scholarly journals AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12

2007 ◽  
Vol 17 (4) ◽  
pp. 451-460 ◽  
Author(s):  
M. Babcock ◽  
S. Yatsenko ◽  
P. Stankiewicz ◽  
J. R. Lupski ◽  
B. E. Morrow
Keyword(s):  
Human Genome ◽  
Genome Architecture ◽  
Chromosome 22Q11.2

scholarly journals Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture

PLoS Genetics ◽  
2005 ◽  
Vol preprint (2007) ◽  
pp. e119
Author(s):  
Adrian Gherman ◽  
Peter E. Chen ◽  
Tanya Teslovich ◽  
Pawel Stankiewicz ◽  
Marjorie Withers ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Architecture ◽  
Population Bottlenecks

scholarly journals An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate

2020 ◽  
Author(s):  
Holly Ruess ◽  
Jeon Lee ◽  
Carlos Guzman ◽  
Venkat Malladi ◽  
Iván D’Orso
Keyword(s):  
Human Genome ◽  
Large Scale ◽  
Clinical Decision Making ◽  
Integration Site ◽  
Large Body ◽  
Suppressive Therapy ◽  
Genome Architecture ◽  
Transcription Activity ◽  
Chromatin States ◽  
Hiv 1

ABSTRACTA large body of work has revealed fundamental principles of HIV-1 integration into the human genome. However, the effect of the integration site to proviral transcription activity has so far remained elusive. Here we combine open-source, large-scale datasets including epigenetics, transcriptome, and 3D genome architecture to interrogate the chromatin states, transcription activity landscape, and nuclear sub-compartments around HIV-1 integration sites in CD4+ T cells to decipher human genome codes shaping the transcription of proviral classes defined based on their position and orientation in the genome. Using a Hidden Markov Model, we describe the importance of specific chromatin states and genome architecture in the control of HIV-1 transcription activity. Additionally, implementation of a machine-learning logistic regression model reveals upstream chromatin accessibility, transcription activity, and categorical nuclear sub-compartments as optimal features predicting HIV-1 transcriptional outcomes. We finally demonstrate clinical relevance by interrogating the positions of intact proviruses persisting in patients under suppressive therapy and provide a compass compatible with clinical decision-making.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Science ◽  
2021 ◽  
Vol 372 (6545) ◽  
pp. 984-989
Author(s):  
Claire Hoencamp ◽  
Olga Dudchenko ◽  
Ahmed M. O. Elbatsh ◽  
Sumitabha Brahmachari ◽  
Jonne A. Raaijmakers ◽  
...  
Keyword(s):  
Human Genome ◽  
Physical Model ◽  
Common Ancestor ◽  
Three Dimensional ◽  
Tree Of Life ◽  
Genome Architecture ◽  
Last Common Ancestor ◽  
Eukaryotic Evolution ◽  
3D Genome ◽  
3D Genomics

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.

scholarly journals Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture

PLoS Genetics ◽  
2007 ◽  
Vol 3 (7) ◽  
pp. e119 ◽  
Author(s):  
Adrian Gherman ◽  
Peter E Chen ◽  
Tanya M Teslovich ◽  
Pawel Stankiewicz ◽  
Marjorie Withers ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Architecture ◽  
Population Bottlenecks

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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