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https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#1
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
April 25, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28446664/analysis-of-competing-hiv-1-splice-donor-sites-uncovers-a-tight-cluster-of-splicing-regulatory-elements-within-exon-2-2b
#2
Anna-Lena Brillen, Lara Walotka, Frank Hillebrand, Lisa Müller, Marek Widera, Stephan Theiss, Heiner Schaal
The HIV-1 accessory protein Vif is essential for viral replication by counteracting the host restriction factor APOBEC3G (A3G), and balanced levels of both proteins are required for efficient viral replication. Non-coding exons 2/2b contain the Vif start codon between their alternatively used splice donors 2 and 2b (D2 and D2b). For the vif mRNA, intron 1 must be removed, while intron 2 must be retained. Thus, splice acceptor 1 (A1) must be activated by U1 snRNP binding to either D2 or D2b, while splicing at D2 or D2b must be prevented...
April 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28446598/the-histone-variant-h2a-z-promotes-efficient-cotranscriptional-splicing-in-s-cerevisiae
#3
Lauren T Neves, Stephen Douglass, Roberto Spreafico, Srivats Venkataramanan, Tracy L Kress, Tracy L Johnson
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446597/the-histone-variant-h2a-z-promotes-splicing-of-weak-introns
#4
Kelly E Nissen, Christina M Homer, Colm J Ryan, Michael Shales, Nevan J Krogan, Kristin L Patrick, Christine Guthrie
Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28445889/genetic-polymorphisms-in-aromatase-cyp19a1-are-not-associated-with-gonadal-phenotypes-in-red-eared-slider-turtle-hatchlings-developed-at-a-pivotal-temperature
#5
Yuiko Matsumoto, David Crews
Embryonic gonad sex in many reptilian species is determined by the incubation temperature of the egg, a differentiation process known as temperature-dependent sex determination (TSD). Incubation at the pivotal temperature (PvT) results in approximately an equal number of offspring of both sexes. We investigated the potential contribution of genetic variations that drives the gonadal differentiation into testes or ovaries under this temperature in the red-eared slider turtle (Trachemys scripta). Four male and 4 female hatchlings of eggs that had been incubated at the PvT were examined for polymorphisms at an approximately 23-kb region of the aromatase (cyp19a1) gene...
April 27, 2017: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/28445705/mutation-characterization-and-heterodimer-analysis-of-patients-with-leukocyte-adhesion-deficiency-including-one-novel-mutation
#6
Shahram Teimourian, Martin De Boer, Dirk Roos, Anna Isaian, Ehsan Moghanloo, Sharhzad Lashkary, Bita Hassani, Hasan Mollanoori, Vahid Babaei, Asaad Azarnezhad
BACKGROUND AND AIM: Leukocyte adhesion deficiency type 1 (LAD-I) is a rare, autosomal recessive disorder of neutrophil migration, characterized by severe, recurrent bacterial infections, inadequate pus formation and impaired wound healing. The ITGB2 gene encodes the β2 integrin subunit (CD18) of the leukocyte adhesion cell molecules, and mutations in this gene cause LAD-I. The aim of the current study was to investigate the mutations in patients diagnosed with LAD-I and functional studies of the impact of two previously reported and a novel mutation on the expression of the CD18/CD11a heterodimer...
April 23, 2017: Immunology Letters
https://www.readbyqxmd.com/read/28444389/smithrnas-could-mitochondria-bend-nuclear-regulation
#7
Andrea Pozzi, Federico Plazzi, Liliana Milani, Fabrizio Ghiselli, Marco Passamonti
Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans. We sequenced sncRNA libraries from isolated mitochondria of Ruditapes philippinarum (Mollusca Bivalvia) gonads, a species with doubly uniparental inheritance of mitochondria (DUI), and identified several putative sncRNAs of mitochondrial origin...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28444238/high-purity-circular-rna-isolation-method-rpad-reveals-vast-collection-of-intronic-circrnas
#8
Amaresh C Panda, Supriyo De, Ioannis Grammatikakis, Rachel Munk, Xiaoling Yang, Yulan Piao, Dawood B Dudekula, Kotb Abdelmohsen, Myriam Gorospe
High-throughput RNA sequencing methods coupled with specialized bioinformatic analyses have recently uncovered tens of thousands of unique circular (circ)RNAs, but their complete sequences, genes of origin and functions are largely unknown. Given that circRNAs lack free ends and are thus relatively stable, their association with microRNAs (miRNAs) and RNA-binding proteins (RBPs) can influence gene expression programs. While exoribonuclease treatment is widely used to degrade linear RNAs and enrich circRNAs in RNA samples, it does not efficiently eliminate all linear RNAs...
