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https://www.readbyqxmd.com/read/29928011/the-ubx-polycomb-response-element-bypasses-an-unpaired-fab-8-insulator-via-cis-transvection-in-drosophila
#1
Danfeng Lu, Zhuoran Li, Lingling Li, Liping Yang, Guijun Chen, Deying Yang, Yue Zhang, Vikrant Singh, Sheryl Smith, Yu Xiao, Erlin Wang, Yunshuang Ye, Wei Zhang, Lei Zhou, Yikang Rong, Jumin Zhou
Chromatin insulators or boundary elements protect genes from regulatory activities from neighboring genes or chromatin domains. In the Drosophila Abdominal-B (Abd-B) locus, the deletion of such elements, such as Frontabdominal-7 (Fab-7) or Fab-8 led to dominant gain of function phenotypes, presumably due to the loss of chromatin barriers. Homologous chromosomes are paired in Drosophila, creating a number of pairing dependent phenomena including transvection, and whether transvection may affect the function of Polycomb response elements (PREs) and thus contribute to the phenotypes are not known...
2018: PloS One
https://www.readbyqxmd.com/read/29927971/genome-wide-identification-and-classification-of-myb-superfamily-genes-in-peach
#2
Chunhua Zhang, Ruijuan Ma, Jianlan Xu, Juan Yan, Lei Guo, Juan Song, Ruchao Feng, Mingliang Yu
The MYB transcription factor superfamily is one of the largest superfamilies modulating various biological processes in plants. Over the past few decades, many MYB superfamily genes have been identified and characterized in some plant species. However, genes belonging to the MYB superfamily in peach (Prunus persica) have not been comprehensively identified and characterized although the genome sequences of peach were released several years ago. In total, this study yielded a set of 256 MYB superfamily genes that was divided into five subfamilies: the R2R3-MYB (2R-MYB), R1R2R3-MYB (3R-MYB), MYB-related (1R-MYB), 4R-MYB, and Atypical-MYB subfamilies...
2018: PloS One
https://www.readbyqxmd.com/read/29927700/adaptations-of-vancomycin-intermediate-sequence-type-72-methicillin-resistant-staphylococcus-aureus-for-daptomycin-nonsusceptibility
#3
Gi Yong Lee, Kyung Mi Kang, Seung Hyun Back, Jin Yang Baek, So Hyun Kim, Jong-Hwan Park, Soo-Jin Yang
In Korea, the major clonal type of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is sequence type 72 (ST72) with staphylococcal cassette chromosome mec (SCCmec) type IV (ST72-MRSA-IV). In this study, we used a previously well-characterized isogenic pair of ST72 vancomycin (VAN) susceptible-and VAN intermediate-MRSA strains (VSSA303 and VISA072) and several VSSA strains complemented with plasmids expressing single-point mutated genes (dprAG196C , femAF92C , vraRE127K , and vraSRE127K ) identified in the VISA strain...
June 21, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29925315/arks-chromosome-scale-scaffolding-of-human-genome-drafts-with-linked-read-kmers
#4
Lauren Coombe, Jessica Zhang, Benjamin P Vandervalk, Justin Chu, Shaun D Jackman, Inanc Birol, René L Warren
BACKGROUND: The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach...
June 20, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29924489/reconstitution-of-mitotic-chromatids-in-vitro
#5
Keishi Shintomi, Tatsuya Hirano
The mitotic chromosome, which is composed of a pair of sister chromatids, is a large macromolecular assembly that ensures faithful transmission of genetic information into daughter cells. Despite its fundamental importance, how a nucleosome fiber is folded and assembled into a large-scale chromatid structure remains poorly understood. To address this question, we have established a biochemically tractable system in which mitotic chromatids can be reconstituted in vitro by mixing a simple substrate (sperm nucleus) and a limited number of purified factors...
June 2018: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/29922330/estimation-of-recombination-rate-and-maternal-linkage-disequilibrium-in-half-sibs
#6
Alexander Hampel, Friedrich Teuscher, Luis Gomez-Raya, Michael Doschoris, Dörte Wittenburg
A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been proposed for estimating these parameters in half-sibs without phasing the progeny. It, however, overlooks the fact that the underlying likelihood function may have two maxima...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29915389/structural-basis-of-meiotic-chromosome-synapsis-through-sycp1-self-assembly
#7
James M Dunce, Orla M Dunne, Matthew Ratcliff, Claudia Millán, Suzanne Madgwick, Isabel Usón, Owen R Davies
Meiotic chromosomes adopt unique structures in which linear arrays of chromatin loops are bound together in homologous chromosome pairs by a supramolecular protein assembly, the synaptonemal complex. This three-dimensional scaffold provides the essential structural framework for genetic exchange by crossing over and subsequent homolog segregation. The core architecture of the synaptonemal complex is provided by SYCP1. Here we report the structure and self-assembly mechanism of human SYCP1 through X-ray crystallographic and biophysical studies...
