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methylation sequencing

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https://www.readbyqxmd.com/read/30517874/madid-a-versatile-approach-to-map-protein-dna-interactions-highlights-telomere-nuclear-envelope-contact-sites-in-human-cells
#1
Michal Sobecki, Charbel Souaid, Jocelyne Boulay, Vincent Guerineau, Daan Noordermeer, Laure Crabbe
Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understanding biological processes. DNA adenine methyltransferase identification (DamID) has emerged as a comprehensive method to map genome-wide occupancy of proteins of interest. A caveat of DamID is the specificity of Dam methyltransferase for GATC motifs that are not homogenously distributed in the genome. Here, we developed an optimized method named MadID, using proximity labeling of DNA by the methyltransferase M.EcoGII...
December 4, 2018: Cell Reports
https://www.readbyqxmd.com/read/30517357/level-vi-lymph-nodes-an-anatomic-study-of-lymph-nodes-located-between-the-recurrent-laryngeal-nerve-and-the-right-common-carotid-artery
#2
Samir Omar Saleh, Flávio Carneiro Hojaij, Ana Maria Itezeroti, Cristina Pires Camargo, Kassem Samir Saleh, Mauro Figueiredo Carvalho de Andrade, Flávia Emi Akamatsu, Alfredo Luiz Jacomo
OBJECTIVE: to describe the presence of lymph nodes and their relationships with demographic and anthropometric characteristics in a specific region, not yet described in anatomy compendiums, called by us Recurrent Carotid Recess (RCR) and located among the right recurrent laryngeal nerve, the right common carotid artery, and the right inferior thyroid artery. METHODS: 32 right cervical regions were harvested from cadavers within 24 hours post-mortem. The fibro-fatty tissue of the RCR was resected and prepared with formalin fixation...
November 29, 2018: Revista do Colégio Brasileiro de Cirurgiões
https://www.readbyqxmd.com/read/30517207/longer-tomm40-poly-t-variants-associated-with-higher-fddnp-pet-medial-temporal-tau-and-amyloid-binding
#3
Prabha Siddarth, Alison C Burggren, David A Merrill, Linda M Ercoli, Zanjbeel Mahmood, Jorge R Barrio, Gary W Small
BACKGROUND: The translocase of outer mitochondrial membrane 40 (TOMM40), which lies in linkage disequilibrium with the apolipoprotein E (APOE) gene, has been implicated in Alzheimer's disease (AD). TOMM40 influences AD pathology through mitochondrial neurotoxicity, and the medial temporal lobe (MTL) is the most likely brain region for identifying early manifestations of AD-related morphology changes. While early reports indicated that the longer length poly-T allele of TOMM40 increases risk for AD, these findings have not been consistently replicated in further studies...
2018: PloS One
https://www.readbyqxmd.com/read/30515146/reduction-in-methane-emissions-from-acidified-dairy-slurry-is-related-to-inhibition-of-methanosarcina-species
#4
Jemaneh Habtewold, Robert Gordon, Vera Sokolov, Andrew VanderZaag, Claudia Wagner-Riddle, Kari Dunfield
Liquid dairy manure treated with sulfuric acid was stored in duplicate pilot-scale storage tanks for 120 days with continuous monitoring of CH4 emissions and concurrent examination of changes in the structure of bacterial and methanogenic communities. Methane emissions were monitored at the site using laser-based Trace Gas Analyzer whereas quantitative real-time polymerase chain reaction and massively parallel sequencing were employed to study bacterial and methanogenic communities using 16S rRNA and methyl-coenzyme M Reductase A ( mcrA ) genes/transcripts, respectively...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30514778/genetic-epigenetic-and-immunologic-profiling-of-mmr-deficient-relapsed-glioblastoma
#5
Stefano Indraccolo, Giuseppe Lombardi, Matteo Fassan, Lorenza Pasqualini, Silvia Giunco, Raffaella Marcato, Alessandra Gasparini, Cinzia Candiotto, Silvia Nalio, Pasquale Fiduccia, Giuseppe Nicolò Fanelli, Ardi Pambuku, Alessandro Della Puppa, Domenico D'Avella, Laura Bonaldi, Marina P Gardiman, Roberta Bertorelle, Anita De Rossi, Vittorina Zagonel
PURPOSE: In-depth characterization of recurrent glioblastoma (rGBM) might contribute to a better understanding of the mechanisms behind tumor progression and enable rGBM treatment with targeted drugs. EXPERIMENTAL DESIGN: In this study, GBM samples were collected at diagnosis and recurrence from adult patients treated with Stupp protocol. Expression of mismatch repair (MMR) proteins was evaluated by IHC, followed by whole exome sequencing (WES) of tumor samples showing loss of MSH6 reactivity...
