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Frontiers in Genetics

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https://www.readbyqxmd.com/read/28523015/transcription-factors-in-fungi-tfome-dynamics-three-major-families-and-dual-specificity-tfs
#1
Ekaterina Shelest
Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28515739/patterns-of-inter-chromosomal-gene-conversion-on-the-male-specific-region-of-the-human-y-chromosome
#2
REVIEW
Beniamino Trombetta, Eugenia D'Atanasio, Fulvio Cruciani
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28507561/deletion-extents-are-not-the-cause-of-clinical-variability-in-22q11-2-deletion-syndrome-does-the-interaction-between-dgcr8-and-mirna-cnvs-play-a-major-role
#3
Veronica Bertini, Alessia Azzarà, Annalisa Legitimo, Roberta Milone, Roberta Battini, Rita Consolini, Angelo Valetto
In humans, the most common genomic disorder is the hemizygous deletion of the chromosome 22q11.2 region, that results in the "22q11.2 deletion syndrome" (22q11.2DS). A peculiarity of 22q11.2DS is its great phenotypic variability that makes this pathology a classic example of a syndrome with variable expressivity and incomplete penetrance. The reasons for this variability have not been elucidated yet, and the molecular substrates underlying the different clinical features of 22q11.2DS are still debated. A cohort of 21 patients has been analyzed by array CGH in order to detect some of the genetic differences that may influence this variability...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28487723/genome-silencing-and-elimination-insights-from-a-selfish-b-chromosome
#4
REVIEW
John C Aldrich, Patrick M Ferree
B chromosomes are non-essential components of numerous plant and animal genomes. Because many of these "extra" chromosomes enhance their own transmission in ways that are detrimental to the rest of the genome, they can be thought of as genome parasites. An extreme example is a paternally inherited B chromosome known as paternal sex ratio (PSR), which is found in natural populations of the jewel wasp Nasonia vitripennis. In order to ensure its own propagation, PSR severely biases the wasp sex ratio by converting diploid female-destined embryos into transmitting haploid males...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28473845/pancreatic-islet-protein-complexes-and-their-dysregulation-in-type-2-diabetes
#5
Helle Krogh Pedersen, Valborg Gudmundsdottir, Søren Brunak
Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes by considering their biological context, such as tissue-specific protein interaction partners. Pancreatic islets are a key T2D tissue and many of the known genetic risk variants lead to impaired islet function, hence a better understanding of the islet-specific dysregulation in the disease-state is essential to unveil the full potential of person-specific profiles...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28458684/modeling-the-attractor-landscape-of-disease-progression-a-network-based-approach
#6
Atefeh Taherian Fard, Mark A Ragan
Genome-wide regulatory networks enable cells to function, develop, and survive. Perturbation of these networks can lead to appearance of a disease phenotype. Inspired by Conrad Waddington's epigenetic landscape of cell development, we use a Hopfield network formalism to construct an attractor landscape model of disease progression based on protein- or gene-correlation networks of Parkinson's disease, glioma, and colorectal cancer. Attractors in this landscape correspond to normal and disease states of the cell...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28458683/full-chloroplast-genome-assembly-of-11-diverse-watermelon-accessions
#7
Chao Shi, Shuo Wang, Fei Zhao, Hua Peng, Chun-Lei Xiang
No abstract text is available yet for this article.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28458682/finding-a-needle-in-a-haystack-distinguishing-mexican-maize-landraces-using-a-small-number-of-snps
#8
Jose L Caldu-Primo, Alicia Mastretta-Yanes, Ana Wegier, Daniel Piñero
In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a large phenotypic diversity of this crop. This diversity has been classified into "landraces." Previous studies have reported that genomic variation in Mexican maize is better explained by environmental factors, particularly those related with altitude, than by landrace. Still, landraces are extensively used by agronomists, who recognize them as stable and discriminatory categories for the classification of samples...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28450881/line-insertion-polymorphisms-are-abundant-but-at-low-frequencies-across-populations-of-anolis-carolinensis
#9
Robert P Ruggiero, Yann Bourgeois, Stéphane Boissinot
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28443134/characterization-of-x-chromosome-gene-expression-in-bovine-blastocysts-derived-by-in-vitro-fertilization-and-somatic-cell-nuclear-transfer
#10
Byungkuk Min, Jung Sun Park, Kyuheum Jeon, Yong-Kook Kang
To better understand X-chromosome reactivation (XCR) during early development, we analyzed transcriptomic data obtained from bovine male and female blastocysts derived by in-vitro fertilization (IVF) or somatic-cell nuclear transfer (SCNT). We found that X-linked genes were upregulated by almost two-fold in female compared with male IVF blastocysts. The upregulation of X-linked genes in female IVFs indicated a transcriptional dimorphism between the sexes, because the mean autosomal gene expression levels were relatively constant, regardless of sex...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28443133/analysis-of-purified-pancreatic-islet-beta-and-alpha-cell-transcriptomes-reveals-11%C3%AE-hydroxysteroid-dehydrogenase-hsd11b1-as-a-novel-disallowed-gene
#11
Timothy J Pullen, Mark O Huising, Guy A Rutter
We and others have previously identified a group of genes, dubbed "disallowed," whose expression is markedly lower in pancreatic islets than in other mammalian cell types. Forced mis-expression of several members of this family leads to defective insulin secretion, demonstrating the likely importance of disallowance for normal beta cell function. Up to now, transcriptomic comparisons have been based solely on data from whole islets. This raises the possibilities that (a) there may be important differences in the degree of disallowance of family members between beta and other either neuroendocrine cells; (b) beta (or alpha) cell disallowed genes may have gone undetected...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28443132/disease-resistance-and-the-definition-of-genetic-enhancement
