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https://www.readbyqxmd.com/read/29222611/kiwifruit-svp2-controls-developmental-and-drought-stress-pathways
#1
Rongmei Wu, Tianchi Wang, Ben A W Warren, Susan J Thomson, Andrew C Allan, Richard C Macknight, Erika Varkonyi-Gasic
Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy...
December 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29222512/improving-gene-regulatory-network-inference-by-incorporating-rates-of-transcriptional-changes
#2
Jigar S Desai, Ryan C Sartor, Lovely Mae Lawas, S V Krishna Jagadish, Colleen J Doherty
Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29214996/the-role-of-cdx2-as-a-lineage-specific-transcriptional-repressor-for-pluripotent-network-during-the-first-developmental-cell-lineage-segregation
#3
Daosheng Huang, Guoji Guo, Ping Yuan, Amy Ralston, Lingang Sun, Mikael Huss, Tapan Mistri, Luca Pinello, Huck Hui Ng, Guocheng Yuan, Junfeng Ji, Janet Rossant, Paul Robson, Xiaoping Han
The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and trophectoderm (TE). The transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4). However its downstream network in the developing embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify CDX2-regulated targets in vivo...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29211822/insights-from-resolving-protein-dna-interactions-at-near-base-pair-resolution
#4
Bryan J Venters
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task...
December 2, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29208650/transcriptional-profiling-of-saccharomyces-cerevisiae-reveals-the-impact-of-variation-of-a-single-transcription-factor-on-differential-gene-expression-in-4nqo-fermentable-and-non-fermentable-carbon-sources
#5
Xiaqing Rong-Mullins, Michael C Ayers, Mahmoud Summers, Jennifer E G Gallagher
Cellular metabolism can change the potency of a chemical's tumorigenicity. 4-nitroquinoline-1-oxide (4NQO) is a tumorigenic drug widely used on animal models for cancer research. Polymorphisms of the transcription factor, Yrr1, confer different levels of resistance to 4NQO in Saccharomyces cerevisiae To study how different Yrr1 alleles regulate gene expression leading to resistance, transcriptomes of three isogenic Scerevisiae strains carrying different Yrr1 alleles were profiled via RNA sequencing (RNA-Seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) in presence and absence of 4NQO...
December 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29203910/tet-proteins-safeguard-bivalent-promoters-from-de-novo-methylation-in-human-embryonic-stem-cells
#6
Nipun Verma, Heng Pan, Louis C Doré, Abhijit Shukla, Qing V Li, Bobbie Pelham-Webb, Virginia Teijeiro, Federico González, Andrei Krivtsov, Chan-Jung Chang, Eirini P Papapetrou, Chuan He, Olivier Elemento, Danwei Huangfu
TET enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish owing to challenges in distinguishing global versus locus-specific effects. Here we show that TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit prominent bivalent promoter hypermethylation without an overall corresponding decrease in gene expression in the undifferentiated state...
December 4, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29192968/a-regression-framework-for-assessing-covariate-effects-on-the-reproducibility-of-high-throughput-experiments
#7
Qunhua Li, Feipeng Zhang
The outcome of high-throughput biological experiments is affected by many operational factors in the experimental and data-analytical procedures. Understanding how these factors affect the reproducibility of the outcome is critical for establishing workflows that produce replicable discoveries. In this article, we propose a regression framework, based on a novel cumulative link model, to assess the covariate effects of operational factors on the reproducibility of findings from high-throughput experiments. In contrast to existing graphical approaches, our method allows one to succinctly characterize the simultaneous and independent effects of covariates on reproducibility and to compare reproducibility while controlling for potential confounding variables...
