The relationship between higher-order chromatin structure and transcription

2006 ◽  
Vol 73 ◽  
pp. 59-66 ◽  
Author(s):  
Nick Gilbert ◽  
Wendy A. Bickmore
Keyword(s):  
Chromatin Structure ◽  
Sucrose Gradient ◽  
Gene Density ◽  
Open Chromatin ◽  
Genome Wide ◽  
Silent Genes ◽  
High Gene ◽  
The Relationship ◽  
High Gene Density ◽  
Active Genes

It has generally been assumed that transcriptionally active genes are in an ‘open’ chromatin structure and that silent genes have a ‘closed’ chromatin structure. Here we re-assess this axiom in the light of genome-wide studies of chromatin fibre structure. Using a combination of sucrose gradient sedimentation and genomic microarrays of the human genome, we argue that open chromatin fibres originate from regions of high gene density, whether or not those genes are transcriptionally active.

scholarly journals MOLECULAR MAPPING OF A GENE CLUSTER FLANKING THE DROSOPHILA DOPA DECARBOXYLASE GENE

Genetics ◽  
1984 ◽  
Vol 106 (4) ◽  
pp. 679-694
Author(s):  
Denise Gilbert ◽  
Jay Hirsh ◽  
T R F Wright
Keyword(s):  
Gene Cluster ◽  
Molecular Mapping ◽  
Gene Density ◽  
Dopa Decarboxylase ◽  
Chromosomal Dna ◽  
Potential Significance ◽  
High Gene ◽  
Complementation Groups ◽  
High Gene Density

ABSTRACT Nine lethal complementation groups flanking the Drosophila Dopa decarboxylase (Ddc) gene, have been localized within 100 kb of cloned chromosomal DNA. Six of these complementation groups are within 23 kb of DNA, and all ten complementation groups, including Ddc, lie within 78-82 kb of DNA. The potential significance of this unusually high gene density is discussed.

Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: First post-treatment mitosis versus viable offspring

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 128-132 ◽  
Author(s):  
G Künzel ◽  
K I Gecheff ◽  
I Schubert
Keyword(s):  
Distribution Patterns ◽  
Gene Density ◽  
Post Treatment ◽  
Recombination Rates ◽  
Chromosomal Distribution ◽  
Chromosome Breaks ◽  
Translocation Breakpoints ◽  
High Gene ◽  
Radiation Induced ◽  
High Gene Density

Translocation breakpoints (TBs) induced by ionizing radiation are nonrandomly distributed along barley chromosomes. When first post-treatment mitoses were evaluated, centromeres and the heterochromatin-containing proximal segments tended to be more than randomly involved, and terminal segments to be less than randomly involved in translocations. Contrary to this, small chromosomal regions in median and distal arm positions, characterized by high recombination rates and high gene density, were identified as preferred sites for the origination of viable translocations, probably due to deviations in chromatin organization. Apparently, the position of a TB has an influence on the rate of viability versus elimination of the carrier cells. Surprisingly, TBs within centromeres and heterochromatin-containing segments seem to be more harmful for survival than those induced in gene-rich regions.Key words: Hordeum vulgare, radiation-induced chromosome breaks, translocation lines, breakpoint distribution.

A 1.8-Mb YAC Contig in Xp11.23: Identification of CpG Islands and Physical Mapping of CA Repeats in a Region of High Gene Density

Genomics ◽  
1994 ◽  
Vol 21 (2) ◽  
pp. 337-343 ◽  
Author(s):  
Michael P. Coleman ◽  
Andrea H. Németh ◽  
Louise Campbell ◽  
Chandrajit P. Raut ◽  
Jean Weissenbach ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Cpg Islands ◽  
Gene Density ◽  
High Gene ◽  
Yac Contig ◽  
High Gene Density

Characterization of the amphioxus presenilin gene in a high gene-density genomic region illustrates duplication during the vertebrate lineage

