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https://www.readbyqxmd.com/read/29145496/insights-into-soybean-transcriptome-reconfiguration-under-hypoxic-stress-functional-regulatory-structural-and-compositional-characterization
#1
Thiago J Nakayama, Fabiana A Rodrigues, Norman Neumaier, Juliana Marcolino-Gomes, Hugo B C Molinari, Thaís R Santiago, Eduardo F Formighieri, Marcos F Basso, José R B Farias, Beatriz M Emygdio, Ana C B de Oliveira, Ângela D Campos, Aluízio Borém, Frank G Harmon, Liliane M Mertz-Henning, Alexandre L Nepomuceno
Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits...
2017: PloS One
https://www.readbyqxmd.com/read/29145159/potential-link-between-m-6-a-modification-and-systemic-lupus-erythematosus
#2
REVIEW
Lian-Ju Li, Yin-Guang Fan, Rui-Xue Leng, Hai-Feng Pan, Dong-Qing Ye
The field of m(6)A modification and epitranscriptomics has recently attracted much attention. More methods allowing for precise m(6)A site profiling and location are developed and crucial players of m(6)A modification machinery are increasingly identified. Although some challenges remain, m(6)A modification is found to modulate almost all aspects of RNA metabolism, such as splicing, stability, structure, translation, and export. Thus, m(6)A modification adds a new layer of post-transcriptional gene expression regulation, and it is implicated in T cell response to HIV infection, type I interferon production, and T cell differentiation and homeostasis...
November 13, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29143012/%C3%AE-alanine-and-n-terminal-cationic-substituents-affect-polyamide-dna-binding
#3
Beibei Liu, Shuo Wang, Karl Aston, Kevin J Koeller, Shahrzad Fanny Hakami Kermani, Carlos H Castañeda, M José Scuderi, Rensheng Luo, James K Bashkin, W David Wilson
Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA-DNA binding affinity and include flexible modules, such as β-alanine (β) motifs to replace pyrroles (Py), and increasing compound charge using N-terminal cationic substituents. To better understand the variations in kinetics and affinities caused by these modifications on PA-DNA interactions, a comprehensive set of PAs with different numbers and positions of β and different types of N-cationic groups was systematically designed and synthesized to bind their cognate sequence, the λB motif...
November 16, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29142233/crystal-structure-of-the-n-terminal-domain-of-human-cdc73-and-its-implications-for-the-hyperparathyroidism-jaw-tumor-hpt-jt-syndrome
#4
Wei Sun, Xiao-Lin Kuang, Yan-Ping Liu, Li-Fei Tian, Xiao-Xue Yan, Wenqing Xu
CDC73/Parafibromin is a critical component of the Paf1 complex (PAF1C), which is involved in transcriptional elongation and histone modifications. Mutations of the human CDC73/HRPT2 gene are associated with hyperparathyroidism-jaw tumor (HPT-JT) syndrome, an autosomal dominant disorder. CDC73/parafibromin was initially recognized as a tumor suppressor by inhibiting cell proliferation via repression of cyclin D1 and c-myc genes. In recent years, it has also shown oncogenic features by activating the canonical Wnt/β-catenin signal pathway...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142126/hpv-replication-regulation-by-acetylation-of-a-conserved-lysine-in-the-e2-protein
#5
Yanique Thomas, Elliot J Androphy
The Papillomavirus (PV) E2 protein is a sequence specific DNA binding protein that recruits cellular factors to its genome in infected epithelial cells. E2 also binds to and loads the viral E1 DNA helicase at the origin of replication. Post-translational modifications (PTMs) of PV E2 have been identified as potential regulators E2 functions. We recently reported lysine (K) 111 as a target of p300 acetylation in bovine (B)PV. The di-lysines at 111 and 112 are conserved in almost all papillomaviruses. We pursued a mutational approach to query the functional significance of lysine in human (H)PV E2...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29142071/chromatin-histone-modifications-and-rigidity-affect-nuclear-morphology-independent-of-lamins
#6
Andrew D Stephens, Patrick Z Liu, Edward J Banigan, Luay M Almassalha, Vadim Backman, Stephen A Adam, Robert D Goldman, John F Marko
Nuclear shape and architecture influence gene localization, mechanotransduction, transcription, and cell function. Abnormal nuclear morphology and protrusions termed "blebs" are diagnostic markers for many human afflictions including heart disease, aging, progeria, and cancer. Nuclear blebs are associated with both lamin and chromatin alterations. A number of prior studies suggest that lamins dictate nuclear morphology, but the contributions of altered chromatin compaction remain unclear. We show that chromatin histone modification state dictates nuclear rigidity, and modulating it is sufficient to both induce and suppress nuclear blebs...
