scholarly journals PARP mediated chromatin unfolding is coupled to long-range enhancer activation

2017 ◽  
Author(s):  
Nezha S. Benabdallah ◽  
Iain Williamson ◽  
Robert S. Illingworth ◽  
Shelagh Boyle ◽  
Graeme R. Grimes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Sonic Hedgehog ◽  
Large Scale ◽  
Target Gene ◽  
Neural Progenitor Cells ◽  
Gene Activation ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Chromatin Reorganization

AbstractEnhancers are critical regulators of gene expression and can be located far from their target gene. It is widely assumed that mechanisms of enhancer action involve reorganization of three-dimensional chromatin architecture, but this is poorly understood. Here we identify a novel mechanism of long-range enhancer associated chromatin reorganization. At the Sonic hedgehog (Shh) locus we observe large-scale decompaction of chromatin between Shh and its brain enhancers in neural progenitor cells. We show that the chromatin unfolding is dependent on activation of the enhancers, not the promoter, is impeded by chromatin-bound proteins located between the enhancer and promoter, and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. We suggest that large-scale chromatin decompaction, analogous to the inducible puffs in Drosophila polytene chromosomes, represents a new mechanism of chromatin reorganization coupled to long-range gene activation from mammalian enhancers and that seems incompatible with a chromatin-looping model of enhancer-promoter communication

scholarly journals A platform for brain-wide imaging and reconstruction of individual neurons

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Michael N Economo ◽  
Nathan G Clack ◽  
Luke D Lavis ◽  
Charles R Gerfen ◽  
Karel Svoboda ◽  
...  
Keyword(s):  
Long Range ◽  
High Speed ◽  
Large Scale ◽  
Three Dimensional ◽  
Image Data ◽  
Mammalian Brain ◽  
Projection Neurons ◽  
Computational Tools ◽  
Two Photon ◽  
Axonal Arbors

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.

scholarly journals Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences

2021 ◽  
Vol 118 (18) ◽  
pp. e2020125118
Author(s):  
Yoshiaki Kita ◽  
Hirozumi Nishibe ◽  
Yan Wang ◽  
Tsutomu Hashikawa ◽  
Satomi S. Kikuchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Neural Circuit ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Control Of Gene Expression ◽  
Cellular Resolution

Precise spatiotemporal control of gene expression in the developing brain is critical for neural circuit formation, and comprehensive expression mapping in the developing primate brain is crucial to understand brain function in health and disease. Here, we developed an unbiased, automated, large-scale, cellular-resolution in situ hybridization (ISH)–based gene expression profiling system (GePS) and companion analysis to reveal gene expression patterns in the neonatal New World marmoset cortex, thalamus, and striatum that are distinct from those in mice. Gene-ontology analysis of marmoset-specific genes revealed associations with catalytic activity in the visual cortex and neuropsychiatric disorders in the thalamus. Cortically expressed genes with clear area boundaries were used in a three-dimensional cortical surface mapping algorithm to delineate higher-order cortical areas not evident in two-dimensional ISH data. GePS provides a powerful platform to elucidate the molecular mechanisms underlying primate neurobiology and developmental psychiatric and neurological disorders.

FLT3ITD Target Enhancers Are Primed but Inaccessible in Fetal Hematopoietic Progenitors

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1228-1228
Author(s):  
Yanan Li ◽  
Riddhi M Patel ◽  
Emily Casey ◽  
Jeffrey A. Magee
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Gene Activation ◽  
Chromatin Accessibility ◽  
Luciferase Reporter ◽  
Enhancer Activity ◽  
Target Gene Expression