April 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28444194/evolution-of-the-3r-myb-gene-family-in-plants
#9
Guanqiao Feng, J Gordon Burleigh, Edward L Braun, Wenbin Mei, W Brad Barbazuk
Plant 3R-MYB transcription factors are an important subgroup of the MYB super family in plants; however, their evolutionary history and functions remain poorly understood. We identified 225 3R-MYB proteins from 65 plant species, including algae and all major lineages of land plants. Two segmental duplication events preceding the common ancestor of angiosperms have given rise to three subgroups of the 3R-MYB proteins. Five conserved introns in the domain region of the 3R-MYB genes were identified, which arose through a step-wise pattern of intron gain during plant evolution...
April 20, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28443463/decreased-expression-of-hsa_circ_0001895-in-human-gastric-cancer-and-its-clinical-significances
#10
Yongfu Shao, Linbo Chen, Rongdan Lu, Xinjun Zhang, Bingxiu Xiao, Guoliang Ye, Junming Guo
Circular RNAs are a special class of endogenous RNAs characterized by jointing 3' and 5' ends together via exon or intron circularization. Recent studies found that circular RNAs are involved in the development of some human diseases. However, little is known about their roles in human gastric cancer. In this study, we chose hsa_circ_0001895 as a targeted circRNA to investigate its clinical significances in gastric cancer patients. Hsa_circ_0001895 expression levels in five gastric cancer cell lines and 257 specimens of tissues were measured by real-time quantitative reverse transcription polymerase chain reaction...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28443131/a-bioinformatics-based-alternative-mrna-splicing-code-that-may-explain-some-disease-mutations-is-conserved-in-animals
#11
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/28442397/molecular-cloning-characterization-and-expression-analysis-of-heat-shock-protein-90-in-albino-northern-snakehead-channa-argus
#12
Aiguo Zhou, Shaolin Xie, Zhenlu Wang, Muhammad Junaid, Lanfen Fan, Chao Wang, Qiao Ye, Yanfeng Chen, De-Sheng Pei, Jixing Zou
The great albino northern snakehead Channa argus is habitual to only the Sichuan Jialing Rivers System in China, making its introduction difficult to other riverine systems. Here, we characterized heat shock protein 90 (AcaHSP90) and probed its molecular responses toward the environmental stressors that C. argus can face during its introduction and breeding in the other southern latitudes of China. To serve the purpose, cDNA encoding of AcaHSP90 were cloned and characterized in albino C. argus. The cDNA was 2752bps that contained an open reading frame (ORF), encoding a 726-amino-acid polypeptide of 83...
April 22, 2017: Gene
https://www.readbyqxmd.com/read/28441946/the-protein-subunit-of-telomerase-displays-patterns-of-dynamic-evolution-and-conservation-across-different-metazoan-taxa
#13
Alvina G Lai, Natalia Pouchkina-Stantcheva, Alessia Di Donfrancesco, Gerda Kildisiute, Sounak Sahu, A Aziz Aboobaker
BACKGROUND: Most animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Given the importance of TERT and telomere biology in core metazoan life history traits, like ageing and the control of somatic cell proliferation, we hypothesised that TERT would have patterns of sequence and regulatory evolution reflecting the diverse life histories across the Animal Kingdom. RESULTS: We performed a complete investigation of the evolutionary history of TERT across animals...
April 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28441456/genome-wide-association-study-of-facial-morphology-reveals-novel-associations-with-frem1-and-park2
#14
Myoung Keun Lee, John R Shaffer, Elizabeth J Leslie, Ekaterina Orlova, Jenna C Carlson, Eleanor Feingold, Mary L Marazita, Seth M Weinberg
Several studies have now shown evidence of association between common genetic variants and quantitative facial traits in humans. The reported associations generally involve simple univariate measures and likely represent only a small fraction of the genetic loci influencing facial morphology. In this study, we applied factor analysis to a set of 276 facial linear distances derived from 3D facial surface images of 2187 unrelated individuals of European ancestry. We retained 23 facial factors, which we then tested for genetic associations using a genome-wide panel of 10,677,593 single nucleotide polymorphisms (SNPs)...
