Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Did the modulation of expression noise shape the evolution of three dimensional genome organizations in eukaryotes?

ABSTRACT: The pervasive role of distant chromatin interactions in transcriptional regulation is increasingly becoming evident. There is a possibility that the greater diversity in chromatin interactions of a genomic locus could contribute to stochastic variation in its gene expression. However, this issue has not been addressed. Here, I present a few lines of evidence, which suggest that the variation in trans chromatin interactions might occur at the cost of expression noise. Genomic regions with nucleosome depletion, abundant and rapid transcription and with essential gene clusters exhibit relatively fewer trans chromatin interactions in the nucleus. Moreover, loci with greater number of interactions tend to show higher expression noise. Based on these observations, I hypothesize that the three dimensional organization of eukaryotic genomes might have evolved under a selective pressure to minimize the expression noise of essential gene clusters in the nucleus.

SUBMITTER: Sandhu KS

PROVIDER: S-EPMC3414405 | biostudies-literature | 2012 May-Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Did the modulation of expression noise shape the evolution of three dimensional genome organizations in eukaryotes?

Sandhu Kuljeet Singh KS

Nucleus (Austin, Tex.) 20120501 3

The pervasive role of distant chromatin interactions in transcriptional regulation is increasingly becoming evident. There is a possibility that the greater diversity in chromatin interactions of a genomic locus could contribute to stochastic variation in its gene expression. However, this issue has not been addressed. Here, I present a few lines of evidence, which suggest that the variation in trans chromatin interactions might occur at the cost of expression noise. Genomic regions with nucleos ...[more]

PMID: 22572956

Similar Datasets

Three Dimensional Organization of Genome Might Have Guided the Dynamics of Gene Order Evolution in Eukaryotes.

Project description:In eukaryotes, genes are nonrandomly organized into short gene-dense regions or "gene-clusters" interspersed by long gene-poor regions. How these gene-clusters have evolved is not entirely clear. Gene duplication may not account for all the gene-clusters since the genes in most of the clusters do not exhibit significant sequence similarity. In this study, using genome-wide data sets from budding yeast, fruit-fly, and human, we show that: 1) long-range evolutionary repositioning of genes strongly associate with their spatial proximity in the nucleus; 2) presence of evolutionary DNA break-points at involved loci hints at their susceptibility to undergo long-range genomic rearrangements; and 3) correlated epigenetic and transcriptional states of engaged genes highlight the underlying evolutionary constraints. The significance of observation 1, 2, and 3 are particularly stronger for the instances of inferred evolutionary gain, as compared with loss, of linear gene-clustering. These observations suggest that the long-range genomic rearrangements guided through 3D genome organization might have contributed to the evolution of gene order. We further hypothesize that the evolution of linear gene-clusters in eukaryotic genomes might have been mediated through spatial interactions among distant loci in order to optimize co-ordinated regulation of genes. We model this hypothesis through a heuristic model of gene-order evolution.

| S-EPMC4824123 | biostudies-literature

Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome.

Project description:Despite recent advances, the underlying functional constraints that shape the three-dimensional organization of eukaryotic genome are not entirely clear. Through comprehensive multivariate analyses of genome-wide datasets, we show that cis and trans interactions in yeast genome have significantly distinct functional associations. In particular, (i) the trans interactions are constrained by coordinated replication and co-varying mutation rates of early replicating domains through interactions among early origins, while cis interactions are constrained by coordination of late replication through interactions among late origins; (ii)cis and trans interactions exhibit differential preference for nucleosome occupancy; (iii)cis interactions are also constrained by the essentiality and co-fitness of interacting genes. Essential gene clusters associate with high average interaction frequency, relatively short-range interactions of low variance, and exhibit less fluctuations in chromatin conformation, marking a physically restrained state of engaged loci that, we suggest, is important to mitigate the epigenetic errors by restricting the spatial mobility of loci. Indeed, the genes with lower expression noise associate with relatively short-range interactions of lower variance and exhibit relatively higher average interaction frequency, a property that is conserved across Escherichia coli,yeast, and mESCs. Altogether, our observations highlight the coordination of replication and the minimization of expression noise, not necessarily co-expression of genes, as potent evolutionary constraints shaping the spatial organization of yeast genome.

| S-EPMC4833423 | biostudies-literature

Shape-Programmable Three-Dimensional Microfluidic Structures.