The FLT3 Internal Tandem Duplication (FLT3ITD) is common somatic mutation in acute myeloid leukemia (AML). We have previously shown that FLT3ITD fails to induce changes in HSC self-renewal, myelopoiesis and leukemogenesis during fetal stages of life. FLT3ITD signal transduction pathways are hyperactivated in fetal progenitors, but FLT3ITD target genes are not. This suggests that postnatal-specific transcription factors may be required to help induce FLT3ITD target gene expression. Alternatively, repressive histone modifications may impose a barrier to FLT3ITD target gene activation in fetal HPCs that is relaxed during postnatal development. To resolve these possibilities, we used ATAC-seq, as well as H3K4me1, H3K27ac and H3K27me3 ChIP-seq, to identify cis-elements that putatively control FLT3ITD target gene expression in fetal and adult hematopoietic progenitor cells (HPCs). We identified many enhancer elements (ATAC-seq peaks with H3K4me1 and H3K27ac) that exhibited increased chromatin accessibility and activity in FLT3ITD adult HPCs relative to wild type adult HPCs. These elements were enriched near FLT3ITD target genes. HOMER analysis showed enrichment for STAT5, ETS, RUNX1 and IRF binding motifs within the FLT3ITD target enhancers, but motifs for temporally dynamic transcription factors were not identified. We cloned a subset of the enhancers and confirmed that they could synergize with their promoter to activate a luciferase reporter. For representative enhancers, STAT5 binding sites were required to activate the enhancer - as anticipated - and RUNX1 repressed enhancer activity. We tested whether accessibility or priming changed between fetal and adult stages of HPC development. FLT3ITD-dependent changes in chromatin accessibility were not observed in fetal HPCs, though the enhancers were primed early in development as evidenced by the presence of H3K4me1. Repressive H3K27me3 were not present at FLT3ITD target enhancers in either or adult HPCs. The data show that FLT3ITD target enhancers are demarcated early in hematopoietic development, long before they become responsive to FLT3ITD signaling. Repressive marks do not appear to create an epigenetic barrier to enhancer activation in the fetal stage. Instead, age-specific transcription factors are likely required to pioneer enhancer elements so that they can respond to STAT5 and other FLT3ITD effectors. Disclosures No relevant conflicts of interest to declare.

scholarly journals RelA Ser276 Phosphorylation Is Required for Activation of a Subset of NF-κB-Dependent Genes by Recruiting Cyclin-Dependent Kinase 9/Cyclin T1 Complexes

2008 ◽  
Vol 28 (11) ◽  
pp. 3623-3638 ◽  
Author(s):  
David E. Nowak ◽  
Bing Tian ◽  
Mohammad Jamaluddin ◽  
Istvan Boldogh ◽  
Leoncio A. Vergara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Gene Activation ◽  
Elongation Factor ◽  
Genetic Network ◽  
Transcriptional Elongation ◽  
Cyclin Dependent Kinase ◽  
Pol Ii ◽  
Target Gene Expression ◽  
Cyclin T1

ABSTRACT NF-κB plays a central role in cytokine-inducible inflammatory gene expression. Previously we empirically determined the identity of 92 members of the genetic network under direct NF-κB/RelA control that show marked heterogeneity in magnitude of transcriptional induction and kinetics of peak activation. To investigate this network further, we have applied a recently developed two-step chromatin immunoprecipitation assay that accurately reflects association and disassociation of RelA binding to its chromatin targets. Although inducible RelA binding occurs with similar kinetics on all NF-κB-dependent genes, serine 276 (Ser276)-phosphorylated RelA binding is seen primarily on a subset of genes that are rapidly induced by tumor necrosis factor (TNF), including Gro-β, interleukin-8 (IL-8), and IκBα. Previous work has shown that TNF-inducible RelA Ser276 phosphorylation is controlled by a reactive oxygen species (ROS)-protein kinase A signaling pathway. To further understand the role of phospho-Ser276 RelA in target gene expression, we inhibited its formation by ROS scavengers and antioxidants, treatments that disrupt phospho-Ser276 formation but not the translocation and DNA binding of nonphosphorylated RelA. Here we find that phospho-Ser276 RelA is required only for activation of IL-8 and Gro-β, with IκBα being unaffected. These data were confirmed in experiments using RelA−/− murine embryonic fibroblasts reconstituted with a RelA Ser276Ala mutation. In addition, we observe that phospho-Ser276 RelA binds the positive transcription elongation factor b (P-TEFb), a complex containing the cyclin-dependent kinase 9 (CDK-9) and cyclin T1 subunits. Inhibition of P-TEFb activity by short interfering RNA (siRNA)-mediated knockdown shows that the phospho-Ser276 RelA-P-TEFb complex is required for IL-8 and Gro-β gene activation but not for IκBα gene activation. These studies indicate that TNF induces target gene expression by heterogeneous mechanisms. One is mediated by phospho-Ser276 RelA formation and chromatin targeting of P-TEFb controlling polymerase II (Pol II) recruitment and carboxy-terminal domain phosphorylation on the IL-8 and Gro-β genes. The second involves a phospho-Ser276 RelA-independent activation of genes preloaded with Pol II, exemplified by the IκBα gene. Together, these data suggest that the binding kinetics, selection of genomic targets, and mechanisms of promoter induction by RelA are controlled by a phosphorylation code influencing its interactions with coactivators and transcriptional elongation factors.