2017: PloS One
https://www.readbyqxmd.com/read/28440677/no-association-between-estrogen-receptor-gene-polymorphisms-and-premature-thelarche-in-girls
#15
Hae Sang Lee, Jong Seo Yoon, Cheol Hwan So, Kyung Hee Kim, Jin Soon Hwang
OBJECTIVE: Premature thelarche (PT) is a benign, nonprogressive condition defined as isolated breast development. While the pathophysiology of PT remains unclear, increased sensitivity to estrogen may cause PT. The aim of this study was to investigate the association between polymorphisms in the estrogen receptor alpha (ERα) gene and PT in girls. METHODS: In this case-control study, we examined 96 girls referred for early breast development (before the age of 8 years)...
April 25, 2017: Gynecological Endocrinology
https://www.readbyqxmd.com/read/28440310/klf5-mediates-odontoblastic-differentiation-through-regulating-dentin-specific-extracellular-matrix-gene-expression-during-mouse-tooth-development
#16
Zhuo Chen, Qi Zhang, Han Wang, Wentong Li, Feng Wang, Chunyan Wan, Shuli Deng, Hui Chen, Yixin Yin, Xiaoyan Li, Zhijian Xie, Shuo Chen
Klf5, a member of the Krüppel-like transcription factor family, has essential roles during embryonic development, cell proliferation, differentiation, migration and apoptosis. This study was to define molecular mechanism of Klf5 during the odontoblastic differentiation. The expression of Klf5, odontoblast-differentiation markers, Dspp and Dmp1 was co-localized in odontoblastic cells at different stages of mouse tooth development and mouse dental papilla mesenchymal cells. Klf5 was able to promote odontoblastic differentiation and enhance mineral formation of mouse dental papilla mesenchymal cells...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438684/two-spliced-isoforms-of-the-sex-determination-gene-fruitless-in-the-chinese-mitten-crab-eriocheir-sinensis
#17
Peiyao Li, Yuan Liu, Danli Luo, Chengwen Song, Zhaoxia Cui
The fruitless (fru) gene plays an important role in sex determination pathway and courtship behavior of Drosophila melanogaster. In the present study, two fru isoforms (Esfru1 and Esfru2) were identified from the Chinese mitten crab Eriocheir sinensis. Sequence analysis showed that Esfru1 and Esfru2 were encoded by the same genomic locus and generated by alternative splicing of pre-mRNA. Esfru1 had all introns completely spliced out, while Esfru2 had a longer exon1 with an additional 78bp sequence. They both contained a conserved BTB domain which was also found in D...
April 21, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28438527/the-baf-brg1-brm-associated-factor-chromatin-remodeling-complex-exhibits-ethanol-sensitivity-in-fetal-neural-progenitor-cells-and-regulates-transcription-at-the-mir-9-2-encoding-gene-locus
#18
Sasha G Burrowes, Nihal A Salem, Alexander M Tseng, Sridevi Balaraman, Marisa R Pinson, Cadianna Garcia, Rajesh C Miranda
Fetal alcohol spectrum disorders are a leading cause of intellectual disability worldwide. Previous studies have shown that developmental ethanol exposure results in loss of microRNAs (miRNAs), including miR-9, and loss of these miRNAs, in turn, mediates some of ethanol's teratogenic effects in the developing brain. We previously found that ethanol increased methylation at the miR-9-2 encoding gene locus in mouse fetal neural stem cells (NSC), advancing a mechanism for epigenetic silencing of this locus and consequently, miR-9 loss in NSCs...
April 7, 2017: Alcohol
https://www.readbyqxmd.com/read/28438387/structural-insights-into-the-mechanism-of-group-ii-intron-splicing
#19
REVIEW
Chen Zhao, Anna Marie Pyle
While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity...
April 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28436939/an-inflammatory-bowel-disease-risk-variant-in-inava-decreases-pattern-recognition-receptor-induced-outcomes
#20
Jie Yan, Matija Hedl, Clara Abraham
Inflammatory bowel disease (IBD) is characterized by dysregulation in both cytokines and responses to intestinal microbes, and proper regulation of pattern recognition receptor (PRR) signaling is critical for intestinal immune homeostasis. Altered functions for the IBD risk locus containing rs7554511, which encompasses the C1orf106 gene (recently named INAVA), and roles for the protein encoded by the INAVA gene are unknown. Here, we investigated the role of INAVA and INAVA genotype in regulating PRR-initiated outcomes in primary human cells...
April 24, 2017: Journal of Clinical Investigation
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