88 research outputs found
Global identification of functional microRNA-mRNA interactions in Drosophila
MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila
Determinants of promoter and enhancer transcription directionality in metazoans
Divergent transcription from promoters and enhancers is pervasive in many species, but it remains unclear if it is a general feature of all eukaryotic cis regulatory elements. To address this, here we define cis regulatory elements in C. elegans, D. melanogaster and H. sapiens and investigate the determinants of their transcription directionality. In all three species, we find that divergent transcription is initiated from two separate core promoter sequences and promoter regions display competition between histone modifications on the +1 and -1 nucleosomes. In contrast, promoter directionality, sequence composition surrounding promoters, and positional enrichment of chromatin states, are different across species. Integrative models of H3K4me3 levels and core promoter sequence are highly predictive of promoter and enhancer directionality and support two directional classes, skewed and balanced. The relative importance of features to these models are clearly distinct for promoters and enhancers. Differences in regulatory architecture within and between metazoans are therefore abundant, arguing against a unified eukaryotic model
FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells
The chromatin regulator FACT (facilitates chromatin transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using Caenorhabditis elegans, we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACT's role as a barrier to cell fate conversion is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts. Such activity is unexpected because FACT is known as a positive regulator of gene expression, and previously described reprogramming barriers typically repress gene expression. While FACT depletion in human fibroblasts results in decreased expression of many genes, a number of FACT-occupied genes, including reprogramming-promoting factors, show increased expression upon FACT depletion, suggesting a repressive function of FACT. Our findings identify FACT as a cellular reprogramming barrier in C. elegans and humans, revealing an evolutionarily conserved mechanism for cell fate protection
Dynamic Behavior in Piezoresponse Force Microscopy
Frequency dependent dynamic behavior in Piezoresponse Force Microscopy (PFM)
implemented on a beam-deflection atomic force microscope (AFM) is analyzed
using a combination of modeling and experimental measurements. The PFM signal
comprises contributions from local electrostatic forces acting on the tip,
distributed forces acting on the cantilever, and three components of the
electromechanical response vector. These interactions result in the bending and
torsion of the cantilever, detected as vertical and lateral PFM signals. The
relative magnitudes of these contributions depend on geometric parameters of
the system, the stiffness and frictional forces of tip-surface junction, and
operation frequencies. The dynamic signal formation mechanism in PFM is
analyzed and conditions for optimal PFM imaging are formulated. The
experimental approach for probing cantilever dynamics using frequency-bias
spectroscopy and deconvolution of electromechanical and electrostatic contrast
is implemented.Comment: 65 pages, 15 figures, high quality version available upon reques
Quasi Two-dimensional Transfer of Elastic Waves
A theory for multiple scattering of elastic waves is presented in a random
medium bounded by two ideal free surfaces, whose horizontal size is infinite
and whose transverse size is smaller than the mean free path of the waves. This
geometry is relevant for seismic wave propagation in the Earth crust. We derive
a time-dependent, quasi-2D radiative transfer equation, that describes the
coupling of the eigenmodes of the layer (surface Rayleigh waves, SH waves, and
Lamb waves). Expressions are found that relate the small-scale fluctuations to
the life time of the modes and to their coupling rates. We discuss a diffusion
approximation that simplifies the mathematics of this model significantly, and
which should apply at large lapse times. Finally, coherent backscattering is
studied within the quasi-2D radiative transfer equation for different source
and detection configurations.Comment: REVTeX, 36 pages with 10 figures. Submitted to Phys. Rev.
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