keyword
MENU ▼
Read by QxMD icon Read
search

ChIP seq

keyword
https://www.readbyqxmd.com/read/28107636/visceral-white-adipose-tissue-following-chronic-intermittent-and-sustained-hypoxia-in-mice
#1
David Gozal, Alex Gileles-Hillel, Rene Cortese, Yan Li, Isaac Almendros, Zhuanhong Qiao, Ahamed A Khalyfa, Jorge Andrade, Abdelnaby Khalyfa
BACKGROUND: Angiogenesis, a process induced by hypoxia in visceral white adipose tissue (vWAT) in the context of obesity, mediates obesity-induced metabolic dysfunction and insulin resistance. Chronic intermittent hypoxia (IH) and sustained hypoxia (SH) induce body weight reductions and insulin resistance of differing magnitude, suggesting different HIF-1α-related activity. METHODS: 8-week old male C57BL/6J mice (n=10-12/group) were exposed to either IH, SH,or room air (RA)...
January 20, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28105912/dgw-an-exploratory-data-analysis-tool-for-clustering-and-visualisation-of-epigenomic-marks
#2
Saulius Lukauskas, Roberto Visintainer, Guido Sanguinetti, Gabriele B Schweikert
BACKGROUND: Functional genomic and epigenomic research relies fundamentally on sequencing based methods like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high dimensional data sets with visually complex structures, such as multi-modal peaks extended over large genomic regions. Current tools for visualisation and data exploration represent and leverage these complex features only to a limited extent. RESULTS: We present DGW, an open source software package for simultaneous alignment and clustering of multiple epigenomic marks...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103242/genome-wide-binding-of-posterior-hoxa-d-transcription-factors-reveals-subgrouping-and-association-with-ctcf
#3
Ivana Jerković, Daniel M Ibrahim, Guillaume Andrey, Stefan Haas, Peter Hansen, Catrin Janetzki, Irene González Navarrete, Peter N Robinson, Jochen Hecht, Stefan Mundlos
Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28096468/o-glcnac-expression-levels-epigenetically-regulate-colon-cancer-tumorigenesis-by-affecting-the-cancer-stem-cell-compartment-via-modulating-expression-of-transcriptional-factor-mybl1
#4
Huabei Guo, Bing Zhang, Alison V Nairn, Tamas Nagy, Kelley W Moremen, Phillip Buckhaults, Michael Pierce
To study the regulation of colorectal adenocarcinoma progression by O-GlcNAc, we have focused on the O-GlcNAc-mediated epigenetic regulation of human colon cancer stem cells (CCSC). Xenograft tumors from colon tumor cells with OGT knockdown grew significantly slower than those formed from control cells, indicating a reduced proliferation of tumor cells due to inhibition of OGT expression. Significant reduction of CCSC population was observed in the tumor cells after OGT knockdown, while tumor cells treated with O-GlcNAcase inhibitor showed an increased CCSC population, indicating that O-GlcNAc levels regulated the CCSC compartment...
January 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28096379/molecular-mechanism-underlying-juvenile-hormone-mediated-repression-of-precocious-larval-adult-metamorphosis
#5
Takumi Kayukawa, Akiya Jouraku, Yuka Ito, Tetsuro Shinoda
Juvenile hormone (JH) represses precocious metamorphosis of larval to pupal and adult transitions in holometabolous insects. The early JH-inducible gene Krüppel homolog 1 (Kr-h1) plays a key role in the repression of metamorphosis as a mediator of JH action. Previous studies demonstrated that Kr-h1 inhibits precocious larval-pupal transition in immature larva via direct transcriptional repression of the pupal specifier Broad-Complex (BR-C). JH was recently reported to repress the adult specifier gene Ecdysone-induced protein 93F (E93); however, its mechanism of action remains unclear...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28093207/p53-mediates-the-suppression-of-cancer-cell-invasion-by-inducing-lima1-eplin
#6
Tomoko Ohashi, Masashi Idogawa, Yasushi Sasaki, Takashi Tokino
The tumor suppressor gene p53 is frequently mutated in human cancer. p53 executes various functions, such as apoptosis induction and cell cycle arrest, by modulating transcriptional regulation. In this study, LIM domain and Actin-binding protein 1 (LIMA1) was identified as a target of the p53 family using a cDNA microarray. We also evaluated genome-wide occupancy of the p53 protein by performing chromatin immunoprecipitation-sequencing (ChIP-seq) and identified two p53 response elements in the LIMA1 gene. LIMA1 protein levels were increased by treatment with nutlin-3a, a small molecule that activates endogenous p53...
