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https://www.readbyqxmd.com/read/29149270/aniseed-2017-extending-the-integrated-ascidian-database-to-the-exploration-and-evolutionary-comparison-of-genome-scale-datasets
#1
Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah K Lowe, Mickael Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C Titus Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean-Nicolas Volff, Patrick Lemaire
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29146583/comparison-of-chip-seq-data-and-a-reference-motif-set-for-human-krab-c2h2-zinc-finger-proteins
#2
Marjan Barazandeh, Sam Lambert, Mihai Albu, Timothy R Hughes
KRAB C2H2 zinc finger proteins (KZNFs) are the largest and most diverse family of human transcription factors, likely due to diversifying selection driven by novel endogenous retroelements (EREs), but the vast majority lack binding motifs or functional data. Two recent studies analyzed a majority of the human KZNFs using either ChIP-seq (60 proteins) or ChIP-exo (221 proteins) in the same cell type (HEK293). The ChIP-exo paper did not describe binding motifs, however. Thirty-nine proteins are represented in both studies, enabling the systematic comparison of the data sets presented here...
November 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29146582/elucidation-of-the-two-h3k36me3-histone-methyltransferases-set2-and-ash1-in-fusarium-fujikuroi-unravels-their-different-chromosomal-targets-and-a-major-impact-of-ash1-on-genome-stability
#3
Slavica Janevska, Leonie Baumann, Christian M K Sieber, Martin Münsterkötter, Jonas Ulrich, Jörg Kämper, Ulrich Güldener, Bettina Tudzynski
In this work, we present a comprehensive analysis of the H3K36 histone methyltransferases Set2 and Ash1 in the filamentous ascomycete Fusarium fujikuroi In Saccharomyces cerevisiae, one single methyltransferase, Set2, confers all H3K36 methylation, while there are two members of the Set2 family in filamentous fungi, and even more H3K36 methyltransferases in higher eukaryotes. Whereas the yeast Set2 homolog has been analyzed in fungi previously, the second member of the Set2 family, designated Ash1, has not been described for any filamentous fungus...
November 16, 2017: Genetics
https://www.readbyqxmd.com/read/29145608/medreaders-a-database-for-transcription-factors-that-bind-to-methylated-dna
#4
Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang
Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29140464/hocomoco-towards-a-complete-collection-of-transcription-factor-binding-models-for-human-and-mouse-via-large-scale-chip-seq-analysis
#5
Ivan V Kulakovskiy, Ilya E Vorontsov, Ivan S Yevshin, Ruslan N Sharipov, Alla D Fedorova, Eugene I Rumynskiy, Yulia A Medvedeva, Arturo Magana-Mora, Vladimir B Bajic, Dmitry A Papatsenko, Fedor A Kolpakov, Vsevolod J Makeev
We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29137925/polycomb-repression-complex-2-is-required-for-the-maintenance-of-retinal-progenitor-cells-and-balanced-retinal-differentiation
#6
Naoko Fujimura, Andrea Kuzelova, Anja Ebert, Hynek Strnad, Jitka Lachova, Ondrej Machon, Meinrad Busslinger, Zbynek Kozmik
Polycomb repressive complexes maintain transcriptional repression of genes encoding crucial developmental regulators through chromatin modification. Here we investigated the role of Polycomb repressive complex 2 (PRC2) in retinal development by inactivating its key components Eed and Ezh2. Conditional deletion of Ezh2 resulted in a partial loss of PRC2 function and accelerated differentiation of Müller glial cells. In contrast, inactivation of Eed led to the ablation of PRC2 function at early postnatal stage...
November 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#7
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
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
#8
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/29129929/il-2-imprints-human-naive-b-cell-fate-towards-plasma-cell-through-erk-elk1-mediated-bach2-repression
#9
Nicolas Hipp, Hannah Symington, Cédric Pastoret, Gersende Caron, Céline Monvoisin, Karin Tarte, Thierry Fest, Céline Delaloy
Plasma cell differentiation is a tightly regulated process that requires appropriate T cell helps to reach the induction threshold. To further understand mechanisms by which T cell inputs regulate B cell fate decision, we investigate the minimal IL-2 stimulation for triggering human plasma cell differentiation in vitro. Here we show that the timed repression of BACH2 through IL-2-mediated ERK/ELK1 signalling pathway directs plasma cell lineage commitment. Enforced BACH2 repression in activated B cells unlocks the plasma cell transcriptional program and induces their differentiation into immunoglobulin M-secreting cells...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29129639/determinants-of-histone-h3k4-methylation-patterns
#10
Luis M Soares, P Cody He, Yujin Chun, Hyunsuk Suh, TaeSoo Kim, Stephen Buratowski
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation "gradient" is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29128632/genome-wide-mapping-of-estrogen-receptor-%C3%AE-binding-sites-by-chip-seq-to-identify-genes-related-to-sexual-maturity-in-hens
#11
Miao Guo, Yi Li, Yuxia Chen, Xiaoli Guo, Zhenjie Yuan, Yunliang Jiang
In ovarian follicle development, estrogen acts as a regulatory molecule to mediate proliferation and differentiation of follicular cells. ERα (estrogen receptor α) exerts regulatory function classically by binding directly to the estrogen response element, recruiting co-factors and activating or repressing transcription in response to E2. In this study, we used ChIP-seq to map ERα-binding sites in ovaries of Hy-line Brown commercial hens at 45d, 90d and 160d. In total, 24,886, 21,680 and 23,348 binding sites were identified in the ovaries of hens at 45d, 90d and 160d, which are linked to 86, 83 and 74 genes, respectively...
