keyword
MENU ▼
Read by QxMD icon Read
search

Epigenetics profilling

keyword
https://www.readbyqxmd.com/read/28449120/sigseeker-a-peak-calling-ensemble-approach-for-constructing-epigenetic-signatures
#1
Jens Lichtenberg, Laura Elnitski, David M Bodine
Motivation: Epigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#2
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
April 25, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28448896/differentially-methylated-embryonal-fyn-associated-substrate-efs-gene-as-a-blood-specific-epigenetic-marker-and-its-potential-application-in-forensic-casework
#3
Athina Vidaki, Cecilia Johansson, Federica Giangasparo
DNA methylation patterns have the ability to reveal the activities of genes within a certain tissue at a particular time point. Tissue-specific DNA methylation patterns have been previously investigated for their applicability in the identification of forensically relevant body fluids, however there is still a lack in robust markers. While following a genome-wide scale investigation has a great potential to reveal useful tissue-specific changes, a gene-targeted approach can also lead to significant outcomes, especially in genomic locations not included in the genome-wide experiments...
April 19, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28447422/minimal-residual-disease-in-acute-myelogenous-leukemia
#4
REVIEW
N M Cruz, N Mencia-Trinchant, D C Hassane, M L Guzman
Treatment of acute myelogenous leukemia (AML) over the past four decades remains mostly unchanged and the prognosis for the majority of patients remains poor. Most of the significant advances that have been observed are in defining cytogenetic abnormalities, as well as the genetic and epigenetic profiles of AML patients. While new cytogenetic and genetic aberrations such as the FLT3-ITD and NPM1 mutations are able to guide prognosis for the majority of patients with AML, outcomes are still dismal and relapse rates remain high...
May 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28447382/quantitative-proteomic-analysis-of-ezh2-inhibition-in-acute-myeloid-leukemia-reveals-the-targets-and-pathways-that-precede-the-induction-of-cell-death
#5
Jarrod J Sandow, Giuseppe Infusini, Aliaksei Z Holik, Gabriela Brumatti, Tessa V Averink, Paul G Ekert, Andrew I Webb
PURPOSE: Chromosomal translocation of the Mixed Lineage Leukemia (MLL) locus generates fusion proteins that drive acute myeloid leukemia (AML) resulting in atypical histone methyltransferase activity and alterations in the epigenetic regulation of gene expression. Targeting histone regulators, such as Enhancer of Zeste Homologue 2 (EZH2), has shown promise in AML. Profiling differential protein expression following inhibition of epigenetic regulators in AML may help to identify novel targets for therapeutics...
April 26, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28446964/strategies-for-the-acquisition-of-transcriptional-and-epigenetic-information-in-single-cells
#6
REVIEW
Guang Li, Elda Dzilic, Nick Flores, Alice Shieh, Sean M Wu
As the basic unit of living organisms, each single cell has unique molecular signatures and functions. Our ability to uncover the transcriptional and epigenetic signature of single cells has been hampered by the lack of tools to explore this area of research. The advent of microfluidic single cell technology along with single cell genome-wide DNA amplification methods had greatly improved our understanding of the expression variation in single cells. Transcriptional expression profile by multiplex qPCR or genome-wide RNA sequencing has enabled us to examine genes expression in single cells in different tissues...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28445736/systematic-epigenomic-analysis-reveals-chromatin-states-associated-with-melanoma-progression
#7
Petko Fiziev, Kadir C Akdemir, John P Miller, Emily Z Keung, Neha S Samant, Sneha Sharma, Christopher A Natale, Christopher J Terranova, Mayinuer Maitituoheti, Samirkumar B Amin, Emmanuel Martinez-Ledesma, Mayura Dhamdhere, Jacob B Axelrad, Amiksha Shah, Christine S Cheng, Harshad Mahadeshwar, Sahil Seth, Michelle C Barton, Alexei Protopopov, Kenneth Y Tsai, Michael A Davies, Benjamin A Garcia, Ido Amit, Lynda Chin, Jason Ernst, Kunal Rai
The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. Through systematic epigenomic profiling of 35 epigenetic modifications and transcriptomic analysis, we define chromatin state changes associated with melanomagenesis by using a cell phenotypic model of non-tumorigenic and tumorigenic states. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways...