December 4, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/30514397/significance-of-molecular-classification-of-ependymomas-c11orf95-rela-fusion-negative-supratentorial-ependymomas-are-a-heterogeneous-group-of-tumors
#6
Kohei Fukuoka, Yonehiro Kanemura, Tomoko Shofuda, Shintaro Fukushima, Satoshi Yamashita, Daichi Narushima, Mamoru Kato, Mai Honda-Kitahara, Hitoshi Ichikawa, Takashi Kohno, Atsushi Sasaki, Junko Hirato, Takanori Hirose, Takashi Komori, Kaishi Satomi, Akihiko Yoshida, Kai Yamasaki, Yoshiko Nakano, Ai Takada, Taishi Nakamura, Hirokazu Takami, Yuko Matsushita, Tomonari Suzuki, Hideo Nakamura, Keishi Makino, Yukihiko Sonoda, Ryuta Saito, Teiji Tominaga, Yasuhiro Matsusaka, Keiichi Kobayashi, Motoo Nagane, Takuya Furuta, Mitsutoshi Nakada, Yoshitaka Narita, Yuichi Hirose, Shigeo Ohba, Akira Wada, Katsuyoshi Shimizu, Kazuhiko Kurozumi, Isao Date, Junya Fukai, Yousuke Miyairi, Naoki Kagawa, Atsufumi Kawamura, Makiko Yoshida, Namiko Nishida, Takafumi Wataya, Masayoshi Yamaoka, Naohiro Tsuyuguchi, Takehiro Uda, Mayu Takahashi, Yoshiteru Nakano, Takuya Akai, Shuichi Izumoto, Masahiro Nonaka, Kazuhisa Yoshifuji, Yoshinori Kodama, Masayuki Mano, Tatsuya Ozawa, Vijay Ramaswamy, Michael D Taylor, Toshikazu Ushijima, Soichiro Shibui, Mami Yamasaki, Hajime Arai, Hiroaki Sakamoto, Ryo Nishikawa, Koichi Ichimura
Extensive molecular analyses of ependymal tumors have revealed that supratentorial and posterior fossa ependymomas have distinct molecular profiles and are likely to be different diseases. The presence of C11orf95-RELA fusion genes in a subset of supratentorial ependymomas (ST-EPN) indicated the existence of molecular subgroups. However, the pathogenesis of RELA fusion-negative ependymomas remains elusive. To investigate the molecular pathogenesis of these tumors and validate the molecular classification of ependymal tumors, we conducted thorough molecular analyses of 113 locally diagnosed ependymal tumors from 107 patients in the Japan Pediatric Molecular Neuro-Oncology Group...
December 4, 2018: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/30514346/hypermethylation-of-dmtn-promotes-the-metastasis-of-colorectal-cancer-cells-by-regulating-the-actin-cytoskeleton-through-rac1-signaling-activation
#7
Ya-Ping Ye, Hong-Li Jiao, Shu-Yang Wang, Zhi-Yuan Xiao, Dan Zhang, Jun-Feng Qiu, Ling-Jie Zhang, Ya-Li Zhao, Ting-Ting Li, Li-Liang, Wen-Ting Liao, Yan-Qing Ding
BACKGROUND: Colorectal cancer (CRC) is one of the most common digestive malignant tumors, and DMTN is a transcriptionally differentially expressed gene that was identified using CRC mRNA sequencing data from The Cancer Genome Atlas (TCGA). Our preliminary work suggested that the expression of DMTN was downregulated in CRC, and the Rac1 signaling pathway was significantly enriched in CRC tissues with low DMTN expression. However, the specific functions and underlying molecular mechanisms of DMTN in the progression of CRC and the upstream factors regulating the downregulation of the gene remain unclear...
December 4, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/30513997/dna-methylation-diversification-at-the-integrated-organellar-dna-like-sequence
#8
Takanori Yoshida, Yoshiaki Tarutani, Tetsuji Kakutani, Akira Kawabe
Plants have a lot of diversity in epigenetic modifications such as DNA methylation in their natural populations or cultivars. Although many studies observing the epigenetic diversity within and among species have been reported, the mechanisms how these variations are generated are still not clear. In addition to the de novo spontaneous epi-mutation, the intra- and inter-specific crossing can also cause a change of epigenetic modifications in their progenies. Here we report an example of diversification of DNA methylation by crossing and succeeding selfing...
December 3, 2018: Genes
https://www.readbyqxmd.com/read/30513969/first-record-of-an-invasive-fruit-fly-belonging-to-bactrocera-dorsalis-complex-diptera-tephritidae-in-europe
#9
Francesco Nugnes, Elia Russo, Gennaro Viggiani, Umberto Bernardo
Emerging pests are increasingly threatening fruit orchard health across the Mediterranean area. Tephritidae, representing serious threats for Europe, are numerous, and the fruit flies Bactrocera zonata and those belonging to Bactrocera dorsalis complex are among the most alarming species. These species are highly polyphagous and B. zonata has already spread to some Mediterranean countries. Due to these ongoing threats, in the Campania Region (southern Italy), a survey with traps and infested fruits analysis was performed with the aim of detecting the presence of species of Bactrocera dorsalis complex...
