577 results found
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Information content differentiates enhancers from silencers in mouse photoreceptors

    Ryan Z Friedman et al.
    Silencers and enhancers targeted by a common transcription factor in photoreceptors are distinguished by the number and diversity of binding transcription factor binding sites they contain.
    1. Developmental Biology
    2. Neuroscience

    Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation

    Maria-Daniela Cirnaru et al.
    RNAseq and ATACseq are utilized to identify transcription factors participating in striatal compartmentation into striosome and matrix, and roles for Stat1, Olig2, and Foxf2 are validated in vitro and in vivo.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions

    Charanya Kumar et al.
    Reconstitution of orientation-specific R-loop-replisome collisions with purified proteins reveals the differential impact of R-loop-associated RNA:DNA hybrids and G-quadruplexes on replication fork progression.
    1. Biochemistry and Chemical Biology
    2. Physics of Living Systems

    Mechanically transduced immunosorbent assay to measure protein-protein interactions

    Christopher J Petell et al.
    METRIS is a method that reports a mechanical readout of protein-protein interactions and due to its unique properties, it will allow many protein-protein interactions to be quantitatively measured easily that are currently laborious to measure with conventional methods.
    1. Cancer Biology
    2. Chromosomes and Gene Expression

    YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation

    Lizhi He et al.
    YAP and TAZ, the ultimate targets of the Hippo signaling pathway, are transcriptional co-activators of AP-1 proteins and STAT3 through which they are important for breast cellular transformation.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species

    Natalia Petrenko, Kevin Struhl
    Although the preinitiation complex for transcriptional initiation by RNA polymerase II contains highly conserved general transcription factors, there are kinetic and compositional differences in the initiation process among eukaryotic species.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

    Luka Bacic et al.
    Analysis of conformational heterogeneity in cryo-EM data by a recently developed deep learning method reveals the structure and dynamics of the oncogenic chromatin remodeler ALC1 bound to a poly-ADP-ribosylated nucleosome.
    1. Developmental Biology
    2. Physics of Living Systems

    Cost-precision trade-off relation determines the optimal morphogen gradient for accurate biological pattern formation

    Yonghyun Song, Changbong Hyeon
    The morphogen profiles that pattern the fruit fly attain desired levels of spatial precision in a cost-effective manner.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation

    Teresa Romeo Luperchio et al.
    Chromatin/transcriptome profiling in multiple mouse models with mutations in epigenetic machinery (EM) reveals shared abnormalities including many IgA-relevant genes, indicating that this kind of joint analysis may elucidate the multigenic nature of EM disorders.
    1. Genetics and Genomics
    2. Neuroscience

    Neuronal calmodulin levels are controlled by CAMTA transcription factors

    Thanh Thi Vuong-Brender et al.
    CAMTA transcription factors are evolutionarily conserved regulators of neuronal levels of the major Ca2+ sensor calmodulin.

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