Project description:Microfluidic devices are gaining extensive interest due to their potential applications in wide-ranging areas, including lab-on-a-chip devices, fluid delivery, and artificial vascular networks. Most current microfluidic devices are in a planar design with fixed configurations once formed, which limits their applications such as in engineered vascular networks in biology and programmable drug delivery systems. Here, shape-programmable three-dimensional (3D) microfluidic structures, which are assembled from a bilayer of channel-embedded polydimethylsiloxane (PDMS) and shape-memory polymers (SMPs) via compressive buckling, are reported. 3D microfluidics in diverse geometries including those in open-mesh configurations are presented. In addition, they can be programmed into temporary shapes and recover their original shape under thermal stimuli due to the shape memory effect of the SMP component, with fluid flow in the microfluidic channels well maintained in both deformed and recovered shapes. Furthermore, the shape-fixing effect of SMPs enables freestanding open-mesh 3D microfluidic structures without the need for a substrate to maintain the 3D shape as used in previous studies. By adding magnetic particles into the PDMS layer, magnetically responsive 3D microfluidic structures are enabled to achieve fast, remote programming of the structures via a portable magnet. A 3D design phase diagram is constructed to show the effects of the magnetic PDMS/SMP thickness ratio and the volume fraction of magnetic particles on the shape programmability of the 3D microfluidic structures. The developed shape-programmable, open-mesh 3D microfluidic structures offer many opportunities for applications including tissue engineering, drug delivery, and many others.

| S-EPMC9552124 | biostudies-literature

Noise-tolerant single photon sensitive three-dimensional imager.

Project description:Active imagers capable of reconstructing 3-dimensional (3D) scenes in the presence of strong background noise are highly desirable for many sensing and imaging applications. A key to this capability is the time-resolving photon detection that distinguishes true signal photons from the noise. To this end, quantum parametric mode sorting (QPMS) can achieve signal to noise exceeding by far what is possible with typical linear optics filters, with outstanding performance in isolating temporally and spectrally overlapping noise. Here, we report a QPMS-based 3D imager with exceptional detection sensitivity and noise tolerance. With only 0.0006 detected signal photons per pulse, we reliably reconstruct the 3D profile of an obscured scene, despite 34-fold spectral-temporally overlapping noise photons, within the 6 ps detection window (amounting to 113,000 times noise per 20 ns detection period). Our results highlight a viable approach to suppress background noise and measurement errors of single photon imager operation in high-noise environments.

| S-EPMC7026101 | biostudies-literature

Pigeons spontaneously form three-dimensional shape categories.

Project description:We explored the pigeon's representation of the shape of simple three-dimensional objects (geons) rotated in depth (four views each of four geons). Pigeons assigned to the Categorization group had to respond differentially to images of four different geons-termed arch, barrel, brick, and wedge-based on their 3D shape, regardless of the orientation of the object. Pigeons assigned to the Pseudocategorization group had to respond differentially to the same objects based on groupings that did not correspond to object identity, which required the learning of local orientation-dependent features (e.g., a concave curve on top, or the position of an illumination hotspot). The Categorization group, which could employ object-identity representations, quickly achieved highly accurate responding. The Pseudocategorization group, however, failed to achieve reliable above-chance responding. In addition, the reaction times for the Categorization group were significantly shorter than for the Pseudocategorization group. These results indicate that pigeons show a strong, spontaneous tendency to categorize the shapes of different orientations in depth of the same 3D object as similar, if not equivalent; they do so despite the vast differences in image characteristics caused by the variations in orientations, even when such categorization is contrary to the reinforcement contingencies.

| S-EPMC10631373 | biostudies-literature

Correlating SHAPE signatures with three-dimensional RNA structures.