December 3, 2018: Insects
https://www.readbyqxmd.com/read/30513695/n%C3%A2-methyladenosine-m%C3%A2-a-revisiting-the-old-with-focus-on-new-an-arabidopsis-thaliana-centered-review
#10
REVIEW
Susheel Sagar Bhat, Dawid Bielewicz, Artur Jarmolowski, Zofia Szweykowska-Kulinska
N ⁶-methyladenosine (m⁶A) is known to occur in plant and animal messenger RNAs (mRNAs) since the 1970s. However, the scope and function of this modification remained un-explored till very recently. Since the beginning of this decade, owing to major technological breakthroughs, the interest in m⁶A has peaked again. Similar to animal mRNAs, plant mRNAs are also m⁶A methylated, within a specific sequence motif which is conserved across these kingdoms. m⁶A has been found to be pivotal for plant development and necessary for processes ranging from seed germination to floral development...
November 30, 2018: Genes
https://www.readbyqxmd.com/read/30512195/epigenetic-regulation-of-gene-expression-in-chinese-hamster-ovary-cells-in-response-to-the-changing-environment-of-a-batch-culture
#11
Inmaculada Hernandez, Heena Dhiman, Gerald Klanert, Vaibhav Jadhav, Norbert Auer, Michael Hanscho, Martina Baumann, Anna Esteve-Codina, Marc Dabad, Jessica Gómez, Tyler Alioto, Angelika Merkel, Emanuele Raineri, Simon Heath, Daniel Rico, Nicole Borth
The existence of dynamic cellular phenotypes in changing environmental conditions is of major interest for cell biologists aiming to understand the mechanism and sequence of regulation of gene expression. In the context of therapeutic protein production by Chinese Hamster Ovary (CHO) cells, a detailed temporal understanding of cell-line behavior and control is necessary to achieve more predictable and reliable process performance. Of particular interest are data on dynamic, temporally resolved transcriptional regulation of genes in response to altered substrate availability and culture conditions...
December 4, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30511518/-precision-screening-and-treatment-of-human-papilloma-virus-related-cervical-cancer
#12
Zheng Hu, Ding Ma
Cervical cancer is a complex disease caused by both genetic susceptibility and environmental factors. Inherited genomic variance, high-risk human papilloma virus (HPV) infection/integration, genome methylation and somatic mutation could all constitute one machine learning model, laying the ground for molecular classification and the precision medicine of cervical cancer. Therefore, for cervical screening, next generation sequencing (NGS)-based HPV DNA and other molecular tests as well as dynamic machine learning models would accurately predict patients with potential to develop the cancer, thereby reducing the burden of repeated screening...
February 25, 2018: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
https://www.readbyqxmd.com/read/30510602/hypermethylation-of-apc2-is-a-predictive-epigenetic-biomarker-for-chinese-colorectal-cancer
#13
Yuan He, Li-Yue Sun, Jing Wang, Rui Gong, Qiong Shao, Zi-Chen Zhang, Zu-Lu Ye, Hai-Yun Wang, Rui-Hua Xu, Jian-Yong Shao
Objective: To investigate methylation of the adenomatosis polyposis coli homologue (APC2) promoter and its correlation with prognostic implications in Chinese colorectal cancer (CRC). Methods: The mRNA expression of APC2 in colorectal tissues was evaluated using the database of The Cancer Genome Atlas (TCGA). Methylation analysis of APC2 in tumor ( n = 66) and corresponding adjacent formalin-fixed and paraffin-embedded (FFPE) tissues ( n = 44) was performed by Sequenom EpiTYPER® and verified by cloning-based bisulfite sequencing analysis...
2018: Disease Markers
https://www.readbyqxmd.com/read/30510283/whole-genome-mbd-seq-and-rrbs-analyses-reveal-that-hypermethylation-of-gastrointestinal-hormone-receptors-is-associated-with-gastric-carcinogenesis
#14
Hee-Jin Kim, Tae-Wook Kang, Keeok Haam, Mirang Kim, Seon-Kyu Kim, Seon-Young Kim, Sang-Il Lee, Kyu-Sang Song, Hyun-Yong Jeong, Yong Sung Kim
DNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis...