November 8, 2017: Gene
https://www.readbyqxmd.com/read/29126285/remap-2018-an-updated-atlas-of-regulatory-regions-from-an-integrative-analysis-of-dna-binding-chip-seq-experiments
#12
Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoit Ballester
With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126155/isl1-mediates-mesenchymal-expansion-in-the-developing-external-genitalia-via-regulation-of-bmp4-fgf10-and-wnt5a
#13
Saunders T Ching, Carlos R Infante, Wen Du, Amnon Sharir, Sungdae Park, Douglas B Menke, Ophir D Klein
Genital malformations are among the most common human birth defects, and both genetic and environmental factors can contribute to these malformations. Development of the external genitalia in mammals relies on complex signaling networks, and disruption of these signaling pathways can lead to genital defects. Islet-1 (ISL1), a member of the LIM/Homeobox family of transcription factors, has been identified as a major susceptibility gene for classic bladder exstrophy in humans, a common form of the bladder exstrophy-epispadias complex (BEEC), and is implicated in a role in urinary tract development...
November 8, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29126153/an-empirical-bayes-test-for-allelic-imbalance-detection-in-chip-seq
#14
Qi Zhang, Sündüz Keles
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has enabled discovery of genomic regions enriched with biological signals such as transcription factor binding and histone modifications. Allelic-imbalance (ALI) detection is a complementary analysis of ChIP-seq data for associating biological signals with single nucleotide polymorphisms (SNPs). It has been successfully used in elucidating functional roles of non-coding SNPs. Commonly used statistical approaches for ALI detection are often based on binomial testing and mixture models, both of which rely on strong assumptions on the distribution of the unobserved allelic probability, and have significant practical shortcomings...
November 3, 2017: Biostatistics
https://www.readbyqxmd.com/read/29121271/genome-wide-identification-of-arabidopsis-lbd29-target-genes-reveals-the-molecular-events-behind-auxin-induced-cell-reprograming-during-callus-formation
#15
Chongyi Xu, Huifen Cao, Enjun Xu, Shiqi Zhang, Yuxin Hu
Auxin-induced callus formation represents an important cell reprograming process during in vitro regeneration of plants, in which the pericycle or pericycle-like cells within plant organs are reprogramed into the pluripotent cell mass termed callus that is generally required for subsequent regeneration of root or shoot. However, the molecular events behind cell reprograming during auxin-induced callus formation are largely elusive. We previously identified that auxin-induced LBD transcription factors act as the master regulators to trigger auxin-induced callus formation...
November 7, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29116820/gsmc-combining-parallel-gibbs-sampling-with-maximal-cliques-for-hunting-dna-motif
#16
Chao Pei, Shu-Lin Wang, Jianwen Fang, Wei Zhang
Regulatory elements are responsible for regulating gene transcription. Therefore, identification of these elements is a tremendous challenge in the field of gene expression. Transcription factors (TFs) play a key role in gene regulation by binding to target promoter sequences. A set of conserved sequence patterns with a highly similar structure that is bound by a TF is called a motif. Motif discovery has been a difficult problem over the past decades. Meanwhile, it is a foundation stone in meeting this challenge...
November 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29115924/transcription-factor-e2f1-promotes-emt-by-regulating-zeb2-in-small-cell-lung-cancer
#17
Tingting Wang, Xufang Chen, Weiwei Qiao, Lijun Kong, Daqing Sun, Zunling Li
BACKGROUND: Epithelial-mesenchymal transition (EMT) is an early event in tumour invasion and metastasis, and widespread and distant metastasis at early stages is the typical biological behaviour in small cell lung cancer (SCLC). Our previous reports showed that high expression of the transcription factor E2F1 was involved in the invasion and metastasis of SCLC, but the role of E2F1 in the process of EMT in SCLC is unknown. METHODS: Immunohistochemistry was performed to evaluate the expressions of EMT related markers...
November 7, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29114022/hupb-is-a-bacterial-nucleoid-associated-protein-with-an-indispensable-eukaryotic-like-tail
#18
Joanna Hołówka, Damian Trojanowski, Katarzyna Ginda, Bartosz Wojtaś, Bartłomiej Gielniewski, Dagmara Jakimowicz, Jolanta Zakrzewska-Czerwińska
In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29114019/native-elongating-transcript-sequencing-reveals-global-anti-correlation-between-sense-and-antisense-nascent-transcription-in-fission-yeast
#19
Maxime Wery, Camille Gautier, Marc Descrimes, Mayuko Yoda, Hervé Vennin-Rendos, Valérie Migeot, Daniel Gautheret, Damien Hermand, Antonin Morillon
Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site...
November 7, 2017: RNA
https://www.readbyqxmd.com/read/29101361/high-intensity-uv-laser-chip-seq-for-the-study-of-protein-dna-interactions-in-living-cells
#20
Arndt Steube, Tino Schenk, Alexander Tretyakov, Hans Peter Saluz
Genome-wide mapping of transcription factor binding is generally performed by chemical protein-DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein-DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces an efficient and instant formation of covalent "zero-length" crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a "snapshot" of direct protein-DNA interactions in their natural environment...
November 3, 2017: Nature Communications
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