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https://www.readbyqxmd.com/read/29220666/chromatin-accessibility-dynamics-during-ipsc-reprogramming
#1
Dongwei Li, Jing Liu, Xuejie Yang, Chunhua Zhou, Jing Guo, Chuman Wu, Yue Qin, Lin Guo, Jiangping He, Shenyong Yu, He Liu, Xiaoshan Wang, Fang Wu, Junqi Kuang, Andrew P Hutchins, Jiekai Chen, Duanqing Pei
Cell-fate decisions remain poorly understood at the chromatin level. Here, we map chromatin remodeling dynamics during induction of pluripotent stem cells. ATAC-seq profiling of MEFs expressing Oct4-Sox2-Klf4 (OSK) reveals dynamic changes in chromatin states shifting from open to closed (OC) and closed to open (CO), with an initial burst of OC and an ending surge of CO. The OC loci are largely composed of genes associated with a somatic fate, while the CO loci are associated with pluripotency. Factors/conditions known to impede reprogramming prevent OSK-driven OC and skew OC-CO dynamics...
December 7, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/29201435/endothelial-nitric-oxide-synthase-gene%C3%A2-polymorphisms-in-patients-with-slow%C3%A2-coronary-flow
#2
Nurzen Sezgin, Abdullah Tekin, Fatma Belgin Atac, Hasibe Verdi, Alpay Turan Sezgin
Background and aims: The aim of this study was to explore potential associations of the intron 4 variable number of tandem repeats (VNTR) and E298A polymorphisms of the endothelial nitric oxide synthase (eNOS) gene with slow coronary flow (SCF). The association between plasma nitrate and nitrite (NO x ) concentrations and eNOS gene polymorphisms was also assessed. Materials and methods: The intron 4 VNTR and E298A polymorphisms of the eNOS gene were evaluated in the isolated DNA blood samples obtained from the SCF patient group (n = 30) and healthy group consisted of age- and sex-matched controls (n = 61)...
September 2017: Interventional Medicine & Applied Science
https://www.readbyqxmd.com/read/29192626/neutrophil-lymphocyte-ratio-predicts-postoperative-pain-after-orthognathic-surgery
#3
H C Turgut, M Alkan, M S Ataç, S K Altundağ, S Bozkaya, B Şimşek, B Işik, M Arslan
BACKGROUND AND AIM: Postoperative pain is well known and usually disturbing complication of surgery. Inflammation plays an important role in the development and progression of postoperative pain. We aimed to investigate possible relationship between preoperatively measured neutrophil-lymphocyte ratio (NLR) - as an inflammation marker - and postoperative analgesic demand in patients underwent orthognathic surgery. MATERIALS AND METHODS: We retrospectively investigated medical and anesthesia records of 177 patients underwent orthognathic surgery...
October 2017: Nigerian Journal of Clinical Practice
https://www.readbyqxmd.com/read/29181276/i-atac-interactive-pipeline-for-the-management-and-pre-processing-of-atac-seq-samples
#4
Zeeshan Ahmed, Duygu Ucar
Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors...
2017: PeerJ
https://www.readbyqxmd.com/read/29180017/role-of-osteopontin-and-its-regulation-in-pancreatic-islet
#5
Mengyin Cai, Pradeep Bompada, Albert Salehi, Juan R Acosta, Rashmi B Prasad, David Atac, Markku Laakso, Leif Groop, Yang De Marinis
Osteopontin (OPN) is involved in various physiological processes and also implicated in multiple pathological states. It has been suggested that OPN may have a role in type 2 diabetes (T2D) by protecting pancreatic islets and interaction with incretins. However, the regulation and function of OPN in islets, especially in humans, remains largely unexplored. In this study, we performed our investigations on both diabetic mouse model SUR1-E1506K+/+ and islets from human donors. We demonstrated that OPN protein, secretion and gene expression was elevated in the diabetic SUR1-E1506K+/+ islets...
November 24, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29171645/cardiovascular-risk-factors-and-white-matter-hyperintensities-in-patients-with-migraine-without-aura
#6
Ceyla Ataç Uçar, Hafize Nalan Güneş, Cemile Sencer Demircan, Burcu Gökçe Çokal, Selda Keskin Güler, Tahir Kurtuluş Yoldaş
OBJECTIVES: White matter hyperintensities (WMHs) are observed in patients with migraine with aura (MWA) and without aura (MWO), but there are a limited number of studies regarding patients with MWA. In this study, we aimed to investigate the cardiovascular risk factors which may play a role in the development of WMHs in patients with MWO. METHODS: This observational, analytical, case-control study was conducted between June 2016 and January 2017. It included 21 patients with MWO who had WMHs on brain MRI and 19 patients with MWO who tested normal on MRI (control group) at the Neurology Department Outpatient Polyclinic, Ankara Training and Research Hospital...