November 29, 2017: Biometrics
https://www.readbyqxmd.com/read/29187863/smooth-an-hnrnp-l-homolog-might-decrease-mitochondrial-metabolism-by-post-transcriptional-regulation-of-isocitrate-dehydrogenase-idh-and-other-metabolic-genes-in-the-sub-acute-phase-of-traumatic-brain-injury
#8
Arko Sen, Katherine Gurdziel, Jenney Liu, Wen Qu, Oluwademi O Nuga, Rayanne B Burl, Maik Hüttemann, Roger Pique-Regi, Douglas M Ruden
Traumatic brain injury (TBI) can cause persistent pathological alteration of neurons. This may lead to cognitive dysfunction, depression and increased susceptibility to life threatening diseases, such as epilepsy and Alzheimer's disease. To investigate the underlying genetic and molecular basis of TBI, we subjected w1118Drosophila melanogaster to mild closed head trauma and found that mitochondrial activity is reduced in the brains of these flies 24 h after inflicting trauma. To determine the transcriptomic changes after mild TBI, we collected fly heads 24 h after inflicting trauma, and performed RNA-seq analyses...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29187152/a-proximity-based-graph-clustering-method-for-the-identification-and-application-of-transcription-factor-clusters
#9
Maxwell Spadafore, Kayvan Najarian, Alan P Boyle
BACKGROUND: Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions...
November 29, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29186514/permissive-zones-for-the-centromere-binding-protein-parb-on-the-caulobacter-crescentus-chromosome
#10
Ngat T Tran, Clare E Stevenson, Nicolle F Som, Anyarat Thanapipatsiri, Adam S B Jalal, Tung B K Le
Proper chromosome segregation is essential in all living organisms. In Caulobacter crescentus, the ParA-ParB-parS system is required for proper chromosome segregation and cell viability. The bacterial centromere-like parS DNA locus is the first to be segregated following chromosome replication. parS is bound by ParB protein, which in turn interacts with ParA to partition the ParB-parS nucleoprotein complex to each daughter cell. Here, we investigated the genome-wide distribution of ParB on the Caulobacter chromosome using a combination of in vivo chromatin immunoprecipitation (ChIP-seq) and in vitro DNA affinity purification with deep sequencing (IDAP-seq)...
November 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29185442/synergistic-gene-expression-during-the-acute-phase-response-is-characterized-by-transcription-factor-assisted-loading
#11
Ido Goldstein, Ville Paakinaho, Songjoon Baek, Myong-Hee Sung, Gordon L Hager
The cytokines interleukin 1β and 6 (IL-1β, IL-6) mediate the acute phase response (APR). In liver, they regulate the secretion of acute phase proteins. Using RNA-seq in primary hepatocytes, we show that these cytokines regulate transcription in a bifurcated manner, leading to both synergistic and antagonistic gene expression. By mapping changes in enhancer landscape and transcription factor occupancy (using ChIP-seq), we show that synergistic gene induction is achieved by assisted loading of STAT3 on chromatin by NF-κB...
November 29, 2017: Nature Communications
https://www.readbyqxmd.com/read/29181276/i-atac-interactive-pipeline-for-the-management-and-pre-processing-of-atac-seq-samples
#12
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/29178831/software-for-rapid-time-dependent-chip-sequencing-analysis-tdca
#13
Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David Vocadlo
BACKGROUND: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited...
November 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29177743/topoisomerase-ii-chromatin-immunoprecipitation
#14
Kayleigh A Smith, Ian G Cowell, Caroline A Austin
Chromatin immunoprecipitation is a method to isolate a protein of interest coupled to DNA following cross-linking with formaldehyde and to quantify the relative abundance or occupancy of the protein at specific genomic loci. After immunoprecipitation of protein-DNA complexes protein-DNA cross-links are reversed and the DNA is extracted. Various methods exist to identify binding sites and determine relative occupancy of the protein of interest; these include quantitative PCR, probing microarrays or sequencing the isolated DNA (ChIP-seq)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29177735/mapping-e-coli-topoisomerase-iv-binding-and-activity-sites
#15
Hafez El Sayyed, Olivier Espéli
