View article
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis Open
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we …
View article
The chromatin accessibility landscape of primary human cancers Open
Cancer chromatin accessibility landscape The Cancer Genome Atlas (TCGA) provides a high-quality resource of molecular data on a large variety of human cancers. Corces et al. used a recently modified assay to profile chromatin accessibility…
View article
Histone Modifications and Cancer Open
Histone posttranslational modifications represent a versatile set of epigenetic marks involved not only in dynamic cellular processes, such as transcription and DNA repair, but also in the stable maintenance of repressive chromatin. In thi…
View article
Comprehensive functional genomic resource and integrative model for the human brain Open
INTRODUCTION Strong genetic associations have been found for a number of psychiatric disorders. However, understanding the underlying molecular mechanisms remains challenging. RATIONALE To address this challenge, the PsychENCODE Consortium…
View article
High-resolution TADs reveal DNA sequences underlying genome organization in flies Open
Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer ( hicexplorer.readthedocs.io ) to ann…
View article
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells Open
Imaging chromatin spatial organization The genome is organized within the nucleus as three-dimensional domains that modulate DNA-templated processes. Bintu et al. used high-throughput Oligopaint labeling and imaging to observe chromatin dy…
View article
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis Open
The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays, which map the genome-wide locations of transcription factor binding sites,…
View article
Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation Open
We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accur…
View article
The epigenetic landscape of T cell exhaustion Open
Epigenetic profiling suggests that exhausted T cells are a distinct cell linage.
View article
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage Open
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can a…
View article
A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing Open
SNF'ing out antitumor immunity Immune checkpoint inhibitors induce durable tumor regressions in some, but not all, cancer patients. Understanding the mechanisms that determine tumor sensitivity to these drugs could potentially expand the n…
View article
Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels Open
Long non-coding (lnc) RNAs are non-coding RNAs longer than 200 nt. lncRNAs primarily interact with mRNA, DNA, protein, and miRNA and consequently regulate gene expression at the epigenetic, transcriptional, post-transcriptional, translatio…
View article
A pathway for mitotic chromosome formation Open
Tracking mitotic chromosome formation How cells pack DNA into fully compact, rod-shaped chromosomes during mitosis has fascinated cell biologists for more than a century. Gibcus et al. delineated the conformational transition trajectory fr…
View article
A human cell atlas of fetal gene expression Open
The genomics of human development Understanding the trajectory of a developing human requires an understanding of how genes are regulated and expressed. Two papers now present a pooled approach using three levels of combinatorial indexing …
View article
Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants Open
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recogniz…
View article
Chromatin organization by an interplay of loop extrusion and compartmental segregation Open
Significance Human DNA is 2 m long and is folded into a 10-μm-sized cellular nucleus. Experiments have revealed two major features of genome organization: Segregation of alternating active and inactive regions into compartments, and format…
View article
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells Open
Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA…
View article
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome Open
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented,…
View article
PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes Open
The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was…
View article
Spatial organization of chromatin domains and compartments in single chromosomes Open
Spatial organization inside the nucleus In eukaryotic cells, DNA is packaged into a complex macromolecular structure called chromatin. Wang et al. have developed an imaging method to map the position of multiple regions on individual chrom…
View article
Metabolic reprogramming and epigenetic modifications on the path to cancer Open
Metabolic rewiring and epigenetic remodeling, which are closely linked and reciprocally regulate each other, are among the well-known cancer hallmarks. Recent evidence suggests that many metabolites serve as substrates or cofactors of chro…
View article
<i>N</i> <sup>6</sup> -methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription Open
A new layer of transcriptional control N 6 -methyladenosine (m 6 A) is the most abundant messenger RNA modification in almost all eukaryotes. Liu et al. now show that m 6 A is also cotranscriptionally added onto various chromosome-associat…
View article
Neutrophil Extracellular Traps and Its Implications in Inflammation: An Overview Open
In addition to physical barriers, neutrophils are considered a part of the first line of immune defense. They can be found in the bloodstream, with a lifespan of 6-8 h, and in tissue, where they can last up to 7 days. The mechanisms that n…
View article
CTCF and cohesin regulate chromatin loop stability with distinct dynamics Open
Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining gen…
View article
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse Open
Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Alt…
View article
Macrophage Ontogeny Underlies Differences in Tumor-Specific Education in Brain Malignancies Open
Extensive transcriptional and ontogenetic diversity exists among normal tissue-resident macrophages, with unique transcriptional profiles endowing the cells with tissue-specific functions. However, it is unknown whether the origins of diff…
View article
An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer Open
Loss of MHC class I (MHC-I) antigen presentation in cancer cells can elicit immunotherapy resistance. A genome-wide CRISPR/Cas9 screen identified an evolutionarily conserved function of polycomb repressive complex 2 (PRC2) that mediates co…