November 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29141987/brachyury-directs-histone-acetylation-to-target-loci-during-mesoderm-development
#7
Arica Beisaw, Pavel Tsaytler, Frederic Koch, Sandra U Schmitz, Maria-Theodora Melissari, Anna D Senft, Lars Wittler, Tracie Pennimpede, Karol Macura, Bernhard G Herrmann, Phillip Grote
T-box transcription factors play essential roles in multiple aspects of vertebrate development. Here, we show that cooperative function of BRACHYURY (T) with histone-modifying enzymes is essential for mouse embryogenesis. A single point mutation (T(Y88A)) results in decreased histone 3 lysine 27 acetylation (H3K27ac) at T target sites, including the T locus, suggesting that T autoregulates the maintenance of its expression and functions by recruiting permissive chromatin modifications to putative enhancers during mesoderm specification...
November 15, 2017: EMBO Reports
https://www.readbyqxmd.com/read/29141961/chromatin-accessibility-dynamics-reveal-novel-functional-enhancers-in-c-elegans
#8
Aaron C Daugherty, Robin W Yeo, Jason D Buenrostro, William J Greenleaf, Anshul Kundaje, Anne Brunet
Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism Caenorhabditis elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29141554/insight-into-the-role-of-long-non-coding-rnas-during-osteogenesis-in-mesenchymal-stem-cells
#9
Sibei Huo, Yachuan Zhou, Xinyu He, Mian Wan, Wei Du, Xin Xu, Ling Ye, Xuedong Zhou, Liwei Zheng
BACKGROUND: Long non-coding RNAs (LncRNAs) are non-protein coding transcripts longer than 200 nucleotides in length. Instead of being "transcriptional noise", lncRNAs are emerging as a key modulator in various biological processes and disease development. Mesenchymal stem cells can be isolated from various adult tissues, such as bone marrow and dental tissues. The differentiation processes into multiple lineages, such as osteogenic differentiation, are precisely orchestrated by molecular signals in both genetic and epigenetic ways...
November 15, 2017: Current Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29141227/in-situ-fixation-redefines-quiescence-and-early-activation-of-skeletal-muscle-stem-cells
#10
Léo Machado, Joana Esteves de Lima, Odile Fabre, Caroline Proux, Rachel Legendre, Anikó Szegedi, Hugo Varet, Lars Roed Ingerslev, Romain Barrès, Frédéric Relaix, Philippos Mourikis
State of the art techniques have been developed to isolate and analyze cells from various tissues, aiming to capture their in vivo state. However, the majority of cell isolation protocols involve lengthy mechanical and enzymatic dissociation steps followed by flow cytometry, exposing cells to stress and disrupting their physiological niche. Focusing on adult skeletal muscle stem cells, we have developed a protocol that circumvents the impact of isolation procedures and captures cells in their native quiescent state...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29139132/light-and-temperature-cues-multitasking-receptors-and-transcriptional-integrators
#11
REVIEW
Jorge J Casal, Julia I Qüesta
The combined information provided by light and temperature cues helps to optimise plant body architecture and physiology. Plants possess elaborate systems to sense and respond to these stimuli. Simultaneous perception of light and temperature by dual receptors such as phytochrome B and phototropin leads to immediate signalling convergence. Conversely, cue asynchronies initiate separate pathways and the information of the earliest cue is stored, awaiting the arrival of the later cue to control transcription...
