1,243 results found
    1. Genetics and Genomics

    On the mechanistic nature of epistasis in a canonical cis-regulatory element

    Mato Lagator et al.
    Thermodynamic framework accurately predicts the sign of epistasis and its environment dependence for a canonical cis-regulatory element.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration

    Jun Wan et al.
    A new paradigm of DNA methylation mediated gene activation and chromatin remodeling provides a general framework to dissect the biological functions of DNA methylation readers and effectors.
    1. Computational and Systems Biology

    Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells

    Dana M King et al.
    The independent effects of transcription factor binding sites are large regardless of sequence context, but the interactions between sites are context dependent.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network

    Maxwell J Roeske et al.
    The conserved biochemical activity of the duplicate Bab transcription factors were integrated into the regulatory hierarchy of an evolving gene regulatory network by binding site gains in a target gene's cis-regulatory region.
    1. Developmental Biology
    2. Evolutionary Biology

    An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1

    David S Lorberbaum et al.
    The seemingly simple, constitutive response of the patched/Ptch1 gene to Hedgehog signaling is in fact regulated by large batteries of context-specific Hedgehog-responsive enhancers in both fly and mouse, allowing tissue-specific tuning of the Hedgehog pathway in animal development and evolution.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Cis-regulatory basis of sister cell type divergence in the vertebrate retina

    Daniel P Murphy et al.
    While photoreceptor and bipolar cells exhibit very similar cis-regulatory grammars, subtle differences in homeodomain motif enrichment represent a key distinction driving the divergence in their transcriptomes.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm

    Xinan H Yang et al.
    Transcription-factor-dependent noncoding RNA transcription illuminates components of a transcription-factor-dependent gene regulatory network that includes enhancer-associated long noncoding RNAs and is necessary for cardiac rhythm.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Community effects in regulation of translation

    Paul M Macdonald et al.
    Regulatory elements in an mRNA that act in cis to influence translation can also exert their effects in trans, in a process dependent on assembly of the mRNAs into particles.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells

    Patrick Laurette et al.
    The PBAF chromatin-remodelling complex is essential for the proliferation of melanocytes and melanoma cells and is recruited to critical regulatory elements by physical and functional interactions with MITF, a transcription factor and master regulator of melanoma.
    1. Developmental Biology
    2. Genetics and Genomics

    CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity

    Xiang-Ru Shannon Xu et al.
    Dissection of a cis-regulatory element (CRM) in its native chromosomal context using CRISPR/Cas9 editing and novel 'Active Genetics' reveals new features of CRM function and insights into how such regulatory elements change during evolution.

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