174 results found
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A test of the pioneer factor hypothesis using ectopic liver gene activation

    Jeffrey L Hansen, Kaiser J Loell, Barak A Cohen
    Pioneering activity may be a property of all transcription factors with sufficient affinity for their targets rather than a property of specific classes of transcription factors.
    1. Chromosomes and Gene Expression

    Translation affects mRNA stability in a codon-dependent manner in human cells

    Qiushuang Wu, Santiago Gerardo Medina ... Ariel Alejandro Bazzini
    Genomic-profiles and reporters reveal that the three-nucleotide ‘words’ read by the ribosome, codons, have a strong effect on mRNA stability, impacting the homeostatic mRNA and protein levels in human cells.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs

    Zeyang Shen, Rick Z Li ... Christopher K Glass
    Collaborative transcription factors (TFs) exhibit a dominant pattern of a relaxed range of spacing and substantial tolerance of spacing alterations resulting from naturally occurring insertions and deletions in comparison to genetic variants directly affecting TF binding sites.
    1. Cancer Biology

    Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance

    Matthew F Pech, Linda E Fong ... Jeffrey Settleman
    CRISPR/Cas9 screens reveal a role for the ubiquitin ligase substrate adaptor DCAF15 in the immune surveillance of cancer cells by natural killer cells.
    1. Chromosomes and Gene Expression

    Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

    Hajnalka L Pálinkás, Angéla Békési ... Beáta G Vértessy
    Human genomic DNA contains uracil in the late replicating, constitutive heterochromatic regions, while treatment with drugs perturbing thymidylate biosynthesis shifts the uracil distribution pattern towards the euchromatin in UNG-inhibited cells.
    1. Genetics and Genomics

    Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors

    Joseph M Replogle, Jessica L Bonnar ... Marco Jost
    Newly developed, highly active CRISPR interference single guide RNA libraries and effectors together enable high-quality genetic screens across cell models.
    1. Genetics and Genomics

    Genome-wide quantification of the effects of DNA methylation on human gene regulation

    Amanda J Lea, Christopher M Vockley ... Jenny Tung
    mSTARR-seq identifies regions of the genome where DNA methylation causally impacts gene expression, providing a map of which epigenetic marks may influence trait variation.
    1. Cell Biology

    Splicing variation of BMP2K balances abundance of COPII assemblies and autophagic degradation in erythroid cells

    Jaroslaw Cendrowski, Marta Kaczmarek ... Marta Miaczynska
    Erythroid-enriched BMP2K kinase, in addition to its predicted function in endocytosis, regulates distribution and abundance of COPII assemblies and autophagic degradation through opposing actions of its two splicing variants.
    1. Computational and Systems Biology

    Detection of new pioneer transcription factors as cell-type-specific nucleosome binders

    Yunhui Peng, Wei Song ... Anna R Panchenko
    A computational method has been developed for predicting the cell-type-specific binding of transcription factors to nucleosomes, and involves integration of ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure.
    1. Cell Biology
    2. Computational and Systems Biology

    circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA

    Trine Line Hauge Okholm, Andreas Bjerregaard Kamstrup ... Christian Kroun Damgaard
    A dysregulated circular RNA in bladder cancer controls oncogenic pathways by tethering specific RNA-binding proteins, which in turn inhibits their normal functions.

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