scholarly journals SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells

Open Biology ◽  
2016 ◽  
Vol 6 (11) ◽  
pp. 160197 ◽  
Author(s):  
Nezha S. Benabdallah ◽  
Philippe Gautier ◽  
Betul Hekimoglu-Balkan ◽  
Laura A. Lettice ◽  
Shipra Bhatia ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Long Range ◽  
Sonic Hedgehog ◽  
Neural Progenitor Cells ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Neural Progenitor ◽  
Chromatin Profiling

The expression of genes with key roles in development is under very tight spatial and temporal control, mediated by enhancers. A classic example of this is the sonic hedgehog gene ( Shh ), which plays a pivotal role in the proliferation, differentiation and survival of neural progenitor cells both in vivo and in vitro. Shh expression in the brain is tightly controlled by several known enhancers that have been identified through genetic, genomic and functional assays. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells, here we report the identification of a novel long-range enhancer for Shh—Shh-brain-enhancer-6 (SBE6)—that is located 100 kb upstream of Shh and that is required for the proper induction of Shh expression during this differentiation programme. This element is capable of driving expression in the vertebrate brain. Our study illustrates how a chromatin-focused approach, coupled to in vivo testing, can be used to identify new cell-type specific cis -regulatory elements, and points to yet further complexity in the control of Shh expression during embryonic brain development.

ANALYSIS AND SIMULATION OF LONG-RANGE CORRELATIONS IN CURVED SPACE

2009 ◽  
Vol 20 (08) ◽  
pp. 1211-1232 ◽  
Author(s):  
ALI REZA MEHRABI ◽  
MUHAMMAD SAHIMI
Keyword(s):  
Long Range ◽  
Large Scale ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Amorphous Semiconductors ◽  
Curved Space ◽  
Long Range Correlations ◽  
Planar Surfaces ◽  
Positively Curved ◽  
Industrial Problem

Numerical simulation and analysis of long-range correlations in curved space are studied. The study is motivated by the problem of constructing accurate models of large-scale porous media which usually contain long-range correlations in their various properties (such as their permeability, porosity, and elastic moduli) within and between their strata that are typically curved layers. The problem is, however, relevant to many other important models and phenomena in which extended correlations in curved space play a prominent role. Examples include the nonlinear σ-model in a curved space, models for describing the long-range structural correlations of amorphous semiconductors that consist of polytopes (tilings of positively-curved three-dimensional space), long-range correlations in the extrapolar total zone, and models in which the Universe is created by bubble nucleations and contain long-range correlations in the fluctuations in the curved spacetime. The study is also relevant to the important industrial problem of designing highly curved objects, such as cars and ships, which use composite materials that contain extended correlations in their property values. We study such correlations along two- and three-dimensional curves, as well as curved surfaces. We show that such correlations are well-defined only on developable surfaces, i.e. those that can be flattened to form planar surfaces without any stretching or distortion, and preserve the distance between two points on such surfaces after the stretching. If a given curved surface is not developable, but can be approximated as piecewise developable, one may still define and analyze extended correlations on it. Representative examples are presented and analyzed.

