scholarly journals CpG islands’ clustering uncovers early development genes in the human genome

2018 ◽  
Vol 15 (2) ◽  
pp. 473-485
Author(s):  
Vladimir Babenko ◽  
Anton Bogomolov ◽  
Roman Babenko ◽  
Elvira Galieva ◽  
Yuriy Orlov
Keyword(s):  
Human Genome ◽  
Early Development ◽  
Cpg Islands ◽  
Replication Timing ◽  
Gene Content ◽  
Embryonic Stage ◽  
Open Chromatin ◽  
Nonhomologous Recombination ◽  
Early Embryonic Stage ◽  
Encoding Genes

We address the problem of the annotation of CpG islands (CGIs) clusters in the human genome. Upon analyzing gene content within CGIs clusters, piRNA, tRNA, and miRNA-encoding genes were found as well as CpG-rich homeobox genes reported previously. Chromosome-wide CGI density is positively correlated with replication timing, confirming that CGIs may serve as open chromatin markers. Early embryonic stage expressed KRAB-ZNF genes abundant at chromosome 19 were found to be interlinked with CGI clusters. We detected that a number of long CGIs and CGI clusters are, in fact, tandem copies with multiple annotated macrosatellites and paralogous genes. This finding implies that tandem expansion of CGIs may serve as a substrate for nonhomologous recombination events.

scholarly journals The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 342
Author(s):  
Giorgio Bernardi
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Interphase Nucleus ◽  
Cpg Islands ◽  
Open Chromatin ◽  
Short Sequence ◽  
Dna Structures ◽  
Chromatin Interactions ◽  
Dna Size

The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two “spatial compartments”, A and B, identified on the basis of chromatin interactions; and (3) of “forests and prairies” characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, “super-families” of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a “genomic code” by DNA sequences that pervade the genome and leave no room for “junk”.

Data Mining Technique Applied To DNA Sequencing

2015 ◽  
Vol 2 (7) ◽  
pp. 18
Author(s):  
R. Jamuna
Keyword(s):  
Data Mining ◽  
Dna Methylation ◽  
Markov Chain ◽  
Human Genome ◽  
Transition Probabilities ◽  
Markov Chain Model ◽  
Effective Means ◽  
Cpg Islands ◽  
Chain Model ◽  
The Given

CpG islands (CGIs) play a vital role in genome analysis as genomic markers.  Identification of the CpG pair has contributed not only to the prediction of promoters but also to the understanding of the epigenetic causes of cancer. In the human genome [1] wherever the dinucleotides CG occurs the C nucleotide (cytosine) undergoes chemical modifications. There is a relatively high probability of this modification that mutates C into a T. For biologically important reasons the mutation modification process is suppressed in short stretches of the genome, such as ‘start’ regions. In these regions [2] predominant CpG dinucleotides are found than elsewhere. Such regions are called CpG islands. DNA methylation is an effective means by which gene expression is silenced. In normal cells, DNA methylation functions to prevent the expression of imprinted and inactive X chromosome genes. In cancerous cells, DNA methylation inactivates tumor-suppressor genes, as well as DNA repair genes, can disrupt cell-cycle regulation. The most current methods for identifying CGIs suffered from various limitations and involved a lot of human interventions. This paper gives an easy searching technique with data mining of Markov Chain in genes. Markov chain model has been applied to study the probability of occurrence of C-G pair in the given   gene sequence. Maximum Likelihood estimators for the transition probabilities for each model and analgously for the  model has been developed and log odds ratio that is calculated estimates the presence or absence of CpG is lands in the given gene which brings in many  facts for the cancer detection in human genome.

Synthesis and phosphorylation of uvomorulin during mouse early development

Development ◽  
1992 ◽  
Vol 115 (1) ◽  
pp. 313-318 ◽  
Author(s):  
M. Sefton ◽  
M.H. Johnson ◽  
L. Clayton
Keyword(s):  
Cell Adhesion ◽  
Early Development ◽  
Adhesion Molecule ◽  
Cell Adhesion Molecule ◽  
Blastocyst Stage ◽  
Embryonic Stage ◽  
Cell Stage ◽  
Mouse Oocytes ◽  
Maternal Mrna ◽  
Embryonic Genome

The cell adhesion molecule, uvomorulin, is synthesised in both the 135 × 10(3) M(r) precursor and 120 × 10(3) M(r) mature forms on maternal mRNA templates in unfertilized and newly fertilized mouse oocytes. Synthesis on maternal message ceases during the 2-cell stage to resume later on mRNA encoded presumptively by the embryonic genome. Uvomorulin is detectable by immunoblotting at all stages upto the blastocyst stage, but shows variations in its total amount and processing with embryonic stage. Whilst only trace levels of phosphorylated uvomorulin are detectable in early and late 4-cell embryos, uvomorulin in 8-cell embryos is phosphorylated.

