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https://www.readbyqxmd.com/read/29773710/arginine-methylation-is-required-for-canonical-wnt-signaling-and-endolysosomal-trafficking
#1
Lauren V Albrecht, Diego Ploper, Nydia Tejeda-Muñoz, Edward M De Robertis
Arginine methylation has emerged as a widespread and reversible protein modification with the potential to regulate a multitude of cellular processes, but its function is poorly understood. Endolysosomes play an important role in Wnt signaling, in which glycogen synthase kinase 3 (GSK3) becomes sequestered inside multivesicular bodies (MVBs) by the process known as microautophagy, causing the stabilization of many proteins. Up to 20% of cellular proteins contain three or more consecutive putative GSK3 sites, and of these 33% also contain methylarginine (meArg) modifications...
May 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29773648/ten-eleven-translocation-2-demethylates-the-mmp9-promoter-and-its-down-regulation-in-preeclampsia-impairs-trophoblast-migration-and-invasion
#2
Xiaoliang Li, Chunlian Wu, Ying Shen, Ke Wang, Li Tang, Mi Zhou, Ming Yang, Tianying Pan, Xinghui Liu, Wenming Xu
Preeclampsia is the most common clinical disorder in pregnancy and might result from disordered uterine environments caused by epigenetic modifications, including deregulation of DNA methylation/demethylation. Recent research has indicated that 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC) via oxidation by ten-eleven translocation (TET) enzymes, is involved in DNA methylation-related plasticity. Here, we report that TET2 expression and 5hmC abundance are significantly altered in the placentas from preeclampsia patients...
May 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29772716/kinetic-basis-of-the-bifunctionality-of-ssoii-dna-methyltransferase
#3
Nadezhda A Timofeyeva, Alexandra Yu Ryazanova, Maxim V Norkin, Tatiana S Oretskaya, Olga S Fedorova, Elena A Kubareva
Type II restriction⁻modification (RM) systems are the most widespread bacterial antiviral defence mechanisms. DNA methyltransferase SsoII (M.SsoII) from a Type II RM system SsoII regulates transcription in its own RM system in addition to the methylation function. DNA with a so-called regulatory site inhibits the M.SsoII methylation activity. Using circular permutation assay, we show that M.SsoII monomer induces DNA bending of 31° at the methylation site and 46° at the regulatory site. In the M.SsoII dimer bound to the regulatory site, both protein subunits make equal contributions to the DNA bending, and both angles are in the same plane...
May 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29772549/long-non-coding-rna-and-polycomb-an-intricate-partnership-in-cancer-biology
#4
Cyrinne Achour, Francesca Aguilo
High-throughput analyses have revealed that the vast majority of the transcriptome does not code for proteins. These non-translated transcripts, when larger than 200 nucleotides, are termed long non-coding RNAs (lncRNAs), and play fundamental roles in diverse cellular processes. LncRNAs are subject to dynamic chemical modification, adding another layer of complexity to our understanding of the potential roles that lncRNAs play in health and disease. Many lncRNAs regulate transcriptional programs by influencing the epigenetic state through direct interactions with chromatin-modifying proteins...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29772444/functional-relevance-of-satb1-in-immune-regulation-and-tumorigenesis
#5
REVIEW
Krishna P Sunkara, Gaurav Gupta, Philip M Hansbro, Kamal Dua, Mary Bebawy
The Special AT-rich Sequence Binding Protein 1 (SATB1) is a chromatin organiser and transcription factor which regulates numerous cellular processes such as differentiation, proliferation and apoptosis through effects on gene expression. SATB1 undergoes various post-translational modifications, which determine its interaction with co-activators and co-repressors to induce regulation of gene transcription. SATB1 is an identified oncogene, its increased expression is associated with poor prognosis in many cancers...
May 14, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29770276/the-evaluation-of-anoxia-responsive-e2f-dna-binding-activity-in-the-red-eared-slider-turtle-trachemys-scripta-elegans
#6
Kyle K Biggar, Kenneth B Storey
In many cases, the DNA-binding activity of a transcription factor does not change, while its transcriptional activity is greatly influenced by the make-up of bound proteins. In this study, we assessed the protein composition and DNA-binding ability of the E2F transcription factor complex to provide insight into cell cycle control in an anoxia tolerant turtle through the use of a modified ELISA protocol. This modification also permits the use of custom DNA probes that are tailored to a specific DNA binding region, introducing the ability to design capture probes for non-model organisms...