April 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28444293/regulation-of-hematopoiesis-and-immune-responses-by-long-noncoding-rnas
#8
Wooseok Seo, Ichiro Taniuchi
Since the first draft of the human genome sequence was released in 2001, unprecedentedly rapid progress has been made in whole genome-wide approaches by utilizing next-generation-sequencing technologies. The last decade alone has generated enormous data in the forms of exome sequencing, transcriptomes, transcription factor occupancy, genomic variation profiling and epigenetic modifications. One of the most striking realizations from sequencing studies has been the discovery and characterization of noncoding RNAs...
April 22, 2017: International Immunology
https://www.readbyqxmd.com/read/28441149/epigenetic-regulatory-mutations-and-epigenetic-therapy-for-multiple-myeloma
#9
Daphné Dupéré-Richer, Jonathan D Licht
PURPOSE OF REVIEW: Next generation sequencing and large-scale analysis of patient specimens has created a more complete picture of multiple myeloma (MM) revealing that epigenetic deregulation is a prominent factor in MM pathogenesis. RECENT FINDINGS: Over half of MM patients have mutations in genes encoding epigenetic modifier enzymes. The DNA methylation profile of MM is related to the stage of the disease and certain classes of mutations in epigenetic modifiers are more prevalent upon disease relapse, suggesting a role in disease progression...
April 22, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28439859/genome-wide-profiling-of-histone-modifications-and-histone-variants-in-arabidopsis-thaliana-and-marchantia-polymorpha
#10
Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, Tomokazu Kawashima
Histone modifications and histone variants barcode the genome and play major roles in epigenetic regulations. Chromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is a well-established method to investigate the landscape of epigenetic marks at a genomic level. Here, we describe procedures for conducting ChIP, subsequent NGS library construction, and data analysis on histone modifications and histone variants in Arabidopsis thaliana. We also describe an optimized nuclear isolation procedure to prepare chromatin for ChIP in the liverwort, Marchantia polymorpha, which is the emerging model plant ideal for evolutionary studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439397/transcriptomic-analysis-of-maternally-provisioned-cues-for-phenotypic-plasticity-in-the-annual-killifish-austrofundulus-limnaeus
#11
Amie L Romney, Jason E Podrabsky
BACKGROUND: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause...
2017: EvoDevo
https://www.readbyqxmd.com/read/28439113/microrna-expression-profiling-defines-the-impact-of-electronic-cigarettes-on-human-airway-epithelial-cells
#12
Siva Kumar Solleti, Soumyaroop Bhattacharya, Ausaf Ahmad, Qian Wang, Jared Mereness, Tirumalai Rangasamy, Thomas J Mariani
While all forms of tobacco exposure have negative health effects, the significance of exposure to electronic cigarettes (eCig) is not fully understood. Here, we studied the global effects of eCig on the micro RNA (miRNA) transcriptome in human lung epithelial cells. Primary human bronchial epithelial (NHBE) cells differentiated at air-liquid interface were exposed to eCig liquid. Exposure of NHBE to any eCig liquid resulted in the induction of oxidative stress-response genes including GCLM, GCLC, GPX2, NQO1 and HO-1...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438736/altered-microrna-expression-is-responsible-for-the-pro-osteogenic-phenotype-of-interstitial-cells-in-calcified-human-aortic-valves
#13
Rui Song, David A Fullerton, Lihua Ao, Ke-Seng Zhao, T Brett Reece, Joseph C Cleveland, Xianzhong Meng
BACKGROUND: The transition of aortic valve interstitial cells (AVICs) to myofibroblastic and osteoblast-like phenotypes plays a critical role in calcific aortic valve disease progression. Several microRNAs (miRs) are implicated in stem cell differentiation into osteoblast. We hypothesized that an epigenetic mechanism regulates valvular pro-osteogenic activity. This study examined miR profile in AVICs of calcified valves and identified miRs responsible for AVIC phenotypic transition. METHODS AND RESULTS: AVICs were isolated from normal and diseased valves...
April 24, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28438071/time-to-re-evaluate-art-protocols-in-the-light-of-advances-in-knowledge-about-methylation-and-epigenetics-an-opinion-paper
#14
Yves Menezo, Brian Dale, Kay Elder
DNA methylation is a biochemical process that modifies gene expression without changing the underlying DNA sequence, and this represents the molecular basis for imprinting and epigenetics. Recent reports have revealed alterations in DNA methylation profiles in the placenta of babies born from assisted reproductive technologies (ART). This supports several previous observations that suggested an increase in the prevalence of imprinting diseases following ART treatment, and also fits our observations regarding the metabolism and requirements of early human embryos...