June 18, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29914373/characterization-of-the-populus-rab-family-genes-and-the-function-of-ptrabe1b-in-salt-tolerance
#8
Jin Zhang, Yu Li, Bobin Liu, Lijuan Wang, Li Zhang, Jianjun Hu, Jun Chen, Huanquan Zheng, Mengzhu Lu
BACKGROUND: Rab proteins form the largest family of the Ras superfamily of small GTP-binding proteins and regulate intracellular trafficking pathways. However, the function of the Rab proteins in woody species is still an open question. RESULTS: Here, a total of 67 PtRabs were identified in Populus trichocarpa and categorized into eight subfamilies (RabA-RabH). Based on their chromosomal distribution and duplication blocks in the Populus genome, a total of 27 PtRab paralogous pairs were identified and all of them were generated by whole-genome duplication events...
June 18, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29914364/an-integrated-omics-analysis-of-the-epigenetic-landscape-of-gene-expression-in-human-blood-cells
#9
Elizabeth M Kennedy, George N Goehring, Michael H Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K Smith, Karen N Conneely
BACKGROUND: Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. RESULTS: We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells...
June 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29909608/nfatc3-pla2g15-fusion-transcript-identified-by-rna-sequencing-promotes-tumor-invasion-and-proliferation-in-colorectal-cancer-cell-lines
#10
Jee-Eun Jang, Hwang-Phill Kim, Sae-Won Han, Hoon Jang, Si-Hyun Lee, Sang-Hyun Song, Duhee Bang, Tae-You Kim
Purpose: This study was designed to identify novel fusion transcripts (FTs) and their functional significance in colorectal cancer lines. Materials and Methods: We performed paired-end RNA sequencing of 28 colorectal cancer (CRC) cell lines. FT candidates were identified using TopHat-fusion, ChimeraScan, and FusionMap tools and further experimental validation was conducted through reverse transcription-polymerase chain reaction and Sanger sequencing. FT was depleted in human CRC line and the effects on cell proliferation, cell migration, and cell invasion were analyzed...
June 14, 2018: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/29907648/the-spectrum-of-replication-errors-in-the-absence-of-error-correction-assayed-across-the-whole-genome-of-escherichia-coli
#11
Brittany A Niccum, Heewook Lee, Wazim MohammedIsmail, Haixu Tang, Patricia L Foster
When the DNA polymerase that replicates the Escherichia coli chromosome, DNA Pol III, makes an error, there are two primary defenses against mutation: proofreading by the epsilon subunit of the holoenzyme and mismatch repair. In proofreading deficient strains, mismatch repair is partially saturated and the cell's response to DNA damage, the SOS response, may be partially induced. To investigate the nature of replication errors, we used mutation accumulation experiments and whole genome sequencing to determine mutation rates and mutational spectra across the entire chromosome of strains deficient in proofreading, mismatch repair, and the SOS response...
June 15, 2018: Genetics
https://www.readbyqxmd.com/read/29907647/determinants-of-base-pair-substitution-patterns-revealed-by-whole-genome-sequencing-of-dna-mismatch-repair-defective-escherichia-coli
#12
Patricia L Foster, Brittany A Niccum, Ellen Popodi, Jesse P Townes, Heewook Lee, Wazim MohammedIsmail, Haixu Tang
Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defective E. coli strains yielded ≈30,000 base-pair substitutions, revealing mutational patterns across the entire chromosome. The base-pair substitution spectrum was dominated by A:T > G:C transitions, which occurred predominantly at the center base of 5'N A C3'+5'G T N3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations...
June 15, 2018: Genetics
https://www.readbyqxmd.com/read/29907612/predicting-human-genes-susceptible-to-genomic-instability-associated-with-alu-alu-mediated-rearrangements
#13
Xiaofei Song, Christine R Beck, Renqian Du, Ian M Campbell, Zeynep Coban-Akdemir, Shen Gu, Amy M Breman, Pawel Stankiewicz, Grzegorz Ira, Chad A Shaw, James R Lupski
Alu elements, the short interspersed element numbering >1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMR) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test dataset consisting of 78 million Alu pairs and predicted ~18% of them are potentially susceptible to AAMR...
June 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29907536/methicillin-resistant-staphylococcus-aureus-nasal-carriage-and-infection-among-patients-with-diabetic-foot-ulcer
#14
Shin-Yi Lin, Nai-Yu Lin, Yu-Yao Huang, Chi-Chun Hsieh, Yhu-Chering Huang
PURPOSE: To evaluate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage in patients with diabetic foot ulcer (DFU) in Taiwan, and to assess the concordance between colonizing and clinical MRSA isolates from the patients. METHOD: A total of 354 nasal specimens were collected from 112 to 242 diabetic patients with and without foot ulcer, respectively. MRSA clinical isolates from DFU wound cultures were collected for comparison. RESULTS: Nasal carriage rate of S...