2018: PeerJ
https://www.readbyqxmd.com/read/29769529/methionine-metabolism-influences-genomic-architecture-and-gene-expression-through-h3k4me3-peak-width
#7
Ziwei Dai, Samantha J Mentch, Xia Gao, Sailendra N Nichenametla, Jason W Locasale
Nutrition and metabolism are known to influence chromatin biology and epigenetics through post-translational modifications, yet how this interaction influences genomic architecture and connects to gene expression is unknown. Here we consider, as a model, the metabolically-driven dynamics of H3K4me3, a histone methylation mark that is known to encode information about active transcription, cell identity, and tumor suppression. We analyze the genome-wide changes in H3K4me3 and gene expression in response to alterations in methionine availability in both normal mouse physiology and human cancer cells...
May 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29769310/tumor-associated-intronic-editing-of-hnrpll-generates-a-novel-splicing-variant-linked-to-cell-proliferation
#8
Yi-Tung Chen, Ian Yi-Feng Chang, Hsuan Liu, Chung-Pei Ma, Yu-Ping Kuo, Chieh-Tien Shih, Ying-Hsin Shih, Lin Kang, Bertrand Chin-Ming Tan
Processing of the eukaryotic transcriptome is a dynamic regulatory mechanism that confers genetic diversity, and splicing and A-to-I RNA editing are well-characterized examples of such processing. Growing evidence reveals the crosstalk between the splicing and RNA editing, but there is a paucity of substantial evidence for its mechanistic details and contribution in a physiological context. Here, our findings demonstrate that tumor-associated differential RNA editing, in conjunction with splicing machinery, regulates the expression of variants of HNRPLL, a gene encoding splicing factor...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29769081/n-6-methyl-adenosine-level-in-nicotiana-tabacum-is-associated-with-tobacco-mosaic-virus
#9
Zhurui Li, Jing Shi, Lu Yu, Xiaozhen Zhao, Longlu Ran, Deyu Hu, Baoan Song
BACKGROUND: N 6 -methyl-adenosine (m6 A) is a prevalent RNA modification in many species. Abnormal m6 A methylation levels can lead to RNA dysfunction and can cause diseases. Tobacco mosaic virus (TMV) is one of the most devastating viruses for agricultural plants. It has many hosts, particularly including tobacco and other members the family Solanaceae. However, it remains unclear whether the abnormal growth induced by TMV is associated with the m6 A level. METHODS: A rapid and accurate analytical method using ultra-high-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HR - MS/MS) was developed to analyse the adenosine (A), cytidine (C), guanosine (G), uridine (U), and m6 A contents in the tobacco leaf, and the m6 A/G ratio was used to evaluate the m6 A level...
May 16, 2018: Virology Journal
https://www.readbyqxmd.com/read/29767358/sureselect-xt-rna-direct-a-technique-for-expression-analysis-through-sequencing-of-target-enriched-ffpe-total-rna
#10
Jennifer Carter Jones, Alex P Siebold, Carolina Becker Livi, Anne Bergstrom Lucas
Gene expression profiling of samples from biobanks requires a method that can be used with intact as well as partially degraded RNA. High throughput applications can benefit from reducing the number of processing steps including eliminating the poly(A) selection and ribosomal depletion steps. When performing targeted capture, we have found that we can eliminate the upfront poly(A) selection/ribosomal depletion steps that cause bias in standard mRNA-Seq workflows. This target enrichment solution allows for whole transcriptome or customized content to characterize differential gene expression patterns (especially for mid/low level transcripts)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765862/genomic-imprinting-and-the-regulation-of-postnatal-neurogenesis
#11
REVIEW
Anna Lozano-Ureña, Raquel Montalbán-Loro, Anne C Ferguson-Smith, Sacri R Ferrón
Most genes required for mammalian development are expressed from both maternally and paternally inherited chromosomal homologues. However, there are a small number of genes known as " imprinted genes " that only express a single allele from one parent, which is repressed on the gene from the other parent. Imprinted genes are dependent on epigenetic mechanisms such as DNA methylation and post-translational modifications of the DNA-associated histone proteins to establish and maintain their parental identity...
November 9, 2017: Brain Plasticity
https://www.readbyqxmd.com/read/29765519/long-noncoding-rnas-are-associated-with-metabolic-and-cellular-processes-in-the-jejunum-mucosa-of-pre-weaning-calves-in-response-to-different-diets
#12
Rosemarie Weikard, Frieder Hadlich, Harald M Hammon, Doerte Frieten, Caroline Gerbert, Christian Koch, Georg Dusel, Christa Kuehn
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves' intestinal mucosa...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765031/comprehensive-epigenetic-landscape-of-rheumatoid-arthritis-fibroblast-like-synoviocytes
#13
Rizi Ai, Teresina Laragione, Deepa Hammaker, David L Boyle, Andre Wildberg, Keisuke Maeshima, Emanuele Palescandolo, Vinod Krishna, David Pocalyko, John W Whitaker, Yuchen Bai, Sunil Nagpal, Kurtis E Bachman, Richard I Ainsworth, Mengchi Wang, Bo Ding, Percio S Gulko, Wei Wang, Gary S Firestein
Epigenetics contributes to the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first comprehensive epigenomic characterization of RA fibroblast-like synoviocytes (FLS), including histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3), open chromatin, RNA expression and whole-genome DNA methylation. To address complex multidimensional relationship and reveal epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29764956/spotlight-on-the-transglutaminase-2-gene-a-focus-on-genomic-and-transcriptional-aspects
#14
REVIEW
Nicoletta Bianchi, Simone Beninati, Carlo M Bergamini
The type 2 isoenzyme is the most widely expressed transglutaminase in mammals displaying several intra- and extracellular activities depending on its location (protein modification, modulation of gene expression, membrane signalling and stabilization of cellular interactions with the extracellular matrix) in relation to cell death, survival and differentiation. In contrast with the appreciable knowledge about the regulation of the enzymatic activities, much less is known concerning its inducible expression, which is altered in inflammatory and neoplastic diseases...