January 13, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28092692/smile-seq-identifies-binding-motifs-of-single-and-dimeric-transcription-factors
#7
Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern, Riccardo Dainese, Giovanna Ambrosini, Didier Trono, Philipp Bucher, Bart Deplancke
Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28087634/genome-wide-identification-of-regulatory-elements-in-sertoli-cells
#8
Danielle M Maatouk, Anirudh Natarajan, Yoichiro Shibata, Lingyun Song, Gregory E Crawford, Uwe Ohler, Blanche Capel
A current goal of molecular biology is to identify transcriptional networks regulating cell differentiation. However, identifying functional gene regulatory elements has been challenging in the context of developing tissues where material is limited and cell types are mixed. To identify regulatory sites during sex determination, we subjected Sertoli cells from mouse fetal testes to DNaseI-seq and ChIP-seq for H3K27ac. DNaseI-seq identified putative regulatory sites around Sertoli- and pregranulosa-enriched genes; however, active enhancers marked by H3K27ac were enriched proximal only to Sertoli-enriched genes...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28080960/myogenic-regulatory-transcription-factors-regulate-growth-in-rhabdomyosarcoma
#9
Inês M Tenente, Madeline N Hayes, Myron S Ignatius, Karin McCarthy, Marielle Yohe, Sivasish Sindiri, Berkley Gryder, Mariana L Oliveira, Ashwin Ramakrishnan, Qin Tang, Eleanor Y Chen, G Petur Nielsen, Javed Khan, David M Langenau
Rhabdomyosarcoma (RMS) is a pediatric malignacy of muscle with myogenic regulatory transcription factors MYOD and MYF5 being expressed in this disease. Consensus in the field has been that expression of these factors likely reflects the target cell of transformation rather than being required for continued tumor growth. Here, we used a transgenic zebrafish model to show that Myf5 is sufficient to confer tumor-propagating potential to RMS cells and caused tumors to initiate earlier and have higher penetrance...
January 12, 2017: ELife
https://www.readbyqxmd.com/read/28079019/an-efficient-targeted-nuclease-strategy-for-high-resolution-mapping-of-dna-binding-sites
#10
Peter J Skene, Steven Henikoff
We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, CUT&RUN is performed in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, CUT&RUN yielded precise transcription factor profiles while avoiding cross-linking and solubilization issues...
January 12, 2017: ELife
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#11
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28070596/chip-seq-data-analysis-to-define-transcriptional-regulatory-networks
#12
Giulio Pavesi
The first step in the definition of transcriptional regulatory networks is to establish correct relationships between transcription factors (TFs) and their target genes, together with the effect of their regulatory activity (activator or repressor). Fundamental advances in this direction have been made possible by the introduction of experimental techniques such as Chromatin Immunoprecipitation, which, coupled with next-generation sequencing technologies (ChIP-Seq), permit the genome-wide identification of TF binding sites...
January 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28068916/inferring-condition-specific-targets-of-human-tf-tf-complexes-using-chip-seq-data
#13
Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H Andrews, Chao Cheng, Chun-Chi Liu, Jeremy J W Chen
BACKGROUND: Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28064247/genome-wide-analysis-of-the-distinct-types-of-chromatin-interactions-in-arabidopsis-thaliana
#14
Jingjing Wang, Yincong Zhou, Xue Li, Xianwen Meng, Miao Fan, Hongjun Chen, Jitong Xue, Ming Chen
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors...