scholarly journals Differential Target Gene Activation by the Staphylococcus aureus Two-Component System saeRS

2009 ◽  
Vol 192 (3) ◽  
pp. 613-623 ◽  
Author(s):  
Markus Mainiero ◽  
Christiane Goerke ◽  
Tobias Geiger ◽  
Christoph Gonser ◽  
Silvia Herbert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Gene Expression Pattern ◽  
Class Ii ◽  
Class I ◽  
Single Amino Acid ◽  
Single Amino Acid Change

ABSTRACT The saePQRS system of Staphylococcus aureus controls the expression of major virulence factors and encodes a histidine kinase (SaeS), a response regulator (SaeR), a membrane protein (SaeQ), and a lipoprotein (SaeP). The widely used strain Newman is characterized by a single amino acid change in the sensory domain of SaeS (Pro18 in strain Newman [SaeSP], compared with Leu18 in other strains [SaeSL]). SaeSP determines activation of the class I sae target genes (coa, fnbA, eap, sib, efb, fib, sae), which are highly expressed in strain Newman. In contrast, class II target genes (hla, hlb, cap) are not sensitive to the SaeS polymorphism. The SaeSL allele (saeSL ) is dominant over the SaeSP allele, as shown by single-copy integration of saePQRSL in strain Newman, which results in severe repression of class I target genes. The differential effect on target gene expression is explained by different requirements for SaeR phosphorylation. From an analysis of saeS deletion strains and strains with mutated SaeR phosphorylation sites, we concluded that a high level of SaeR phosphorylation is required for activation of class I target genes. However, a low level of SaeR phosphorylation, which can occur independent of SaeS, is sufficient to activate class II target genes. Using inducible saeRS constructs, we showed that the expression of both types of target genes is independent of the saeRS dosage and that the typical growth phase-dependent gene expression pattern is not driven by SaeRS.

scholarly journals Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009039
Author(s):  
Yi Kuang ◽  
Anna Pyo ◽  
Natanel Eafergan ◽  
Brittany Cain ◽  
Lisa M. Gutzwiller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Target Gene ◽  
Gene Activation ◽  
Notch Intracellular Domain ◽  
Repressor Complex ◽  
Notch Activation

Notch signaling controls many developmental processes by regulating gene expression. Notch-dependent enhancers recruit activation complexes consisting of the Notch intracellular domain, the Cbf/Su(H)/Lag1 (CSL) transcription factor (TF), and the Mastermind co-factor via two types of DNA sites: monomeric CSL sites and cooperative dimer sites called Su(H) paired sites (SPS). Intriguingly, the CSL TF can also bind co-repressors to negatively regulate transcription via these same sites. Here, we tested how synthetic enhancers with monomeric CSL sites versus dimeric SPSs bind Drosophila Su(H) complexes in vitro and mediate transcriptional outcomes in vivo. Our findings reveal that while the Su(H)/Hairless co-repressor complex similarly binds SPS and CSL sites in an additive manner, the Notch activation complex binds SPSs, but not CSL sites, in a cooperative manner. Moreover, transgenic reporters with SPSs mediate stronger, more consistent transcription and are more resistant to increased Hairless co-repressor expression compared to reporters with the same number of CSL sites. These findings support a model in which SPS containing enhancers preferentially recruit cooperative Notch activation complexes over Hairless repression complexes to ensure consistent target gene activation.

scholarly journals Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness

2021 ◽  
pp. gr.275901.121
Author(s):  
Alexandre Laverre ◽  
Eric Tannier ◽  
Anamaria Necsulea
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Large Scale ◽  
Target Genes ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Gene Expression Profiles ◽  
Evolutionary Conservation ◽  
Regulatory Elements ◽  
Regulatory Landscapes

Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements is rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter-enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny or contacts with target genes, is significantly associated with gene expression evolution.