Gene ◽  
2001 ◽  
Vol 279 (2) ◽  
pp. 157-164 ◽  
Author(s):  
Amalia Martı́nez-Mir ◽  
Cristian Cañestro ◽  
Roser Gonzàlez-Duarte ◽  
Ricard Albalat
Keyword(s):  
Genomic Region ◽  
Gene Density ◽  
Vertebrate Lineage ◽  
High Gene ◽  
High Gene Density

scholarly journals Strong replicators associated with open chromatin are sufficient to establish an early replicating domain

2018 ◽  
Author(s):  
Caroline Brossas ◽  
Sabarinadh Chilaka ◽  
Antonin Counillon ◽  
Marc Laurent ◽  
Coralie Goncalves ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Binding Sites ◽  
Replication Origin ◽  
Molecular Mechanisms ◽  
Open Chromatin ◽  
Strongly Correlated ◽  
Topologically Associating Domains ◽  
Genome Wide ◽  
Close Physical Proximity ◽  
Temporal Program

AbstractVertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into topologically associating domains. However, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong replication origin and chromatin modifier binding sites capable of shifting a targeted mid-late replicating region for earlier replication. When inserted side-by-side, these modules acted in cooperation, with similar effects on two late-replicating regions. Targeted insertions of these two modules at two chromosomal sites separated by 30 kb brought these two modules into close physical proximity and induced the formation of an early-replicating domain. Thus, combinations of strong origins and cis-elements capable of opening the chromatin structure are the basic units of early-replicating domains, and are absent from late-replicated regions. These findings are consistent with those of genome-wide studies mapping strong initiation sites and open chromatin marks in vertebrate genomes.

Does the High Gene Density in the Sponge NK Homeobox Gene Cluster Reflect Limited Regulatory Capacity?

2008 ◽  
Vol 214 (3) ◽  
pp. 205-217 ◽  
Author(s):  
Bryony Fahey ◽  
Claire Larroux ◽  
Ben J. Woodcroft ◽  
Bernard M. Degnan
Keyword(s):  
Gene Cluster ◽  
Homeobox Gene ◽  
Gene Density ◽  
High Gene ◽  
Regulatory Capacity ◽  
High Gene Density

scholarly journals Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structureThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2011 ◽  
Vol 89 (1) ◽  
pp. 24-34 ◽  
Author(s):  
Heather J. Szerlong ◽  
Jeffrey C. Hansen
Keyword(s):  
Chromatin Structure ◽  
Peer Review Process ◽  
Secondary Structures ◽  
Hierarchical Organization ◽  
Coding Region ◽  
Nucleosomal Array ◽  
Genome Wide ◽  
The Relationship ◽  
Selection Of

Genetic information in eukaryotes is managed by strategic hierarchical organization of chromatin structure. Primary chromatin structure describes an unfolded nucleosomal array, often referred to as “beads on a string”. Chromatin is compacted by the nonlinear rearrangement of nucleosomes to form stable secondary chromatin structures. Chromatin conformational transitions between primary and secondary structures are mediated by both nucleosome-stacking interactions and the intervening linker DNA. Chromatin model system studies find that the topography of secondary structures is sensitive to the spacing of nucleosomes within an array. Understanding the relationship between nucleosome spacing and higher order chromatin structure will likely yield important insights into the dynamic nature of secondary chromatin structure as it occurs in vivo. Genome-wide nucleosome mapping studies find the distance between nucleosomes varies, and regions of uniformly spaced nucleosomes are often interrupted by regions of nonuniform spacing. This type of organization is found at a subset of actively transcribed genes in which a nucleosome-depleted region near the transcription start site is directly adjacent to uniformly spaced nucleosomes in the coding region. Here, we evaluate secondary chromatin structure and discuss the structural and functional implications of variable nucleosome distributions in different organisms and at gene regulatory junctions.

Sign in / Sign up

Export Citation Format

Share Document