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International Journal of Genomics

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https://www.readbyqxmd.com/read/30009162/topological-characterization-of-human-and-mouse-m-5-c-epitranscriptome-revealed-by-bisulfite-sequencing
#1
Zhen Wei, Subbarayalu Panneerdoss, Santosh Timilsina, Jingting Zhu, Tabrez A Mohammad, Zhi-Liang Lu, João Pedro de Magalhães, Yidong Chen, Rong Rong, Yufei Huang, Manjeet K Rao, Jia Meng
Background: Compared with the well-studied 5-methylcytosine (m5 C) in DNA, the role and topology of epitranscriptome m5 C remain insufficiently characterized. Results: Through analyzing transcriptome-wide m5 C distribution in human and mouse, we show that the m5 C modification is significantly enriched at 5' untranslated regions (5'UTRs) of mRNA in human and mouse. With a comparative analysis of the mRNA and DNA methylome, we demonstrate that, like DNA methylation, transcriptome m5 C methylation exhibits a strong clustering effect...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30003085/nonredundant-highly-connected-micrornas-control-functionality-in-breast-cancer-networks
#2
Guillermo de Anda-Jáuregui, Jesús Espinal-Enríquez, Diana Drago-García, Enrique Hernández-Lemus
Alterations to transcriptional regulation are an important factor in breast cancer. Noncoding RNA, such as microRNA (miR), have very influential roles in the transcriptional regulation of genes. Transcriptional regulation can be successfully modeled and analyzed using complex network theory. Particularly, interactions between two distinct classes of biological elements, such as miR and genes, can be approached through the bipartite network formalism. Based on bipartite network properties, it is possible to identify highly influential miRs in the network, such as those that have a large number of connections indicating regulation of a large set of genes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29977903/the-genetic-diversity-and-geographic-differentiation-of-the-wild-soybean-in-northeast-china-based-on-nuclear-microsatellite-variation
#3
Hongkun Zhao, Yumin Wang, Fu Xing, Xiaodong Liu, Cuiping Yuan, Guangxun Qi, Jixun Guo, Yingshan Dong
In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index ( I ) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29967765/transcriptome-and-expression-profiling-analysis-of-recalcitrant-tea-camellia-sinensis-l-seeds-sensitive-to-dehydration
#4
Xiaofang Jin, Dandan Liu, Linlong Ma, Ziming Gong, Dan Cao, Yanli Liu, Yeyun Li, Changjun Jiang
The tea plant ( Camellia sinensis (L.) O. Kuntze) is an economically important woody perennial nonalcoholic health beverage crop. Tea seeds are categorized as recalcitrant and are sensitive to dehydration treatment. However, the molecular basis of this phenomenon has not been investigated. Thus, we analyzed the genome-wide expression profiles of three dehydration stages using RNA-Seq and digital gene expression (DGE) technologies. We performed de novo assembly and obtained a total of 91,925 nonredundant unigenes, of which 58,472 were extensively annotated...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29951522/overexpression-of-a-new-zinc-finger-protein-transcription-factor-osctzfp8-improves-cold-tolerance-in-rice
#5
Yong-Mei Jin, Rihua Piao, Yong-Feng Yan, Mojun Chen, Ling Wang, Hongxia He, Xiaoxiao Liu, Xing-Ai Gao, Wenzhu Jiang, Xiu-Feng Lin
Cold stress is one of the most important abiotic stresses in rice. C2 H2 zinc finger proteins play important roles in response to abiotic stresses in plants. In the present study, we isolated and functionally characterized a new C2 H2 zinc finger protein transcription factor OsCTZFP8 in rice. OsCTZFP8 encodes a C2 H2 zinc finger protein, which contains a typical zinc finger motif, as well as a potential nuclear localization signal (NLS) and a leucine-rich region (L-box). Expression of OsCTZFP8 was differentially induced by several abiotic stresses and was strongly induced by cold stress...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29951521/advancing-genomics-for-drug-development-and-safety-evaluation
#6
EDITORIAL
Zhichao Liu, Joshua Xu, Zhining Wen
No abstract text is available yet for this article.