October 2017: Aǧrı: Ağrı (Algoloji) Derneği'nin Yayın Organıdır, the Journal of the Turkish Society of Algology
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#7
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
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/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#9
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29126307/universal-correction-of-enzymatic-sequence-bias-reveals-molecular-signatures-of-protein-dna-interactions
#10
André L Martins, Ninad M Walavalkar, Warren D Anderson, Chongzhi Zang, Michael J Guertin
Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126117/dynamic-reorganization-of-open-chromatin-underlies-diverse-transcriptomes-during-spermatogenesis
#11
So Maezawa, Masashi Yukawa, Kris G Alavattam, Artem Barski, Satoshi H Namekawa
During spermatogenesis, germ cells undergo massive cellular reconstruction and dynamic chromatin remodeling to facilitate highly diverse transcriptomes, which are required for the production of functional sperm. However, it remains unknown how germline chromatin is organized to promote the dynamic, complex transcriptomes of spermatogenesis. Here, using ATAC-seq, we establish the varied landscape of open chromatin during spermatogenesis. We identify the reorganization of accessible chromatin in intergenic and intronic regions during the mitosis-to-meiosis transition...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29115649/role-of-inflammatory-markers-in-decreasing-negative-appendectomy-rate-a-study-based-on-computed-tomography-findings
#12
Ebru Ozan, Gökçe Kaan Ataç, Kaan Alişar, Aslıhan Alhan
BACKGROUND: This study aimed to investigate the role of inflammatory markers in decreasing negative appendectomy rate (NAR) based on their relation with findings of acute appendicitis (AA) on computed tomography (CT). METHODS: Ninety-two patients who underwent CT examination with suspected AA were included. We investigated the relation between CT findings of AA and laboratory inflammatory markers and also performed receiver operating characteristic (ROC) analysis to calculate cut-off values of inflammatory markers and CT findings of AA...
November 2017: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29113963/gain-of-function-of-asxl1-truncating-protein-in-the-pathogenesis-of-myeloid-malignancies
#13
Hui Yang, Stefan Kurtenbach, Ying Guo, Ines Lohse, Michael A Durante, Jianping Li, Zhaomin Li, Hassan Al-Ali, Lingxiao Li, Zizhen Chen, Matthew G Field, Peng Zhang, Shi Chen, Shohei Yamamoto, Zhuo Li, Yuan Zhou, Stephen D Nimer, J William Harbour, Claes Wahlestedt, Mingjiang Xu, Feng-Chun Yang
Additional Sex Combs-Like 1 (ASXL1) is mutated at a high frequency in all forms of myeloid malignancies associated with poor prognosis. We generated a Vav1 promoter driven Flag-Asxl1(Y588X) transgenic mouse model, Asxl1(Y588X) Tg, to express a truncated FLAG-ASXL1(aa1-587) protein in the hematopoietic system. The Asxl1(Y588X) Tg mice had an enlarged hematopoietic stem cell (HSC) pool, shortened survival, and predisposition to a spectrum of myeloid malignancies, thereby recapitulating the characteristics of myeloid malignancy patients with ASXL1 mutations...
November 7, 2017: Blood
https://www.readbyqxmd.com/read/29107597/naked-mole-rat-cells-have-a-stable-epigenome-that-resists-ipsc%C3%A2-reprogramming
#14
Li Tan, Zhonghe Ke, Gregory Tombline, Nicholas Macoretta, Kevin Hayes, Xiao Tian, Ruitu Lv, Julia Ablaeva, Michael Gilbert, Natarajan V Bhanu, Zuo-Fei Yuan, Benjamin A Garcia, Yujiang G Shi, Yang Shi, Andrei Seluanov, Vera Gorbunova
Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and cancer resistance. We observed that the reprogramming efficiency of NMR fibroblasts in response to OSKM was drastically lower than that of mouse fibroblasts. Expression of SV40 LargeT antigen (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was sufficient to improve reprogramming efficiency, suggesting that NMR chromatin may be refractory to reprogramming...