#12
Derek So, Erika Kleiderman, Seydina B Touré, Yann Joly
Recent gene editing experiments carried out in human embryos have raised the question of whether interventions like the introduction of a CCR5-Δ32 deletion, which could provide heritable resistance to HIV infection, ought to be considered enhancements. Many authors have used the term "enhancement" in different ways, some based on patients' biomedical outcomes and others on their social context. These classifications are often considered overly imprecise. Nevertheless, the concept of "enhancement" could affect the ways in which these applications are regulated in different jurisdictions, the availability of coverage by insurers or public health care, and the force of public opinion in shaping future policy on gene editing...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28443131/a-bioinformatics-based-alternative-mrna-splicing-code-that-may-explain-some-disease-mutations-is-conserved-in-animals
#13
Wen Qu, Pablo Cingolani, Barry R Zeeberg, Douglas M Ruden
Deep sequencing of cDNAs made from spliced mRNAs indicates that most coding genes in many animals and plants have pre-mRNA transcripts that are alternatively spliced. In pre-mRNAs, in addition to invariant exons that are present in almost all mature mRNA products, there are at least 6 additional types of exons, such as exons from alternative promoters or with alternative polyA sites, mutually exclusive exons, skipped exons, or exons with alternative 5' or 3' splice sites. Our bioinformatics-based hypothesis is that, in analogy to the genetic code, there is an "alternative-splicing code" in introns and flanking exon sequences, analogous to the genetic code, that directs alternative splicing of many of the 36 types of introns...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28435435/corrigendum-simplified-assay-for-epigenetic-age-estimation-in-whole-blood-of-adults
#14
Laura Vidal-Bralo, Yolanda Lopez-Golan, Antonio Gonzalez
[This corrects the article on p. 126 in vol. 7, PMID: 27471517.].
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28424732/evidence-for-loss-in-identity-de-differentiation-and-trans-differentiation-of-islet-%C3%AE-cells-in-type-2-diabetes
#15
REVIEW
Chad S Hunter, Roland W Stein
The two main types of diabetes mellitus have distinct etiologies, yet a similar outcome: loss of islet β-cell function that is solely responsible for the secretion of the insulin hormone to reduce elevated plasma glucose toward euglycemic levels. Type 1 diabetes (T1D) has traditionally been characterized by autoimmune-mediated β-cell death leading to insulin-dependence, whereas type 2 diabetes (T2D) has hallmarks of peripheral insulin resistance, β-cell dysfunction, and cell death. However, a growing body of evidence suggests that, especially during T2D, key components of β-cell failure involves: (1) loss of cell identity, specifically proteins associated with mature cell function (e...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28421107/sexual-dimorphism-of-mirnas-secreted-by-bovine-in-vitro-produced-embryos
#16
Nicole Gross, Jenna Kropp, Hasan Khatib
Sexual dimorphism of bovine blastocysts has previously been observed through differences in development, cell death, metabolism, telomere length, DNA methylation, and transcriptomics. However, dimorphism in the secretion of miRNAs to culture media has not yet been evaluated. The objectives of this study were to determine if sex-specific blastocyst miRNA secretion occurs and to further investigate the role these miRNAs may have in the interaction between a blastocyst and the maternal environment. In vitro embryo culture was performed and media from male and female blastocysts was collected into sex-specific pools...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28408918/cftr-gene-mutations-in-the-egyptian-population-current-and-future-insights-for-genetic-screening-strategy
#17
Ayman S El-Seedy, Hanaa Shafiek, Alain Kitzis, Véronique Ladevèze
No abstract text is available yet for this article.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28400788/the-lin28-let-7-pathway-in-cancer
#18
REVIEW
Julien Balzeau, Miriam R Menezes, Siyu Cao, John P Hagan
Among all tumor suppressor microRNAs, reduced let-7 expression occurs most frequently in cancer and typically correlates with poor prognosis. Activation of either LIN28A or LIN28B, two highly related RNA binding proteins (RBPs) and proto-oncogenes, is responsible for the global post-transcriptional downregulation of the let-7 microRNA family observed in many cancers. Specifically, LIN28A binds the terminal loop of precursor let-7 and recruits the Terminal Uridylyl Transferase (TUTase) ZCCHC11 that polyuridylates pre-let-7, thereby blocking microRNA biogenesis and tumor suppressor function...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28396681/evolution-of-nucleotide-punctuation-marks-from-structural-to-linear-signals
#19
Nawal El Houmami, Hervé Seligmann
We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28377786/unveiling-the-impact-of-the-genomic-architecture-on-the-evolution-of-vertebrate-micrornas
#20
REVIEW
Gustavo S França, Ludwig C Hinske, Pedro A F Galante, Maria D Vibranovski
Eukaryotic genomes frequently exhibit interdependency between transcriptional units, as evidenced by regions of high gene density. It is well recognized that vertebrate microRNAs (miRNAs) are usually embedded in those regions. Recent work has shown that the genomic context is of utmost importance to determine miRNA expression in time and space, thus affecting their evolutionary fates over long and short terms. Consequently, understanding the inter- and intraspecific changes on miRNA genomic architecture may bring novel insights on the basic cellular processes regulated by miRNAs, as well as phenotypic evolution and disease-related mechanisms...
2017: Frontiers in Genetics
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