November 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/29138868/hdac-inhibitor-lmk%C3%A2-235-promotes-the-odontoblast-differentiation-of-dental-pulp-cells
#12
Zhao Liu, Ting Chen, Qianqian Han, Ming Chen, Jie You, Fuchun Fang, Ling Peng, Buling Wu
The role of dental pulp cells (DPCs) in hard dental tissue regeneration had received increasing attention because DPCs can differentiate into odontoblasts and other tissue‑specific cells. In recent years, epigenetic modifications had been identified to serve an important role in cell differentiation, and histone deacetylase (HDAC) inhibitors have been widely studied by many researchers. However, the effects of HDAC4 and HDAC5 on the differentiation of DPCs and the precise molecular mechanisms remain unclear...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138838/effects-of-scn9a-gene-modification-on-na-channel-and-the-expression-of-nerve-growth-factor-in-a-rat-model-of-diarrhea%C3%A2-predominant-irritable-bowel-syndrome
#13
Yong-Yan Cai, Chen Li, Zhi-Xin Yan, Na Ma, Fang-Fang Li
The aim of the present study was to identify whether the sodium voltage-gated channel alpha subunit 9 (SCN9A) gene modification is a potential treatment for diarrhea‑predominant irritable bowel syndrome (D‑IBS), via regulating the Na+ channel and the expression of nerve growth factor (NGF). The recombinant adenovirus vector of the SCN9A gene was established, and rat colon cells were isolated for SCN9A gene modification. All subjects were divided into four groups: i) The SCN9A‑modified (D‑IBS rat model implanted with SCN9A‑modified colon cells), ii) negative control (NC; D‑IBS rat model implanted with colon cells without SCN9A gene modification), iii) blank (D‑IBS rat model without any treatment) and iv) normal (normal rats without any treatment)...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138532/ubiquitin-specific-protease-2-modulates-the-lipopolysaccharide-elicited-expression-of-proinflammatory-cytokines-in-macrophage-like-hl-60-cells
#14
Hiroshi Kitamura, Takeshi Ishino, Yoshinori Shimamoto, Jun Okabe, Tomomi Miyamoto, Eiki Takahashi, Ichiro Miyoshi
We investigated the regulatory roles of USP2 in mRNA accumulation of proinflammatory cytokines in macrophage-like cells after stimulation with a toll-like receptor (TLR) 4 ligand, lipopolysaccharide (LPS). Human macrophage-like HL-60 cells, mouse macrophage-like J774.1 cells, and mouse peritoneal macrophages demonstrated negative feedback to USP2 mRNA levels after LPS stimulation, suggesting that USP2 plays a significant role in LPS-stimulated macrophages. USP2 knockdown (KD) by short hairpin RNA in HL-60 cells promoted the accumulation of transcripts for 25 of 104 cytokines after LPS stimulation...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/29137925/polycomb-repression-complex-2-is-required-for-the-maintenance-of-retinal-progenitor-cells-and-balanced-retinal-differentiation
#15
Naoko Fujimura, Andrea Kuzelova, Anja Ebert, Hynek Strnad, Jitka Lachova, Ondrej Machon, Meinrad Busslinger, Zbynek Kozmik
Polycomb repressive complexes maintain transcriptional repression of genes encoding crucial developmental regulators through chromatin modification. Here we investigated the role of Polycomb repressive complex 2 (PRC2) in retinal development by inactivating its key components Eed and Ezh2. Conditional deletion of Ezh2 resulted in a partial loss of PRC2 function and accelerated differentiation of Müller glial cells. In contrast, inactivation of Eed led to the ablation of PRC2 function at early postnatal stage...