This methods article described a protocol aiming at mapping E. coli Topoisomerase IV (Topo IV) binding and cleavage activity sites on the genome. The approach is readily applicable to any Type II topoisomerase on a broad variety of gram-positive and gram-negative bacterial species. Conventional ChIP-seq of flag tagged Topo IV subunits and a novel method aimed at trapping only DNA bound to active Topo IV (called NorfliP) are described. NorfliP relies on the ability of norfloxacin, a quinolone drug, to cross-link the 5' ends of the DNA breaks with the catalytic tyrosine of bacterial Type II topoisomerases...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29177663/chromatin-immunoprecipitation-chip-of-heat-shock-protein-90-hsp90
#16
Aneliya Yoveva, Ritwick Sawarkar
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used technique for genome-wide mapping of protein-DNA interactions and epigenetic marks in vivo. Recent studies have suggested an important role of heat shock protein 90 (Hsp90) at chromatin. This molecular chaperone assists other proteins to acquire their mature and functional conformation and helps in the assembly of many complexes. In this chapter, we provide specific details on how to perform Hsp90 ChIP-seq from Drosophila Schneider (S2) cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29174800/ets1-induction-by-the-microenvironment-promotes-ovarian-cancer-metastasis-through-focal-adhesion-kinase
#17
Sunil Tomar, Joshua P Plotnik, James Haley, Joshua Scantland, Subramanyam Dasari, Zahir Sheikh, Robert Emerson, Dean Lenz, Peter C Hollenhorst, Anirban K Mitra
Metastatic colonization involves paracrine/juxtacrine interactions with the microenvironment inducing an adaptive response through transcriptional regulation. However, the identities of transcription factors (TFs) induced by the metastatic microenvironment in ovarian cancer (OC) and their mechanism of action is poorly understood. Using an organotypic 3D culture model recapitulating the early events of metastasis, we identified ETS1 as the most upregulated member of the ETS family of TFs in metastasizing OC cells as they interacted with the microenvironment...
November 21, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29173090/zebrafish-transcription-factor-orfeome-for-gene-discovery-and-regulatory-network-elucidation
#18
Justin King, Justin Foster, James M Davison, John F Rawls, Ghislain Breton
The completion of the zebrafish genome sequence and advances in miniaturization and multiplexing were essential to the creation of techniques such as RNA-seq, ChIP-seq, and high-throughput behavioral and chemical screens. Multiplexing was also instrumental in the recent enhancement of the classic yeast one-hybrid interaction techniques to provide unprecedented discovery capabilities for protein-DNA interactions. Unfortunately its use for zebrafish research is currently hampered by the lack of an open reading frame (ORF) clone collection...
November 27, 2017: Zebrafish
https://www.readbyqxmd.com/read/29167426/epigenetic-targeting-of-bromodomain-protein-brd4-counteracts-cancer-cachexia-and-prolongs-survival
#19
Marco Segatto, Raffaella Fittipaldi, Fabrizio Pin, Roberta Sartori, Kyung Dae Ko, Hossein Zare, Claudio Fenizia, Gianpietro Zanchettin, Elisa Sefora Pierobon, Shinji Hatakeyama, Cosimo Sperti, Stefano Merigliano, Marco Sandri, Panagis Filippakopoulos, Paola Costelli, Vittorio Sartorelli, Giuseppina Caretti
Cancer cachexia is a devastating metabolic syndrome characterized by systemic inflammation and massive muscle and adipose tissue wasting. Although it is responsible for approximately one-third of cancer deaths, no effective therapies are available and the underlying mechanisms have not been fully elucidated. We previously identified the bromodomain and extra-terminal domain (BET) protein BRD4 as an epigenetic regulator of muscle mass. Here we show that the pan-BET inhibitor (+)-JQ1 protects tumor-bearing mice from body weight loss and muscle and adipose tissue wasting...
November 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29158625/comparative-genomic-hybridization-and-transcriptome-sequencing-reveal-that-two-genes-osi_14279-loc_os03g62620-and-osi_10794-loc_os03g14950-regulate-the-mutation-in-the-%C3%AE-rl-rice-mutant
#20
Xulong Wang, Fanhua Wang, Huiqiong Chen, Xiaoyu Liang, Yingmei Huang, Jicai Yi
We previously established the genetic locus of the rolled-leaf mutant, γ-rl, to chromosome 3. In this study, we performed a comparative genomic hybridization (CGH) analysis to identify the genes responsible for the γ-rl mutant phenotype. This was combined with RNA transcriptome sequencing (RNA-seq) to analyze differences in the mRNA expression in seeds 12 h after germination. Using the reference genome of the "indica type" rice from GenBank, we created a chip with 386,000 high density DNA probes designed to target chromosome 3...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
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