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29888248/whole-exome-sequencing-identifies-one-de-novo-variant-in-the-fgd6-gene-in-a-thai-family-with-autism-spectrum-disorder
#7
Chuphong Thongnak, Areerat Hnoonual, Duangkamol Tangviriyapaiboon, Suchaya Silvilairat, Apichaya Puangpetch, Ekawat Pasomsub, Wasun Chantratita, Pornprot Limprasert, Chonlaphat Sukasem
Autism spectrum disorder (ASD) has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29888247/insights-into-the-genome-sequence-of-chromobacterium-amazonense-isolated-from-a-tropical-freshwater-lake
#8
Alexandre Bueno Santos, Patrícia Silva Costa, Anderson Oliveira do Carmo, Gabriel da Rocha Fernandes, Larissa Lopes Silva Scholte, Jeronimo Ruiz, Evanguedes Kalapothakis, Edmar Chartone-Souza, Andréa Maria Amaral Nascimento
Members of the genus Chromobacterium have been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis of Chromobacterium amazonense strain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29862250/genome-wide-expression-profiles-of-hemp-cannabis-sativa-l-in-response-to-drought-stress
#9
Chunsheng Gao, Chaohua Cheng, Lining Zhao, Yongting Yu, Qing Tang, Pengfei Xin, Touming Liu, Zhun Yan, Yuan Guo, Gonggu Zang
Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29862249/comparative-genomics-analysis-of-plasmid-ppv989-94-from-a-clinical-isolate-of-pantoea-vagans-pv989
#10
Lei Xu, Min Yin, Tingyuan Zhu, Yabo Liu, Yuanyuan Ying, Junwan Lu, Chaoqing Lin, Jianchao Ying, Teng Xu, Liyan Ni, Qiyu Bao, Shunfei Lu
Pantoea vagans , a gram-negative bacterium from the genus Pantoea and family Enterobacteriaceae , is present in various natural environments and considered to be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic and sequenced its whole genome. Besides a chromosome DNA molecule, it also harboured three large plasmids. A comparative genomics analysis was performed for the smallest plasmid, pPV989-94. It can be divided into four regions, including three conservative regions related to replication (R1), transfer conjugation (R2), and transfer leading (R3), and one variable region (R4)...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29854720/genome-wide-identification-phylogeny-and-expression-analysis-of-arf-genes-involved-in-vegetative-organs-development-in-switchgrass
#11
Jianli Wang, Zhenying Wu, Zhongbao Shen, Zetao Bai, Peng Zhong, Lichao Ma, Duofeng Pan, Ruibo Zhang, Daoming Li, Hailing Zhang, Chunxiang Fu, Guiqing Han, Changhong Guo
Auxin response factors (ARFs) have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass ( Panicum virgatum L.), a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes ( PvARFs ) were identified in the switchgrass genome (2n = 4x = 36), 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29854719/the-challenges-and-opportunities-in-the-clinical-application-of-noncoding-rnas-the-road-map-for-mirnas-and-pirnas-in-cancer-diagnostics-and-prognostics
#12
REVIEW
Preethi Krishnan, Sambasivarao Damaraju
Discoveries on nonprotein-coding RNAs have induced a paradigm shift in our overall understanding of gene expression and regulation. We now understand that coding and noncoding RNA machinery work in concert to maintain overall homeostasis. Based on their length, noncoding RNAs are broadly classified into two groups-long (>200 nt) and small noncoding RNAs (<200 nt). These RNAs perform diverse functions-gene regulation, splicing, translation, and posttranscriptional modifications. MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) are two classes of small noncoding RNAs that are now classified as master regulators of gene expression...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29854718/characterization-of-transcription-termination-associated-rnas-new-insights-into-their-biogenesis-tailing-and-expression-in-primary-tumors
#13
Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Next-generation sequencing has uncovered novel classes of small RNAs (sRNAs) in eukaryotes, in addition to the well-known miRNAs, siRNAs, and piRNAs. In particular, sRNA species arise from transcription start sites (TSSs) and the transcription termination sites (TTSs) of genes. However, a detailed characterization of these new classes of sRNAs is still lacking. Here, we present a comprehensive study of sRNAs derived from TTSs of expressed genes (TTSa-RNAs) in human cell lines and primary tissues. Taking advantage of sRNA-sequencing, we show that TTSa-RNAs are present in the nuclei of human cells, are loaded onto both AGO1 and AGO2, and their biogenesis does not require DICER and AGO2 endonucleolytic activity...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850479/genomics-approach-of-the-natural-product-pharmacology-for-high-impact-diseases
#14
EDITORIAL
Yong Wang, Qin Feng, Peijian He, Lixin Zhu, Guoxun Chen
No abstract text is available yet for this article.