December 3, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/30509319/comprehensive-methylation-analysis-of-imprinting-associated-differentially-methylated-regions-in-colorectal-cancer
#15
Hidenori Hidaka, Ken Higashimoto, Saori Aoki, Hiroyuki Mishima, Chisa Hayashida, Toshiyuki Maeda, Yasuo Koga, Hitomi Yatsuki, Keiichiro Joh, Hirokazu Noshiro, Ryuichi Iwakiri, Atsushi Kawaguchi, Koh-Ichiro Yoshiura, Kazuma Fujimoto, Hidenobu Soejima
BACKGROUND: Imprinted genes are regulated by DNA methylation at imprinting-associated differentially methylated regions (iDMRs). Abnormal expression of imprinted genes is implicated in imprinting disorders and tumors. In colorectal cancer (CRC), methylation and imprinting status of the IGF2/H19 domain have been studied. However, no comprehensive methylation analysis of iDMRs in CRC has been reported. Furthermore, the relationship between iDMR methylation status and other methylation-related issues, such as CpG island methylator phenotype (CIMP) and long interspersed element-1 (LINE-1) methylation, remains unclear...
December 4, 2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/30508863/acute-exercise-increases-the-expression-of-kir2ds4-by-promoter-demethylation-in-nk-cells
#16
Alexander Schenk, Walter Pulverer, Christine Koliamitra, Claus Juergen Bauer, Suzana Ilic, Rudolf Heer, Robert Schier, Volker Schick, Bernd W Böttiger, Clarissa Gerhäuser, Wilhelm Bloch, Philipp Zimmer
Positive effects of exercise on cancer prevention and progression have been proposed to be mediated by stimulating natural killer (NK) cells. Because NK cell receptors are regulated by epigenetic modifications, we investigated whether acute aerobic exercise and training change promoter DNA methylation and gene expression of the activating KIR2DS4 and the inhibiting KIR3DL1 gene. Sixteen healthy women (50-60 years) performed a graded exercise test (GXT) and were randomized into either a passive control group or an intervention group performing a four-week endurance exercise intervention...
December 3, 2018: International Journal of Sports Medicine
https://www.readbyqxmd.com/read/30505163/descriptions-of-four-new-species-of-bactrocera-and-new-country-records-highlight-the-high-biodiversity-of-fruit-flies-in-vietnam-diptera-tephritidae-dacinae
#17
Luc Leblanc, Camiel Doorenweerd, Michael San Jose, Hong Thai Pham, Daniel Rubinoff
Recent snap-shot surveys for fruit flies in Vietnam in 2015 and 2017 using traps baited with the male Dacinae fruit fly lures methyl eugenol, cue-lure and zingerone, collected 56 species, including 11 new country records and another 11 undescribed species, four of which are described in this paper. This increases the number of described species known to occur in Vietnam from 78 to 93. Species accumulation curves, based on the Chao 2 mean estimate, suggest that we collected 60-85 % of the local fauna at the sites sampled, and that species diversity decreases with increasing latitude...
2018: ZooKeys
https://www.readbyqxmd.com/read/30504727/mir-10b-downregulated-by-dna-methylation-acts-as-a-tumor-suppressor-in-hpv-positive-cervical-cancer-via-targeting-tiam1
#18
Miaomei Yu, Yun Xu, Lili Pan, Yuehua Feng, Kaiming Luo, Qinfeng Mu, Guanghua Luo
BACKGROUND/AIMS: microRNAs (miRNAs) are known to act as oncogenes or tumor suppressors in diverse cancers. Although miR-10b is an oncogene implicated in many tumors, its role in cervical cancer (CC) remains largely unclear. Here, we investigated the function and underlying mechanisms of miR-10b in human CC. METHODS: Quantitative RT-PCR was used to measure miR-10b expression in CC and normal tissues, and its association with clinicopathologic features was analyzed...
November 30, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/30504293/genomics-of-aggressive-b-cell-lymphoma
#19
REVIEW
Allison Rosenthal, Lisa Rimsza
The growing body of genomic information collected and applied to mature aggressive B-cell lymphoma diagnosis and management has exploded over the last few years due to improved technologies with high-throughput capacity, suitable for use on routine formalin-fixed, paraffin-embedded tissue biopsies, and decreasing costs. These techniques have made evaluation of complete DNA sequences, RNA-expression patterns, translocations, copy-number alterations, loss of heterozygosity, and DNA-methylation patterns possible on a genome-wide level...
November 30, 2018: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/30503826/sequencing-based-methods-for-detection-and-quantitation-of-ribose-methylations-in-rna
#20
REVIEW
Nicolai Krogh, Henrik Nielsen
Ribose methylation is one of the most abundant RNA modifications and is found in all domains of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. Recent years have seen the development of several sequencing-based methods for RNA modifications relying on different principles. In this review, we compare mapping and quantitation studies of ribose methylations from yeast and human culture cells...
November 29, 2018: Methods: a Companion to Methods in Enzymology
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