scholarly journals Chromatin domain boundary element search tool for Drosophila

2012 ◽  
Vol 40 (10) ◽  
pp. 4385-4395 ◽  
Author(s):  
Arumugam Srinivasan ◽  
Rakesh K. Mishra
Keyword(s):  
Boundary Element ◽  
Domain Boundary ◽  
Chromatin Domain ◽  
Search Tool

scholarly journals Boundary Element-Associated Factor 32B Connects Chromatin Domains to the Nuclear Matrix

2007 ◽  
Vol 27 (13) ◽  
pp. 4796-4806 ◽  
Author(s):  
Rashmi U. Pathak ◽  
Nandini Rangaraj ◽  
Satish Kallappagoudar ◽  
Krishnaveni Mishra ◽  
Rakesh K. Mishra
Keyword(s):  
Boundary Element ◽  
Dna Sequences ◽  
Nuclear Matrix ◽  
Domain Boundary ◽  
Coiled Coil ◽  
Boundary Elements ◽  
Structural Basis ◽  
Chromatin Domain ◽  
Eukaryotic Genomes

ABSTRACT Chromatin domain boundary elements demarcate independently regulated domains of eukaryotic genomes. While a few such boundary sequences have been studied in detail, only a small number of proteins that interact with them have been identified. One such protein is the boundary element-associated factor (BEAF), which binds to the scs′ boundary element of Drosophila melanogaster. It is not clear, however, how boundary elements function. In this report we show that BEAF is associated with the nuclear matrix and map the domain required for matrix association to the middle region of the protein. This region contains a predicted coiled-coil domain with several potential sites for posttranslational modification. We demonstrate that the DNA sequences that bind to BEAF in vivo are also associated with the nuclear matrix and colocalize with BEAF. These results suggest that boundary elements may function by tethering chromatin to nuclear architectural components and thereby provide a structural basis for compartmentalization of the genome into functionally independent domains.

scholarly journals In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element

Development ◽  
1997 ◽  
Vol 124 (9) ◽  
pp. 1809-1820 ◽  
Author(s):  
J. Mihaly ◽  
I. Hogga ◽  
J. Gausz ◽  
H. Gyurkovics ◽  
F. Karch
Keyword(s):  
Boundary Element ◽  
Domain Boundary ◽  
P Element ◽  
Chromatin Domain ◽  
Homeotic Genes ◽  
Bithorax Complex ◽  
Specific Expression ◽  
Response Element ◽  
Regulatory Domains ◽  
Polycomb Response Element

Parasegmental (PS)-specific expression of the homeotic genes of the bithorax-complex (BX-C) appears to depend upon the subdivision of the complex into a series of functionally independent cis-regulatory domains. Fab-7 is a regulatory element that lies between iab-6 and iab-7 (the PS11- and PS12-specific cis-regulatory domains, respectively). Deletion of Fab-7 causes ectopic expression of iab-7 in PS11 (where normally only iab-6 is active). Two models have been proposed to account for the dominant Fab-7 phenotype. The first considers that Fab-7 functions as a boundary element that insulates iab-6 and iab-7. The second model envisages that Fab-7 contains a silencer element that keeps iab-7 repressed in parasegments anterior to PS12. Using a P-element inserted in the middle of the Fab-7 region (the bit transposon), we have generated an extensive collection of new Fab-7 mutations that allow us to subdivide Fab-7 into a boundary element and a Polycomb-respond element (PRE). The boundary lies within 1 kb of DNA on the proximal side of the bit transposon (towards iab-6). Deletions removing this element alone cause a complex gain- and loss-of-function phenotype in PS11; in some groups of cells, both iab-6 and iab-7 are active, while in others both iab-6 and iab-7 are inactive. Thus, deletion of the boundary allows activating as well as repressing activities to travel between iab-6 and iab-7. We also provide evidences that the boundary region contains an enhancer blocker element. The Polycomb-response element lies within 0.5 kb of DNA immediately distal to the boundary (towards iab-7). Deletions removing the PRE alone do not typically cause any visible phenotype as homozygotes. Interestingly, weak ectopic activation of iab-7 is observed in hemizygous PRE deletions, suggesting that the mechanisms that keep iab-7 repressed in the absence of this element may depend upon chromosome pairing. These results help to reconcile the previously contradictory models on Fab-7 function and to shed light on how a chromatin domain boundary and a nearby PRE concur in the setting up of the appropriate PS-specific expression of the Abd-B gene of the BX-C.

Theory of a Time Domain Boundary Element Development for the Dynamic Analysis of Coupled Multiphase Porous Media

2017 ◽  
Vol 08 (03n04) ◽  
pp. 1750007
Author(s):  
Pooneh Maghoul ◽  
Behrouz Gatmiri
Keyword(s):  
Boundary Element ◽  
Time Domain ◽  
Unsaturated Soils ◽  
Water Pressure ◽  
Domain Boundary ◽  
Fundamental Solutions ◽  
Element Formulation ◽  
Inertia Effects ◽  
Coupled Equations ◽  
The Time Domain

This paper presents an advanced formulation of the time-domain two-dimensional (2D) boundary element method (BEM) for an elastic, homogeneous unsaturated soil subjected to dynamic loadings. Unlike the usual time-domain BEM, the present formulation applies a convolution quadrature which requires only the Laplace-domain instead of the time-domain fundamental solutions. The coupled equations governing the dynamic behavior of unsaturated soils ignoring contributions of the inertia effects of the fluids (water and air) are derived based on the poromechanics theory within the framework of a suction-based mathematical model. In this formulation, the solid skeleton displacements [Formula: see text], water pressure [Formula: see text] and air pressure [Formula: see text] are presumed to be independent variables. The fundamental solutions in Laplace transformed-domain for such a dynamic [Formula: see text] theory have been obtained previously by authors. Then, the BE formulation in time is derived after regularization by partial integrations and time and spatial discretizations. Thereafter, the BE formulation is implemented in a 2D boundary element code (PORO-BEM) for the numerical solution. To verify the accuracy of this implementation, the displacement response obtained by the boundary element formulation is verified by comparison with the elastodynamics problem.

scholarly journals Time Domain Boundary Element Analysis of Wake Fields in Long Accelerator Structures

2008 ◽  
Vol 55 (5) ◽  
pp. 2584-2591 ◽  
Author(s):  
Kazuhiro Fujita ◽  
Hideki Kawaguchi ◽  
Robert Hampel ◽  
Wolfgang F. O. Muller ◽  
Thomas Weiland ◽  
...  
Keyword(s):  
Boundary Element ◽  
Time Domain ◽  
Domain Boundary ◽  
Element Analysis ◽  
Boundary Element Analysis ◽  
Wake Fields
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