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850478/whole-genome-sequencing-and-comparative-genome-analysis-provided-insight-into-the-predatory-features-and-genetic-diversity-of-two-bdellovibrio-species-isolated-from-soil
#15
Omotayo Opemipo Oyedara, Aldo Segura-Cabrera, Xianwu Guo, Temidayo Oluyomi Elufisan, Rafael Alejandro Cantú González, Mario A Rodríguez Pérez
Bdellovibrio spp. are predatory bacteria with great potential as antimicrobial agents. Studies have shown that members of the genus Bdellovibrio exhibit peculiar characteristics that influence their ecological adaptations. In this study, whole genomes of two different Bdellovibrio spp. designated SKB1291214 and SSB218315 isolated from soil were sequenced. The core genes shared by all the Bdellovibrio spp. considered for the pangenome analysis including the epibiotic B. exovorus were 795. The number of unique genes identified in Bdellovibrio spp...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850477/the-progress-of-methylation-regulation-in-gene-expression-of-cervical-cancer
#16
REVIEW
Chunyang Feng, Junxue Dong, Weiqin Chang, Manhua Cui, Tianmin Xu
Cervical cancer is one of the most common gynecological tumors in females, which is closely related to high-rate HPV infection. Methylation alteration is a type of epigenetic decoration that regulates the expression of genes without changing the DNA sequence, and it is essential for the progression of cervical cancer in pathogenesis while reflecting the prognosis and therapeutic sensitivity in clinical practice. Hydroxymethylation has been discovered in recent years, thus making 5-hmC, the more stable marker, attract more attention in the field of methylation research...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850476/the-influence-of-metabolic-syndrome-and-sex-on-the-dna-methylome-in-schizophrenia
#17
Kyle J Burghardt, Jacyln M Goodrich, Brittany N Lines, Vicki L Ellingrod
Introduction: The mechanism by which metabolic syndrome occurs in schizophrenia is not completely known; however, previous work suggests that changes in DNA methylation may be involved which is further influenced by sex. Within this study, the DNA methylome was profiled to identify altered methylation associated with metabolic syndrome in a schizophrenia population on atypical antipsychotics. Methods: Peripheral blood from schizophrenia subjects was utilized for DNA methylation analyses...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850475/the-yabby-genes-of-leaf-and-leaf-like-organ-polarity-in-leafless-plant-monotropa-hypopitys
#18
Anna V Shchennikova, Marya A Slugina, Alexey V Beletsky, Mikhail A Filyushin, Andrey A Mardanov, Olga A Shulga, Elena Z Kochieva, Nikolay V Ravin, Konstantin G Skryabin
Monotropa hypopitys is a mycoheterotrophic, nonphotosynthetic plant acquiring nutrients from the roots of autotrophic trees through mycorrhizal symbiosis, and, similar to other extant plants, forming asymmetrical lateral organs during development. The members of the YABBY family of transcription factors are important players in the establishment of leaf and leaf-like organ polarity in plants. This is the first report on the identification of YABBY genes in a mycoheterotrophic plant devoid of aboveground vegetative organs...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850474/genome-wide-identification-and-characterization-of-fox-genes-in-the-honeybee-apis-cerana-and-comparative-analysis-with-other-bee-fox-genes
#19
Hongyi Nie, Haiyang Geng, Yan Lin, Shupeng Xu, Zhiguo Li, Yazhou Zhao, Songkun Su
The forkhead box (Fox) gene family, one of the most important families of transcription factors, participates in various biological processes. However, Fox genes in Hymenoptera are still poorly known. In this study, 14 Fox genes were identified in the genome of Apis cerana . In addition, 16 (Apis mellifera) , 13 (Apis dorsata) , 16 (Apis florea) , 17 (Bombus terrestris) , 16 (Bombus impatiens) , and 18 (Megachile rotundata) Fox genes were identified in their genomes, respectively. Phylogenetic analyses suggest that FoxA is absent in the genome of A...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29850473/gene-variation-of-endoplasmic-reticulum-aminopeptidases-1-and-2-and-risk-of-blood-pressure-progression-and-incident-hypertension-among-17-255-initially-healthy-women
#20
Robert Y L Zee, Alicia Rivera, Yaritza Inostroza, Paul M Ridker, Daniel I Chasman, Jose R Romero
Recent studies have demonstrated the importance of endoplasmic reticulum aminopeptidase (ERAP) in blood pressure (BP) homeostasis. To date, no large prospective, genetic-epidemiological data are available on genetic variation within ERAP and hypertension risk. The association of 45 genetic variants of ERAP1 and ERAP2 was investigated in 17,255 Caucasian female participants from the Women's Genome Health Study. All subjects were free of hypertension at baseline. During an 18-year follow-up period, 10,216 incident hypertensive cases were identified...
2018: International Journal of Genomics
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