November 14, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/29107594/genes-associated-with-pancreas-development-and-function-maintain-open-chromatin-in-ipscs-generated-from-human-pancreatic-beta-cells
#15
Matthias Thurner, Liraz Shenhav, Agata Wesolowska-Andersen, Amanda J Bennett, Amy Barrett, Anna L Gloyn, Mark I McCarthy, Nicola L Beer, Shimon Efrat
Current in vitro islet differentiation protocols suffer from heterogeneity and low efficiency. Induced pluripotent stem cells (iPSCs) derived from pancreatic beta cells (BiPSCs) preferentially differentiate toward endocrine pancreas-like cells versus those from fibroblasts (FiPSCs). We interrogated genome-wide open chromatin in BiPSCs and FiPSCs via ATAC-seq and identified ∼8.3k significant, differential open chromatin sites (DOCS) between the two iPSC subtypes (false discovery rate [FDR] < 0.05). DOCS where chromatin was more accessible in BiPSCs (Bi-DOCS) were significantly enriched for known regulators of endodermal development, including bivalent and weak enhancers, and FOXA2 binding sites (FDR < 0...
November 14, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/29104531/the-repression-of-atoh1-by-neurogenin1-during-inner-ear-development
#16
Héctor Gálvez, Juan J Tena, Fernando Giraldez, Gina Abelló
Atonal homolog 1 (Atoh1) and Neurogenin1 (Neurog1) are basic Helix-Loop-Helix (bHLH) transcription factors crucial for the generation of hair cells (HCs) and neurons in the inner ear. Both genes are induced early in development, but the expression of Atoh1 is counteracted by Neurog1. As a result, HC development is prevented during neurogenesis. This work aimed at understanding the molecular basis of this interaction. Atoh1 regulation depends on a 3'Atoh1-enhancer that is the site for Atoh1 autoregulation. Reporter assays on chick embryos and P19 cells show that Neurog1 hampers the autoactivation of Atoh1, the effect being cell autonomous and independent on Notch activity...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29067999/myd88-dependent-dendritic-and-epithelial-cell-crosstalk-orchestrates-immune-responses-to-allergens
#17
S Y Thomas, G S Whitehead, M Takaku, J M Ward, X Xu, K Nakano, M R Lyons-Cohen, H Nakano, K M Gowdy, P A Wade, D N Cook
Sensitization to inhaled allergens is dependent on activation of conventional dendritic cells (cDCs) and on the adaptor molecule, MyD88. However, many cell types in the lung express Myd88, and it is unclear how signaling in these different cell types reprograms cDCs and leads to allergic inflammation of the airway. By combining ATAC-seq with RNA profiling, we found that MyD88 signaling in cDCs maintained open chromatin at select loci even at steady state, allowing genes to be rapidly induced during allergic sensitization...
October 25, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/29066026/cd4-cd28-kir-cd11a-hi-t-cells-correlate-with-disease-activity-and-are-characterized-by-a-pro-inflammatory-epigenetic-and-transcriptional-profile-in-lupus-patients
#18
Elizabeth Gensterblum, Paul Renauer, Patrick Coit, Faith M Strickland, Nathan C Kilian, Shaylynn Miller, Mikhail Ognenovski, Jonathan D Wren, Pei-Suen Tsou, Emily E Lewis, Kathleen Maksimowicz-McKinnon, W Joseph McCune, Bruce C Richardson, Amr H Sawalha
OBJECTIVE: The goal of this study was to comprehensively characterize CD4+CD28+ T cells overexpressing CD11a and KIR genes, and examine the relationship between this T cell subset, genetic risk, and disease activity in lupus. METHODS: The size of the CD4+CD28+KIR+CD11a(hi) T cell subset was determined by flow cytometry, and total genetic risk for lupus was calculated in 105 female patients using 43 confirmed genetic susceptibility loci. Primary CD4+CD28+KIR+CD11a(hi) T cells were isolated from lupus patients or were induced from healthy individuals using 5-azacytidine...
October 20, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29057918/yeats2-links-histone-acetylation-to-tumorigenesis-of-non-small-cell-lung-cancer
#19
Wenyi Mi, Haipeng Guan, Jie Lyu, Dan Zhao, Yuanxin Xi, Shiming Jiang, Forest H Andrews, Xiaolu Wang, Mihai Gagea, Hong Wen, Laszlo Tora, Sharon Y R Dent, Tatiana G Kutateladze, Wei Li, Haitao Li, Xiaobing Shi
Recognition of modified histones by "reader" proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival...
October 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29052193/identification-of-open-chromatin-regions-in-plant-genomes-using-atac-seq
#20
Marko Bajic, Kelsey A Maher, Roger B Deal
Identifying and characterizing highly accessible chromatin regions assists in determining the location of genomic regulatory elements and understanding transcriptional regulation. In this chapter, we describe an approach to map accessible chromatin features in plants using the Assay for Transposase-Accessible Chromatin, combined with high-throughput sequencing (ATAC-seq), which was originally developed for cultured animal cells. This technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and simultaneous insertion of sequencing adapters into open chromatin regions of the input nuclei...
2018: Methods in Molecular Biology
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