May 15, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29763857/the-pillars-of-land-plants-new-insights-into-stem-development
#15
REVIEW
Antonio Serrano-Mislata, Robert Sablowski
In spite of its central importance in evolution, plant architecture and crop improvement, stem development remains poorly understood relative to other plant organs. Here, we summarise current knowledge of stem ontogenesis and its regulation, including insights from new image analysis and biophysical approaches. The stem initiates in the rib zone (RZ) of the shoot apical meristem, under transcriptional control by DELLA and BLH proteins. Links have emerged between these regulators and cell proliferation, patterning and oriented growth in the RZ...
May 12, 2018: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29762480/time-course-microarray-analysis-reveals-differences-between-transcriptional-changes-in-tomato-leaves-triggered-by-mild-and-severe-variants-of-potato-spindle-tuber-viroid
#16
Aneta Więsyk, Roksana Iwanicka-Nowicka, Anna Fogtman, Włodzimierz Zagórski-Ostoja, Anna Góra-Sochacka
Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in "Rutgers" tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage; (ii) early symptoms; (iii) full spectrum of symptoms and (iv) the so-called 'recovery' stage, when stem regrowth was observed in severely affected plants...
May 15, 2018: Viruses
https://www.readbyqxmd.com/read/29762370/molecular-regulations-of-mucosal-maltase-expressions
#17
Toshinao Goda, Kazue Honma
Two major α-glucosidase (maltase) genes, sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM), respectively, are expressed in the small intestine. In this review, we have summarized whether jejunal expression of these maltase genes is regulated by dietary manipulations, which may affect carbohydrate availability from the luminal side, through changes in the binding of transcription factors and/or histone code on these genes. Studies using a model of mice fed either a low-starch or a high-starch diet for 7 days, found the mRNA levels of SI, MGAM, and Na-glucose cotransporter (SGLT1) genes in the jejunum to be increased in parallel by feeding a high-starch diet...
June 2018: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/29761511/overexpression-of-the-tashn1-transcription-factor-in-bread-wheat-leads-to-leaf-surface-modifications-improved-drought-tolerance-and-no-yield-penalty-under-controlled-growth-conditions
#18
Huihui Bi, Jianxin Shi, Natalia Kovalchuk, Sukanya Luang, Natalia Bazanova, Larissa Chirkova, Dabing Zhang, Yuri Shavrukov, Anton Stepanenko, Penny Tricker, Peter Langridge, Maria Hrmova, Sergiy Lopato, Nikolai Borisjuk
Transcription factors regulate multiple networks, mediating the responses of organisms to stresses, including drought. Here we investigated the role of the wheat transcription factor TaSHN1 in crop growth and drought tolerance. TaSHN1, isolated from bread wheat, was characterised for molecular interactions and functionality. The overexpression of TaSHN1 in wheat was followed by the evaluation of T2 and T3 transgenic lines for drought tolerance, growth and yield components. Leaf surface changes were analysed by light microscopy, SEM, TEM and GC-MS/GC-FID...
May 14, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29761399/chromatin-immunoprecipitation-in-macrophages
#19
Germain Rousselet
Macrophages are highly polymorphic depending upon their cellular origin and their tissue environment. The different forms that a macrophage can adopt fundamentally reflect different transcription patterns. In addition, macrophages are exquisitely sensitive to a wide variety of signals coming from either infectious agents or damaged tissues. Most of the responses to these signals involve rapid and massive modifications of transcription. The control of transcription relies on the one hand on the posttranslational modification of histones, and on the other hand on the binding on the chromatin of multiple protein complexes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760498/hierarchical-mechanism-of-amino-acid-sensing-by-the-t-box-riboswitch
#20
Krishna C Suddala, Javier Cabello-Villegas, Malgorzata Michnicka, Collin Marshall, Edward P Nikonowicz, Nils G Walter
In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5' half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification...
May 14, 2018: Nature Communications
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