November 15, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28061857/coordinated-regulation-of-acid-resistance-in-escherichia-coli
#15
Patricia Aquino, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K Sayeg, Arion I Stettner, Julia Wang, Brandon G Wong, Winnie S Wong, Stephen L Alexander, Cong Ba, Seth I Bensussen, David B Bernstein, Dana Braff, Susie Cha, Daniel I Cheng, Jang Hwan Cho, Kenny Chou, James Chuang, Daniel E Gastler, Daniel J Grasso, John S Greifenberger, Chen Guo, Anna K Hawes, Divya V Israni, Saloni R Jain, Jessica Kim, Junyu Lei, Hao Li, David Li, Qian Li, Christopher P Mancuso, Ning Mao, Salwa F Masud, Cari L Meisel, Jing Mi, Christine S Nykyforchyn, Minhee Park, Hannah M Peterson, Alfred K Ramirez, Daniel S Reynolds, Nae Gyune Rim, Jared C Saffie, Hang Su, Wendell R Su, Yaqing Su, Meng Sun, Meghan M Thommes, Tao Tu, Nitinun Varongchayakul, Tyler E Wagner, Benjamin H Weinberg, Rouhui Yang, Anastasia Yaroslavsky, Christine Yoon, Yanyu Zhao, Alicia J Zollinger, Anne M Stringer, John W Foster, Joseph Wade, Sahadaven Raman, Natasha Broude, Wilson W Wong, James E Galagan
BACKGROUND: Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored...
January 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28061811/the-nature-and-nurture-of-cell-heterogeneity-accounting-for-macrophage-gene-environment-interactions-with-single-cell-rna-seq
#16
Quin F Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes, Michael D Moore, Rory Bowden
BACKGROUND: Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome's limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic 'snapshots' of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic ('nature') and environmental ('nurture') modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28060339/the-chip-exo-method-identifying-protein-dna-interactions-with-near-base-pair-precision
#17
Andrea A Perreault, Bryan J Venters
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise...
December 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28055034/applying-the-intact-method-to-purify-endosperm-nuclei-and-to-generate-parental-specific-epigenome-profiles
#18
Jordi Moreno-Romero, Juan Santos-González, Lars Hennig, Claudia Köhler
The early endosperm tissue of dicot species is very difficult to isolate by manual dissection. This protocol details how to apply the INTACT (isolation of nuclei tagged in specific cell types) system for isolating early endosperm nuclei of Arabidopsis at high purity and how to generate parental-specific epigenome profiles. As a Protocol Extension, this article describes an adaptation of an existing Nature Protocol that details the use of the INTACT method for purification of root nuclei. We address how to obtain the INTACT lines, generate the starting material and purify the nuclei...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28054639/rapid-recall-ability-of-memory-t-cells-is-encoded-in-their-epigenome
#19
Artem Barski, Suresh Cuddapah, Andrey V Kartashov, Chong Liu, Hiromi Imamichi, Wenjing Yang, Weiqun Peng, H Clifford Lane, Keji Zhao
Even though T-cell receptor (TCR) stimulation together with co-stimulation is sufficient for the activation of both naïve and memory T cells, the memory cells are capable of producing lineage specific cytokines much more rapidly than the naïve cells. The mechanisms behind this rapid recall response of the memory cells are still not completely understood. Here, we performed epigenetic profiling of human resting naïve, central and effector memory T cells using ChIP-Seq and found that unlike the naïve cells, the regulatory elements of the cytokine genes in the memory T cells are marked by activating histone modifications even in the resting state...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28053168/ccnet-database-of-co-expression-networks-with-functional-modules-for-diploid-and-polyploid-gossypium
#20
Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chunchao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas J Provart, Fuguang Li, Zhen Su
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network...
January 4, 2017: Nucleic Acids Research
keyword
keyword
78077
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"