Multi-scale coding of genomic information: From DNA sequence to genome structure and function

2011 ◽  
Vol 498 (2-3) ◽  
pp. 45-188 ◽  
Author(s):  
Alain Arneodo ◽  
Cédric Vaillant ◽  
Benjamin Audit ◽  
Françoise Argoul ◽  
Yves d’Aubenton-Carafa ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Genome Structure ◽  
Structure And Function ◽  
Genomic Information ◽  
Multi Scale ◽  
And Function

scholarly journals Impact of DNA methylation on 3D genome structure

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana Buitrago ◽  
Mireia Labrador ◽  
Juan Pablo Arcon ◽  
Rafael Lema ◽  
Oscar Flores ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromatin Structure ◽  
Chromatin Condensation ◽  
Genome Structure ◽  
Dna Methyltransferases ◽  
Model System ◽  
Structure And Function ◽  
3D Genome ◽  
Cellular Machinery ◽  
And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

2007 ◽  
Vol 58 (6) ◽  
pp. 470 ◽  
Author(s):  
P. Moolhuijzen ◽  
D. S. Dunn ◽  
M. Bellgard ◽  
M. Carter ◽  
J. Jia ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Physical Map ◽  
Genome Structure ◽  
Genetic Research ◽  
Structure And Function ◽  
Wheat Genome ◽  
D Genome ◽  
Genome Sequencing Consortium ◽  
And Function ◽  
Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

scholarly journals Histone chaperone FACT and curaxins: effects on genome structure and function

2019 ◽  
Vol 2019 ◽  
Author(s):  
Han-Wen Chang ◽  
Ekaterina V. Nizovtseva ◽  
Sergey V. Razin ◽  
Tim Formosa ◽  
Katerina V. Gurova ◽  
...  
Keyword(s):  
Genome Structure ◽  
Histone Chaperone ◽  
Structure And Function ◽  
And Function

Microsporidian Genome Structure and Function

Microsporidia ◽  
2014 ◽  
pp. 221-229 ◽  
Author(s):  
Patrick J. Keeling ◽  
Naomi M. Fast ◽  
Nicolas Corradi
Keyword(s):  
Genome Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths

2019 ◽  
Vol 11 (8) ◽  
pp. 2162-2177 ◽  
Author(s):  
David A Ray ◽  
Jenna R Grimshaw ◽  
Michaela K Halsey ◽  
Jennifer M Korstian ◽  
Austin B Osmanski ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Common Ancestor ◽  
Genome Structure ◽  
Detailed Examination ◽  
Structure And Function ◽  
Evolutionary Processes ◽  
Repetitive Nature ◽  
Daunting Task ◽  
And Function

Abstract Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.

scholarly journals Chromosome organization in bacteria: mechanistic insights into genome structure and function

2019 ◽  
Vol 21 (4) ◽  
pp. 227-242 ◽  
Author(s):  
Remus T. Dame ◽  
Fatema-Zahra M. Rashid ◽  
David C. Grainger
Keyword(s):  
Genome Structure ◽  
Structure And Function ◽  
Chromosome Organization ◽  
And Function

scholarly journals Cohesin Releasing Factor WAPL Regulates Genome Structure and Function of Mature T Cells

2021 ◽  
Author(s):  
Yaping Sun ◽  
Gabrielle A. Dotson ◽  
Lindsey A. Muir ◽  
Scott Ronquist ◽  
Katherine Oravecz-Wilson ◽  
...  
Keyword(s):  
T Cells ◽  
Hematopoietic Cell Transplantation ◽  
Genome Structure ◽  
3D Structure ◽  
Three Dimensional ◽  
Structure And Function ◽  
Cell Functions ◽  
And Function

ABSTRACTThe cohesin complex modulates gene expression and cellular functions by shaping three-dimensional (3D) organization of chromatin. WAPL, cohesin’s DNA releasing factor, regulates 3D chromatin architecture. The 3D genome structure and its relevance to mature T cell functions is not well understood. We show that in vivo lymphopenic expansion, and allo-antigen driven proliferation, alters the 3D structure and function of the genome in mature T cells. Conditional deletion of Wapl in T cells reduced long-range genomic interactions, altered chromatin A/B compartments and the topologically associating domains (TAD) of the chromatin in T cells at baseline. Comparison of chromatin structure in normal and WAPL-deficient T cells after lymphopenic and allo-antigen driven stimulation revealed reduced loop extensions with changes in cell cycling genes. WAPL-mediated changes in 3D architecture of chromatin regulated activation, cycling and proliferation of T cells in vitro and in vivo. Finally, WAPL-deficient T cells caused reduced severity of graft-versus-host disease following experimental allogeneic hematopoietic cell transplantation. These data collectively characterize 3D genomic architecture of T cells in vivo and demonstrate biological and clinical implications for its disruption by cohesin releasing factor WAPL.

Sign in / Sign up

Export Citation Format

Share Document