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View article: CUT&TIME captures the history of open chromatin in developing neurons
CUT&TIME captures the history of open chromatin in developing neurons Open
Chromatin structure plays a central role in defining cell identity by regulating gene expression. During development, shifts in chromatin structure facilitate changes in gene expression needed to specify distinct cell types. To understand …
View article: Genetic diversity and regulatory features of human-specific <i>NOTCH2NL</i> duplications
Genetic diversity and regulatory features of human-specific <i>NOTCH2NL</i> duplications Open
SUMMARY NOTCH2NL ( NOTCH2 -N-terminus-like) genes arose from incomplete, recent chromosome 1 segmental duplications implicated in human brain cortical expansion. Genetic characterization of these loci and their regulation is complicated by…
View article: Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition
Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition Open
The three-dimensional (3D) architecture of the genome plays a crucial role in gene regulation and various human diseases. Short-read sequencing methods for measuring 3D genome organization are powerful, but they lack the ability to resolve…
View article: Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon Open
Summary Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assemb…
View article: A haplotype-resolved view of human gene regulation
A haplotype-resolved view of human gene regulation Open
Diploid human cells contain two non-identical genomes, and differences in their regulation underlie human development and disease. We present Fiber-seq Inferred Regulatory Elements (FIRE) and show that FIRE provides a more comprehensive an…
View article: P229: Non-coding variants create an enhancer cluster that causes resistance to thyrotropin via long-range interactions with a microRNA promoter
P229: Non-coding variants create an enhancer cluster that causes resistance to thyrotropin via long-range interactions with a microRNA promoter Open
Resolving whether and how rare noncoding genetic variants cause Mendelian conditions remains challenging owing to the diverse mechanisms by which they cause disease. Here we demonstrate the utility of single-molecule chromatin fiber sequen…
View article: The accessible chromatin landscape of the human genome
The accessible chromatin landscape of the human genome Open
DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present…
View article: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Open
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmen…
View article: Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques
Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques Open
The genome is reprogrammed during development to produce diverse cell types, largely through altered expression and activity of key transcription factors. The accessibility and critical functions of epidermal cells have made them a model f…
View article: eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data Open
Summary The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into c…
View article: Cryptic Promoter Activation Drives <i>POU5F1</i> (<i>OCT4</i>) Expression in Renal Cell Carcinoma
Cryptic Promoter Activation Drives <i>POU5F1</i> (<i>OCT4</i>) Expression in Renal Cell Carcinoma Open
Transcriptional dysregulation drives cancer formation but the underlying mechanisms are still poorly understood. As a model system, we used renal cell carcinoma (RCC), the most common malignant kidney tumor which canonically activates the …
View article: 52 Genetic Loci Influencing Myocardial Mass
52 Genetic Loci Influencing Myocardial Mass Open
Taken together, our findings provide new insights into genes and biological pathways controlling myocardial mass and may help identify novel therapeutic targets.