scholarly journals Microchromosomes Exhibit Distinct Features of Vertebrate Chromosome Structure and Function with Underappreciated Ramifications for Genome Evolution

2020 ◽  
Author(s):  
Blair W Perry ◽  
Drew R Schield ◽  
Richard H Adams ◽  
Todd A Castoe
Keyword(s):  
Chromosome Structure ◽  
Genome Structure ◽  
Structure And Function ◽  
Open Chromatin ◽  
Vertebrate Genome ◽  
Sequencing Data ◽  
Evolutionary Origins ◽  
And Function ◽  
Open Question ◽  
Distinct Features

Abstract Microchromosomes are common yet poorly understood components of many vertebrate genomes. Recent studies have revealed that microchromosomes contain a high density of genes and possess other distinct characteristics compared with macrochromosomes. Whether distinctive characteristics of microchromosomes extend to features of genome structure and organization, however, remains an open question. Here, we analyze Hi-C sequencing data from multiple vertebrate lineages and show that microchromosomes exhibit consistently high degrees of interchromosomal interaction (particularly with other microchromosomes), appear to be colocalized to a common central nuclear territory, and are comprised of a higher proportion of open chromatin than macrochromosomes. These findings highlight an unappreciated level of diversity in vertebrate genome structure and function, and raise important questions regarding the evolutionary origins and ramifications of microchromosomes and the genes that they house.

scholarly journals Comprehensive identification of transposable element insertions using multiple sequencing technologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chu ◽  
Rebeca Borges-Monroy ◽  
Vinayak V. Viswanadham ◽  
Soohyun Lee ◽  
Heng Li ◽  
...  
Keyword(s):  
Transposable Element ◽  
Structure And Function ◽  
Endogenous Retroviruses ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read ◽  
And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

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

An isochore transition zone in the NF1 gene region is a conserved landmark of chromosome structure and function

Genomics ◽  
2005 ◽  
Vol 86 (4) ◽  
pp. 439-445 ◽  
Author(s):  
Claudia Schmegner ◽  
Anke Berger ◽  
Walther Vogel ◽  
Horst Hameister ◽  
Günter Assum
Keyword(s):  
Transition Zone ◽  
Chromosome Structure ◽  
Structure And Function ◽  
Gene Region ◽  
Nf1 Gene ◽  
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

The heart as a functional unit

ESC CardioMed ◽  
2018 ◽  
pp. 76-81
Author(s):  
Philip J. Kilner ◽  
Sonya V. Babu-Narayan
Keyword(s):  
Functional Unit ◽  
Structure And Function ◽  
Morphological Features ◽  
Metabolic Rates ◽  
Evolutionary Origins ◽  
And Function

This chapter and Chapter 3.6 address the interrelatedness of heart form, structure, and function. The principle of reciprocation between the alternate contractions of atrial and ventricular cavities is outlined, and it is explained how it is enhanced with the increased output of exercise by virtue of the directions of the forces associated with changes of momentum through the looped curvatures of the heart. The human heart’s sinuous paths of flow and its fully septated, four-chamber arrangement are features shared by the hearts of other mammals and the birds, which are also warm-blooded with relatively high cardiac outputs for high metabolic rates. These morphological features are not found among the hearts of the exothermic invertebrate phyla such as worms, arthropods, or molluscs. The possible evolutionary origins and potential functional advantages of cardiac septation for mammalian life are considered. This chapter addresses the interrelatedness of macroscopic structural morphodynamics with the fluid morphodynamics of passing blood streams while Chapter 3.6 considers the smaller-scale morphodynamics of myocardium in an attempt to convey a multiscale morphodynamic interpretation of the heart form, structure, and function.

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