November 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29137327/regulation-of-fbxo4-mediated-icam-1-protein-stability-in-metastatic-breast-cancer
#16
Jae-Hyeok Kang, Mi-Young Choi, Yan-Hong Cui, Neha Kaushik, Nizam Uddin, Ki-Chun Yoo, Min-Jung Kim, Su-Jae Lee
Advanced or progressive cancers share common traits such as altered transcriptional modulation, genetic modification, and abnormal post-translational regulation. These processes influence protein stability and cellular activity. Intercellular adhesion molecule-1 (ICAM-1) is involved in the malignant progression of various human cancers, including breast, liver, renal, and pancreatic cancers, but protein stability has not been deal with in metastatic breast cancer. Additionally, the relevance of the stability maintenance of ICAM-1 protein remains obscure...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137147/development-of-pgemini-a-plant-gateway-destination-vector-allowing-the-simultaneous-integration-of-two-cdna-via-a-single-lr-clonase-reaction
#17
Marino Exposito-Rodriguez, Philippe P Laissue, Patricia E López-Calcagno, Philip M Mullineaux, Christine A Raines, Andrew J Simkin
Gateway technology has been used to facilitate the generation of a large number of constructs for the modification of plants for research purposes. However, many of the currently available vectors only allow the integration of a single cDNA of interest into an expression clone. The ability to over-express multiple genes in combination is essential for the study of plant development where several transcripts have a role to play in one or more metabolic processes. The tools to carry out such studies are limited, and in many cases rely on the incorporation of cDNA into expression systems via conventional cloning, which can be both time consuming and laborious...
November 12, 2017: Plants (Basel, Switzerland)
https://www.readbyqxmd.com/read/29136398/molecular-cloning-and-epigenetic-change-detection-of-kiss1-during-seasonal-reproduction-in-chinese-indigenous-sheep
#18
Xiaoyun He, Qiuyue Liu, Xiaoyu Li, Xiaofei Guo, Xiangyu Wang, Wenping Hu, Ran Di, Mingxing Chu
Like most seasonal domesticated species, sheep are short-day breeders, which means that the reproduction axis is activated by short days. The annual photoperiodic cycle affects the amount of daylength information that is transmitted to the hypothalamic-pituitary-gonadal (HPG) axis by regulating pulsatile secretion of gonadotrophin-releasing hormone from the hypothalamus. Kisspeptin, which is encoded by Kiss1, plays a major role in reproductive seasonality. Based on results from our previous Solexa sequencing data obtained from Tan (T) and Small Tail Han (STH) sheep during anoestrus and the breeding season, full-length mRNA information for ovine Kiss1 was obtained; 894bp in T sheep and 1145bp in STH sheep...
November 15, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/29136238/regulation-of-transcriptional-silencing-and-chromodomain-protein-localization-at-centromeric-heterochromatin-by-histone-h3-tyrosine-41-phosphorylation-in-fission-yeast
#19
Bingbing Ren, Hwei Ling Tan, Thi Thuy Trang Nguyen, Ahmed Mahmoud Mohammed Sayed, Ying Li, Yu-Keung Mok, Henry Yang, Ee Sin Chen
Heterochromatin silencing is critical for genomic integrity and cell survival. It is orchestrated by chromodomain (CD)-containing proteins that bind to methylated histone H3 lysine 9 (H3K9me), a hallmark of heterochromatin. Here, we show that phosphorylation of tyrosine 41 (H3Y41p)-a novel histone H3 modification-participates in the regulation of heterochromatin in fission yeast. We show that a loss-of-function mutant of H3Y41 can suppress heterochromatin de-silencing in the centromere and subtelomere repeat regions, suggesting a de-silencing role for H3Y41p on heterochromatin...
November 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29135019/mirnas-participate-in-the-diagnosis-pathogenesis-and-therapy-of-parkinson-s-disease
#20
REVIEW
Xuexin Lu, Zhijie Cui, Shuang Liu, Feng Yin
MicroRNAs (miRNAs), one kind of post-transcriptional modification, mediate transcriptional silencing of various metabolic enzymes that are involved in various life processes, including Parkinson's disease. At present, the pathogenesis of Parkinson's disease is not clear, although many studies suggest that miRNAs play a very important role in the progress of Parkinsonism. This paper reviews the biological characteristics of miRNAs and summarizes the progress of miRNAs in reference to the diagnosis and pathogenesis of Parkinson's disease...
November 14, 2017: Histology and Histopathology
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