June 4, 2018: Journal of Microbiology, Immunology, and Infection, Wei Mian Yu Gan Ran za Zhi
https://www.readbyqxmd.com/read/29902967/ugbs-flex-a-novel-bioinformatics-pipeline-for-imputation-free-snp-discovery-in-polyploids-without-a-reference-genome-finger-millet-as-a-case-study
#15
Peng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M Dida, Russell L Malmberg, Katrien M Devos
BACKGROUND: Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. Furthermore, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species...
June 15, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29902792/xy-sry-positive-ovarian-disorder-of-sex-development-in-cattle
#16
Lisa De Lorenzi, Silvana Arrighi, Elena Rossi, Pierangela Grignani, Carlo Previderè, Stefania Bonacina, Fausto Cremonesi, Pietro Parma
In mammals, the sex of the embryo depends on the SRY gene. In the presence of at least one intact and functional copy of this genetic factor (XY embryo) undifferentiated gonads will develop as testicles that subsequently determine the male phenotype. When this factor is not present, i.e., in subjects with 2 X chromosomes, an alternative pathway induces the development of ovaries, hence a female phenotype. In this case study, we describe a female cattle affected by a disorder of sex development (DSD). The subject, despite having a chromosomal XY constitution, did not develop testicles but ovaries, although they were underdeveloped...
June 13, 2018: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/29902091/a-novel-deletion-downstream-of-the-pax6-gene-identified-in-a-chinese-family-with-congenital-aniridia
#17
Xiaoqi Liu, Yaqi Wu, Zequn Miao, Houbin Zhang, Bo Gong, Xianjun Zhu, Lulin Huang, Yi Shi, Fang Hao, Shi Ma, He Lin, Lejin Wang, Zhenglin Yang
PURPOSE: Congenital aniridia, a severe bilateral panocular visual disorder, is an autosomal dominantly inherited eye anomaly. Mutations in the paired box 6 gene (PAX6) have been shown to be responsible for congenital aniridia in most patients. The purpose of the present study was to report clinical features of a Chinese family with congenital aniridia and to screen novel genetic mutations for congenital aniridia. METHODS: All members of a three-generation family underwent comprehensive ophthalmic examination, and 8 of its 25 members were diagnosed with congenital aniridia...
June 14, 2018: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29899300/cytogenetics-in-arctica-islandica-bivalvia-arctidae-the-longest-lived-non-colonial-metazoan
#18
Daniel García-Souto, Juan J Pasantes
Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects but nothing is known about their chromosomes. In this work, the chromosomes of the ocean quahog Arctica islandica were analysed by means of 4′,6-diamidino-2-phenylindole (DAPI)/propidium iodide (PI) staining and fluorescent in situ hybridization (FISH) with rDNA, histone gene and telomeric probes...
June 13, 2018: Genes
https://www.readbyqxmd.com/read/29898652/intrachromosomal-colocalization-strengthens-co-expression-co-modification-and-evolutionary-conservation-of-neighboring-genes
#19
Shuaibin Lian, Tianliang Liu, Shengli Jing, Hongyu Yuan, Zaibao Zhang, Lin Cheng
BACKGROUND: Gene order and location in chromosomes of species are non-random. Neighboring gene pairs tend to display some similarities, such as co-expression and co-modification. However, the contribution of linear proximity, spatial proximity, and evolutionary proximity to these similarities remain unclear, together with whether the presence of several types of proximity can strengthens the similarities. RESULTS: In this study, we investigated the properties of three kinds of colocalized gene pairs: intrachromosomal colocalized gene pairs, always-neighboring gene pairs, and evolutionary neighboring gene pairs...
June 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29898102/comparative-cytogenetic-analysis-in-erythrolamprus-snakes-serpentes-dipsadidae-from-argentina
#20
Camila Falcione, Alejandra Hernando, María José Bressa
We described the karyotypes of five snake taxa from Argentina: Erythrolamprus almadensis, E. ceii, E. poecilogyrus caesius, E. p. schotti and E. p. sublineatus, and also intergrading individuals between the last two subspecies by conventional staining, chromosome bandings and fluorescent in situ hybridization (FISH) with 28S ribosomal DNA probes. Erythrolamprus ceii and E. almadensis share a diploid chromosome number of 2n= 28, whereas in E. poecilogyrus intraspecific variations were observed: E. p. caesius has 2n= 28, E...
April 2018: Anais da Academia Brasileira de Ciências
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