576 results found
    1. Chromosomes and Gene Expression

    A promoter interaction map for cardiovascular disease genetics

    Lindsey E Montefiori et al.
    Promoter capture Hi-C in human iPSCs and iPSC-derived cardiomyocytes provides a platform to interrogate gene-regulatory dynamics of cardiomyocyte differentiation and directly links thousands of cardiovascular disease risk loci to hundreds of distal target genes.
    1. Computational and Systems Biology

    Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies

    Ye Zheng et al.
    A statistical model rescues multi-mapping reads with high accuracy and demonstrates their impact in all facets of the analysis of genome-wide high throughput conformation capture datasets.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

    Michael R Stadler et al.
    Fruit fly chromosomes are divided into discrete structural domains by regions of decompacted chromatin, suggesting a novel model for the formation of a known class of genetic elements.
    1. Chromosomes and Gene Expression

    Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization

    Pavan Choppakatla et al.
    Linker histone H1.8 shapes mitotic chromosomes by tuning the number and size of condensin-dependent DNA loops and suppressing condensin and DNA topoisomerase II-dependent individualization.
    1. Microbiology and Infectious Disease

    MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

    Martial Marbouty et al.
    Physical contacts of bacteria and phage genomes allow in situ exploration of underdocumented phage families in the gut.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Large domains of heterochromatin direct the formation of short mitotic chromosome loops

    Maximilian H Fitz-James et al.
    Large regions of foreign DNA inserted into mammalian chromosomes assemble into H3K9me3-heterochromatin and result in increased condensin loading with organisation into shorter mitotic chromosome loops than endogenous DNA.
    1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    Chromosome organization by one-sided and two-sided loop extrusion

    Edward J Banigan et al.
    Seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization are reconciled by computationally investigating mechanisms of loop extrusion that are consistent with both.
    1. Stem Cells and Regenerative Medicine
    2. Chromosomes and Gene Expression

    Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

    Paula Freire-Pritchett et al.
    Promoter interactome maps in human embryonic stem cells (ESCs) and ESC-derived early neuroectodermal progenitors link distal enhancers to putative target genes, reveal lineage-specific cis-regulatory architecture and shed light on the logic of gene regulation by multiple enhancers.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver

    Bryan J Matthews, David J Waxman
    Certain types of 3D chromatin loops are easy to predict from existing or easily obtainable 2D information, which benefits gene expression studies in tissues/cells/organisms without extensive pre-existing 3D information.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

    Jinmi Choi et al.
    Temporal changes in genome-wide enhancer transcription activity during a transdifferentiation event reveal additive and synergistic enhancer cooperation.

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