SAF-A promotes origin licensing and replication fork progression to ensure robust DNA replication

2021 ◽  
Author(s):  
Caitlin Connolly ◽  
Saori Takahashi ◽  
Hisashi Miura ◽  
Ichiro Hiratani ◽  
Nick Gilbert ◽  
...  
Keyword(s):  
Dna Replication ◽  
Biological Activities ◽  
Timing Analysis ◽  
Replication Timing ◽  
Synthesis Rate ◽  
Open Chromatin ◽  
Replication Fork Progression ◽  
Chromosome Domains ◽  
Origin Licensing ◽  
In Cells

The organisation of chromatin is closely intertwined with biological activities of chromosome domains, including transcription and DNA replication status. Scaffold attachment factor A (SAF-A), also known as Heteronuclear Ribonucleoprotein Protein U (HNRNPU), contributes to the formation of open chromatin structure. Here we demonstrate that SAF-A promotes the normal progression of DNA replication, and enables resumption of replication after inhibition. We report that cells depleted for SAF-A show reduced origin licensing in G1 phase, and consequently reduced origin activation frequency in S phase. Replication forks progress slowly in cells depleted for SAF-A, also contributing to reduced DNA synthesis rate. Single-cell replication timing analysis revealed that the boundaries between early- and late- replicating domains are blurred in cells depleted for SAF-A. Associated with these defects, SAF-A-depleted cells show elevated gH2A phosphorylation and tend to enter quiescence. Overall we find that SAF-A protein promotes robust DNA replication to ensure continuing cell proliferation.

scholarly journals Particle Swarm Optimization with Reinforcement Learning for the Prediction of CpG Islands in the Human Genome

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e21036 ◽  
Author(s):  
Li-Yeh Chuang ◽  
Hsiu-Chen Huang ◽  
Ming-Cheng Lin ◽  
Cheng-Hong Yang
Keyword(s):  
Particle Swarm Optimization ◽  
Reinforcement Learning ◽  
Human Genome ◽  
Cpg Islands ◽  
Particle Swarm ◽  
Swarm Optimization

scholarly journals Rif1 regulates the replication timing domains on the human genome

2012 ◽  
Vol 31 (18) ◽  
pp. 3667-3677 ◽  
Author(s):  
Satoshi Yamazaki ◽  
Aii Ishii ◽  
Yutaka Kanoh ◽  
Masako Oda ◽  
Yasumasa Nishito ◽  
...  
Keyword(s):  
Human Genome ◽  
Replication Timing

scholarly journals Genomic study of the critical region of chromosome 21 associated to Down syndrome

2011 ◽  
pp. 26-38 ◽  
Author(s):  
Julio César Montoya ◽  
Juliana Soto ◽  
José María Satizábal ◽  
Adalberto Sánchez ◽  
Felipe García
Keyword(s):  
Down Syndrome ◽  
Critical Region ◽  
Cpg Islands ◽  
Distal Portion ◽  
Chromosome 21 ◽  
Open Chromatin ◽  
Nucleotide Polymorphisms ◽  
Limited Information ◽  
Genomic Study ◽  
Public Data

Introduction: Previous reports have identified a region of chromosome 21 known as Down ayndrome critical region (DSCR) in which the expression of some genes would modulate the main clinical characteristics of this pathology. In this sense, there is currently limited information on the architecture of the DSCR associated. Objective: To obtain in silico a detailed vision of the chromatin structure associated with the evaluation of genomic covariables contained in public data bases. Methods: Taking as reference the information consigned in the National Center for Biotechnology Information, the Genome Browser from the University of California at Santa Cruz and from the HapMap project, a chromosome walk along 21 Mb of the distal portion of chromosome 21q arm was performed. In this distal portion, the number of single nucleotide polymorphisms (SNP), number of CpG islands, repetitive elements, recombination frequencies, and topographical state of that chromatin were recorded. Results: The frequency of CpG islands and Ref genes increased in the more distal 1.2 Mb DSCR that contrast with those localized near to the centromere. The highest level of recombination calculated for women was registered in the 21q22.12 to 22.3 bands. DSCR 6 and 9 genes showed a high percentage of methylation in CpG islands in DNA from normal and trisomic fibroblasts. The DSCR2 gene exhibited high levels of open chromatin and also methylation in some lysine residues of the histone H3 as relevant characteristics. Conclusion: The existence of a genomic environment characterized by high values of recombination frequencies and CpG methylation in DSCR 6 and 9 and also DSCR2 genes led us to postulate that in non-disjunction detected in Down syndrome, complex genomic, epigenetic and environmental relationships regulate some processes of meiosis.

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