Dynamics of direct large-small scale couplings in coherently forced turbulence: concurrent physical- and Fourier-space views

1995 ◽  
Vol 283 ◽  
pp. 43-95 ◽  
Author(s):  
P. K. Yeung ◽  
James G. Brasseur ◽  
Qunzhen Wang
Keyword(s):  
Long Range ◽  
Large Scale ◽  
Three Dimensional ◽  
Physical Space ◽  
Small Scale ◽  
Fourier Space ◽  
Distant Interactions ◽  
Long Range Interactions ◽  
Small Scales ◽  
Non Local

As discussed in a recent paper by Brasseur & Wei (1994), scale interactions in fully developed turbulence are of two basic types in the Fourier-spectral view. The cascade of energy from large to small scales is embedded within ‘local-to-non-local’ triadic interactions separated in scale by a decade or less. ‘Distant’ triadic interactions between widely disparate scales transfer negligible energy between the largest and smallest scales, but directly modify the structure of the smallest scales in relationship to the structure of the energy-dominated large scales. Whereas cascading interactions tend to isotropize the small scales as energy moves through spectral shells from low to high wavenumbers, distant interactions redistribute energy within spectral shells in a manner that leads to anisotropic redistributions of small-scale energy and phase in response to anisotropic structure in the large scales. To study the role of long-range interactions in small-scale dynamics, Yeung & Brasseur (1991) carried out a numerical experiment in which the marginally distant triads were purposely stimulated through a coherent narrow-band anisotropic forcing at the large scales readily interpretable in both the Fourier- and physical-space views. It was found that, after one eddy turnover time, the smallest scales rapidly became anisotropic as a direct consequence of the marginally distant triadic group in a manner consistent with the distant triadic equations. Because these asymptotic equations apply in the infinite Reynolds number limit, Yeung & Brasseur argued that the observed long-range effects should be applicable also at high Reynolds numbers.We continue the analysis of forced simulations in this study, focusing (i) on the detailed three-dimensional restructuring of the small scales as predicted by the asymptotic triadic equations, and (ii) on the relationship between Fourier- and physical-space evolution during forcing. We show that the three-dimensional restructuring of small-scale energy and vorticity in Fourier space from large-scale forcing is predicted in some detail by the distant triadic equations. We find that during forcing the distant interactions alter small-scale structure in two ways: energy is redistributed anisotropically within high-wavenumber spectral shells, and phase correlations are established at the small scales by the distant interactions. In the numerical experiments, the long-range interactions create two pairs of localized volumes of concentrated energy in three-dimensional Fourier space at high wavenumbers in which the Fourier modes are phase coupled. Each pair of locally phase-correlated volumes of Fourier modes separately corresponds to aligned vortex tubes in physical space in two orthogonal directions. We show that the dynamics of distant interactions in creating small-scale anisotropy may be described in physical space by differential advection and distortion of small-scale vorticity by the coherent large-scale energy-containing eddies, producing anisotropic alignment of small-scale vortex tubes.Scaling arguments indicate a disparity in timescale between distant triadic interactions and energy-cascading local-to-non-local interactions which increases with scale separation. Consequently, the small scales respond to forcing initially through the distant interactions. However, as energy cascades from the large-scale to the small-scale Fourier modes, the stimulated distant interactions become embedded within a sea of local-to-non-local energy cascading interactions which reduce (but do not eliminate) small-scale anisotropy at later times. We find that whereas the small-scale structure is still anisotropic at these later times, the second-order velocity moment tensor is insensitive to this anisotropy. Third-order moments, on the other hand, do detect the anisotropy. We conclude that whereas a single statistical measure of anisotropy can be used to indicate the presence of anisotropy, a null result in that measure does not necessarily imply that the signal is isotropic. The results indicate that non-equilibrium non-stationary turbulence is particularly sensitive to long-range interactions and deviations from local isotropy.

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