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Genome folding principles uncovered in condensin-depleted mitotic chromosomes
During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I a...
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Author Correction: HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription
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Open AccessSnapshot: a package for clustering and visualizing epigenetic history during cell differentiation
Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to id...
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Open AccessCLIMB: High-dimensional association detection in large scale genomic data
Joint analyses of genomic datasets obtained in multiple different conditions are essential for understanding the biological mechanism that drives tissue-specificity and cell differentiation, but they still rem...
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Article
CTCF blocks antisense transcription initiation at divergent promoters
Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How...
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Article
HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription
The fetal-to-adult switch in hemoglobin production is a model of developmental gene control with relevance to the treatment of hemoglobinopathies. The expression of transcription factor BCL11A, which represses...
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Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells
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Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells
The mechanisms by which the fetal-type β-globin-like genes HBG1 and HBG2 are silenced in adult erythroid precursor cells remain a fundamental question in human biology and have therapeutic relevance to sickle cel...
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Open AccessAuthor Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
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Open AccessCTCF and transcription influence chromatin structure re-configuration after mitosis
During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. We exploited the M- to G1-phase progression to interrogate the contributions of the architectural f...
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Alteration of genome folding via contact domain boundary insertion
Animal chromosomes are partitioned into contact domains. Pathogenic domain disruptions can result from chromosomal rearrangements or perturbation of architectural factors. However, such broad-scale alterations...
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Open AccessExpanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the ...
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Article
Chromatin structure dynamics during the mitosis-to-G1 phase transition
Features of higher-order chromatin organization—such as A/B compartments, topologically associating domains and chromatin loops—are temporarily disrupted during mitosis1,2. Because these structures are thought to...
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Open AccessEstablishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points
Enhancers and promoters are cis-acting regulatory elements associated with lineage-specific gene expression. Previous studies showed that different categories of active regulatory elements are in regions of op...
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Open AccessExploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility
Single-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we intr...
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Open AccessOccupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility
Regulated gene expression controls organismal development, and variation in regulatory patterns has been implicated in complex traits. Thus accurate prediction of enhancers is important for further understandi...
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Open AccessPrinciples of regulatory information conservation between mouse and human
To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human–mouse erythroid progenitor, lymphoblast and ...
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Open AccessA comparative encyclopedia of DNA elements in the mouse genome
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater in...
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An encyclopedia of mouse DNA elements (Mouse ENCODE)
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed fo...
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Ubiquitination, proteasomes and GABAA receptors
Inhibitory neurotransmission by γ-aminobutyric acid (GABA) is regulated by the number and subcellular localization of GABAA receptors in the membrane of the target neuron. A new study suggests that the ubiquitin-...