Project description:Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structural properties of the respective nucleotide, such as different types of base-pairing, stacking, and phosphate-backbone interactions. We find that the RNA SHAPE signal is strongly correlated with cis-Watson-Crick/Watson-Crick base-pairing and is to a remarkable degree not dependent on other structural properties with the exception of stacking. We subsequently generated probabilistic models that estimate the likelihood that a residue with a given SHAPE score participates in base-pairing. We show that several models that take SHAPE scores of adjacent residues into account perform better in predicting base-pairing compared with individual SHAPE scores. This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification.

| S-EPMC3162334 | biostudies-literature

A Landmark-Free Method for Three-Dimensional Shape Analysis.

Project description:BackgroundThe tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is especially true of those investigating smooth or featureless surfaces.MethodsIn this paper, we present a new method to perform this transformation for data obtained from high-resolution scanning technology. This method uses surface scans, instead of landmarks, to calculate a shape difference metric analogous to Procrustes distance and perform superimposition. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also explore some new ways this data can be used; for example, we can calculate an averaged surface directly and visualize point-wise shape information over this surface. Finally, we briefly demonstrate this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis.

| S-EPMC4783062 | biostudies-literature

Active superelasticity in three-dimensional epithelia of controlled shape.

Project description:Fundamental biological processes are carried out by curved epithelial sheets that enclose a pressurized lumen. How these sheets develop and withstand three-dimensional deformations has remained unclear. Here we combine measurements of epithelial tension and shape with theoretical modelling to show that epithelial sheets are active superelastic materials. We produce arrays of epithelial domes with controlled geometry. Quantification of luminal pressure and epithelial tension reveals a tensional plateau over several-fold areal strains. These extreme strains in the tissue are accommodated by highly heterogeneous strains at a cellular level, in seeming contradiction to the measured tensional uniformity. This phenomenon is reminiscent of superelasticity, a behaviour that is generally attributed to microscopic material instabilities in metal alloys. We show that in epithelial cells this instability is triggered by a stretch-induced dilution of the actin cortex, and is rescued by the intermediate filament network. Our study reveals a type of mechanical behaviour-which we term active superelasticity-that enables epithelial sheets to sustain extreme stretching under constant tension.

| S-EPMC6520229 | biostudies-literature

A three-dimensional statistical shape model of the growing mandible.

Project description:Mandibular growth and morphology are important topics in the field of oral and maxillofacial surgery. For diagnostic and planning purposes, a normative database or statistical shape model of the growing mandible can be of great benefit. A collection of 874 cadaveric children's mandibles with dental age between 1 and 12 years old were digitized using computed tomography scanning and reconstructed to three-dimensional models. Point correspondence was achieved using iterative closest point and coherent point drift algorithms. Principal component analysis (PCA) was applied to find the main modes of variation in the data set. The average mandible was presented, along with the first ten PCA modes. The first mode explained 78% of the total variance; combining the first ten modes accumulated to 95% of the total variance. The first mode was strongly correlated with age and hence, with natural growth. This is the largest study on three-dimensional mandibular shape and development conducted thus far. The main limitation is that the samples lack information such as gender and cause of death. Clinical application of the model first requires validation with contemporary samples.

| S-EPMC8458295 | biostudies-literature

Three-Dimensional Krawtchouk Descriptors for Protein Local Surface Shape Comparison.

Project description:Direct comparison of three-dimensional (3D) objects is computationally expensive due to the need for translation, rotation, and scaling of the objects to evaluate their similarity. In applications of 3D object comparison, often identifying specific local regions of objects is of particular interest. We have recently developed a set of 2D moment invariants based on discrete orthogonal Krawtchouk polynomials for comparison of local image patches. In this work, we extend them to 3D and construct 3D Krawtchouk descriptors (3DKDs) that are invariant under translation, rotation, and scaling. The new descriptors have the ability to extract local features of a 3D surface from any region-of-interest. This property enables comparison of two arbitrary local surface regions from different 3D objects. We present the new formulation of 3DKDs and apply it to the local shape comparison of protein surfaces in order to predict ligand molecules that bind to query proteins.

| S-EPMC7009784 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data