April 25, 2017: Human Fertility: Journal of the British Fertility Society
https://www.readbyqxmd.com/read/28434075/associations-of-self-reported-smoking-cotinine-levels-and-epigenetic-smoking-indicators-with-oxidative-stress-among-older-adults-a-population-based-study
#15
Xu Gao, Xīn Gào, Yan Zhang, Lutz Philipp Breitling, Ben Schöttker, Hermann Brenner
Tobacco smoking and oxidative stress (OS) are both related to a wide spectrum of adverse age-related health outcomes, but their association is not yet well-established. We examined the associations of self-reported smoking indicators, serum cotinine levels and smoking-related DNA methylation biomarkers with two urinary proxy markers of OS, 8-isoprostane (8-iso) and 8-hydroxy-2'-deoxyguanosine (8-oxodG), in two independent subsets of older adults recruited in Germany (discovery set: n = 978, validation set: n = 531)...
April 22, 2017: European Journal of Epidemiology
https://www.readbyqxmd.com/read/28433605/stability-of-patient-specific-features-of-altered-dna-replication-timing-in-xenografts-of-primary-human-acute-lymphoblastic-leukemia
#16
Takayo Sasaki, Juan Carlos Rivera-Mulia, Daniel Vera, Jared Zimmerman, Sunny Das, Michelle Padget, Naoto Nakamichi, Bill H Chang, Jeff Tyner, Brian J Druker, Andrew P Weng, Curt I Civin, Connie J Eaves, David M Gilbert
Genome-wide DNA replication timing (RT) profiles reflect the global 3D chromosome architecture of cells. They also provide a comprehensive and unique megabase-scale picture of the cellular epigenetic state. Thus normal differentiation involves reproducible changes in RT and transformation generally perturbs these, although the potential effects of altered RT on the properties of transformed cells remain largely unknown. A major challenge to interrogating these issues in human acute lymphoid leukemia (ALL) is the low proliferative activity of most of the cells, which may be further reduced in cryopreserved samples and difficult to overcome in vitro...
April 19, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28433417/mechanistic-insights-into-epigenetic-modulation-of-ethanol-consumption
#17
Igor Ponomarev, Claire E Stelly, Hitoshi Morikawa, Yuri A Blednov, R Dayne Mayfield, R Adron Harris
There is growing evidence that small-molecule inhibitors of epigenetic modulators, such as histone deacetylases (HDAC) and DNA methyltransferases (DNMT), can reduce voluntary ethanol consumption in animal models, but molecular and cellular processes underlying this behavioral effect are poorly understood. We used C57BL/6J male mice to investigate the effects of two FDA-approved drugs, decitabine (a DNMT inhibitor) and SAHA (an HDAC inhibitor), on ethanol consumption using two tests: binge-like drinking in the dark (DID) and chronic intermittent every other day (EOD) drinking...
March 12, 2017: Alcohol
https://www.readbyqxmd.com/read/28431570/a-relative-quantitative-methylation-sensitive-amplified-polymorphism-msap-method-for-the-analysis-of-abiotic-stress
#18
Piotr T Bednarek, Renata Orłowska, Agnieszka Niedziela
BACKGROUND: We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms...
April 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28430989/gene-fractionation-and-function-in-the-ancient-subgenomes-of-maize
#19
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts...
April 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28428426/transgenerational-transmission-of-environmental-information-in-c-elegans
#20
Adam Klosin, Eduard Casas, Cristina Hidalgo-Carcedo, Tanya Vavouri, Ben Lehner
The environment experienced by an animal can sometimes influence gene expression for one or a few subsequent generations. Here, we report the observation that a temperature-induced change in expression from a Caenorhabditis elegans heterochromatic gene array can endure for at least 14 generations. Inheritance is primarily in cis with the locus, occurs through both oocytes and sperm, and is associated with altered trimethylation of histone H3 lysine 9 (H3K9me3) before the onset of zygotic transcription. Expression profiling reveals that temperature-induced expression from endogenous repressed repeats can also be inherited for multiple generations...
April 21, 2017: Science
keyword
keyword
24025
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"