scholarly journals Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence ofHomo sapiens

2016 ◽  
Vol 8 (9) ◽  
pp. 2774-2788 ◽  
Author(s):  
Gennadi V. Glinsky
Keyword(s):  
Regulatory Networks ◽  
Phenotypic Divergence ◽  
Genomic Regulatory Networks ◽  
Regulatory Dna ◽  
Human Specific

scholarly journals Conservation patterns’ analysis of 18,364 candidate human-specific regulatory sequences revealed two distinct pathways of the human regulatory DNA divergence

2015 ◽  
Author(s):  
Gennadi Glinsky
Keyword(s):  
Transposable Elements ◽  
Regulatory Networks ◽  
Homo Sapiens ◽  
Functional Divergence ◽  
Regulatory Sequences ◽  
Conservation Patterns ◽  
Genomic Regulatory Networks ◽  
Species Specific ◽  
Regulatory Dna ◽  
Human Specific

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the idea that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Here, conservation patterns analysis of 18,364 regulatory DNA segments comprising candidate HSRS was carried out using the most recent releases of the reference genomes’ databases of humans and nonhuman primates (NHP) and defining the sequence conservation threshold as the minimum ratio of bases that must remap of 1.00. Present analyses identified 5,535 candidate HSRS defined by either the acceleration of mutation rates on the human lineage or the functional divergence from chimpanzee that are highly conserved in NHP and appear to evolve by the exaptation of ancestral DNA pathway. This pathway seems mechanistically distinct from the evolution of regulatory DNA driven by the species-specific expansion of transposable elements. It is proposed that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: i) exaptation of the highly conserved ancestral regulatory DNA segments; ii) human-specific insertions of transposable elements.

scholarly journals Effects of reference databases' refinements on the validity of molecular definitions of 15,371 candidate human-specific regulatory sequences

2015 ◽  
Author(s):  
Gennadi Glinsky
Keyword(s):  
Regulatory Networks ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Accurate Definition ◽  
Reference Databases ◽  
Definition Of ◽  
Regulatory Dna ◽  
Sequence Quality ◽  
Human Specific

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the idea that unique to human phenotypes result from human-specific changes to genomic regulatory networks (GRNs). The sequence quality of reference genome databases is essential for the accurate definition of regulatory DNA segments as candidate HSRS. It is unclear how database improvements would affect the validity of the HSRS' definition. Sequence conservation analysis of 15,371 candidate HSRS was carried out using the most recent releases of reference genomes' databases of humans and nonhuman primates (NHP) defining the conservation threshold as the minimum ratio of bases that must remap of 1.00. This analysis identifies 3,793 regulatory DNA segments that lack evidence of human-specific mutations and represent regulatory sequences highly conserved in humans, Bonobo, and Chimpanzee. Present analysis revealed a major database refinement's effect on the validity of HSRS' definition and suggests that human-specific phenotypes may evolve as a results of integration into human-specific GRNs of both conserved in NHP and human-specific genomic regulatory elements.

scholarly journals Human-specific loss of regulatory DNA and the evolution of human-specific traits

Nature ◽  
2011 ◽  
Vol 471 (7337) ◽  
pp. 216-219 ◽  
Author(s):  
Cory Y. McLean ◽  
Philip L. Reno ◽  
Alex A. Pollen ◽  
Abraham I. Bassan ◽  
Terence D. Capellini ◽  
...  
Keyword(s):  
Specific Loss ◽  
Regulatory Dna ◽  
Human Specific

scholarly journals On attracting sets in artificial networks: cross activation

2018 ◽  
Vol 16 ◽  
pp. 01005
Author(s):  
Felix Sadyrbaev
Keyword(s):  
Dynamical Systems ◽  
Differential Equations ◽  
Mathematical Models ◽  
Ordinary Differential Equations ◽  
Critical Points ◽  
Regulatory Networks ◽  
Main Diagonal ◽  
Sigmoidal Function ◽  
Genomic Regulatory Networks ◽  
Over Time

Mathematical models of artificial networks can be formulated in terms of dynamical systems describing the behaviour of a network over time. The interrelation between nodes (elements) of a network is encoded in the regulatory matrix. We consider a system of ordinary differential equations that describes in particular also genomic regulatory networks (GRN) and contains a sigmoidal function. The results are presented on attractors of such systems for a particular case of cross activation. The regulatory matrix is then of particular form consisting of unit entries everywhere except the main diagonal. We show that such a system can have not more than three critical points. At least n–1 eigenvalues corresponding to any of the critical points are negative. An example for a particular choice of sigmoidal function is considered.

scholarly journals Genomic Regulatory Networks and Animal Development

2005 ◽  
Vol 9 (4) ◽  
pp. 449-462 ◽  
Author(s):  
Angelike Stathopoulos ◽  
Michael Levine
Keyword(s):  
Regulatory Networks ◽  
Animal Development ◽  
Genomic Regulatory Networks

scholarly journals Genes and chromosomes: control of development

2004 ◽  
Vol 76 (3) ◽  
pp. 529-540 ◽  
Author(s):  
Oleg Serov ◽  
Irina Serova
Keyword(s):  
Gene Expression ◽  
Molecular Basis ◽  
Regulatory Networks ◽  
Interphase Nucleus ◽  
Developmental Regulation ◽  
Hierarchical Control ◽  
Epigenetic Inheritance ◽  
The Past ◽  
Genomic Regulatory Networks ◽  
Chromosome Level

The past decade has witnessed immense progress in research into the molecular basis behind the developmental regulation of genes. Sets of genes functioning under hierarchical control have been identified, evolutionary conserved systems of genes effecting the cell-to-cell transmission of transmembrane signals and assigned a central role in morphogenesis have been intensively studied; the concept of genomic regulatory networks coordinating expression of many genes has been introduced, to mention some of the major breakthroughs. It should be noted that the temporal and tissue-specific parameters of gene expression are correctly regulated in development only in the context of the chromosome and that they are to a great extent dependent on the position of the gene on the chromosome or the interphase nucleus. Moreover epigenetic inheritance of the gene states through successive cell generations has been conducted exclusively at the chromosome level by virtue of cell or chromosome memory. The ontogenetic memory is an inherent property of the chromosome and cis-regulation has a crucial role in its maintenance.

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