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ChIP-Seq

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https://www.readbyqxmd.com/read/28334916/mocap-large-scale-inference-of-transcription-factor-binding-sites-from-chromatin-accessibility
#1
Xi Chen, Bowen Yu, Nicholas Carriero, Claudio Silva, Richard Bonneau
Differential binding of transcription factors (TFs) at cis-regulatory loci drives the differentiation and function of diverse cellular lineages. Understanding the regulatory interactions that underlie cell fate decisions requires characterizing TF binding sites (TFBS) across multiple cell types and conditions. Techniques, e.g. ChIP-Seq can reveal genome-wide patterns of TF binding, but typically requires laborious and costly experiments for each TF-cell-type (TFCT) condition of interest. Chromosomal accessibility assays can connect accessible chromatin in one cell type to many TFs through sequence motif mapping...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334833/chip-seq-analysis-of-the-luxr-type-regulator-vjbr-reveals-novel-insights-into-the-brucella-virulence-gene-expression-network
#2
Claudia L Kleinman, Gabriela Sycz, Hernán R Bonomi, Romina M Rodríguez, Angeles Zorreguieta, Rodrigo Sieira
LuxR-type transcription factors control diverse physiological functions necessary for bacterial adaptation to environmental changes. In the intracellular pathogen Brucella, the LuxR homolog VjbR has been shown to regulate the expression of virulence factors acting at early stages of the intracellular infection and, directly or indirectly, hundreds of additional genes. However, the precise determination of VjbR direct targets has so far proved elusive. Here, we performed chromatin immunoprecipitation of VjbR followed by next-generation sequencing (ChIP-seq)...
March 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334742/recognition-but-no-repair-of-abasic-site-in-single-stranded-dna-by-human-ribosomal-us3-protein-residing-within-intact-40s-subunit
#3
Anastasia S Grosheva, Dmitry O Zharkov, Joachim Stahl, Alexander V Gopanenko, Alexey E Tupikin, Marsel R Kabilov, Dmitri M Graifer, Galina G Karpova
Isolated human ribosomal protein uS3 has extra-ribosomal functions including those related to base excision DNA repair, e.g. AP lyase activity that nicks double-stranded (ds) DNA 3΄ to the abasic (AP) site. However, the ability of uS3 residing within ribosome to recognize and cleave damaged DNA has never been addressed. Here, we compare interactions of single-stranded (ss) DNA and dsDNA bearing AP site with human ribosome-bound uS3 and with the isolated protein, whose interactions with ssDNA were not yet studied...
January 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#4
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334224/computational-modeling-of-in-vivo-and-in-vitro-protein-dna-interactions-by-multiple-instance-learning
#5
Zhen Gao, Jianhua Ruan
Motivation: The study of transcriptional regulation is still difficult yet fundamental in molecular biology research. While the development of both in vivo and in vitro profiling techniques have significantly enhanced our knowledge of transcription factor (TF)-DNA interactions, computational models of TF-DNA interactions are relatively simple and may not reveal sufficient biological insight. In particular, supervised learning based models for TF-DNA interactions attempt to map sequence-level features ( k -mers) to binding event but usually ignore the location of k -mers, which can cause data fragmentation and consequently inferior model performance...
March 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327288/atrophin-controls-developmental-signaling-pathways-via-interactions-with-trithorax-like
#6
Kelvin Yeung, Ann Boija, Edvin Karlsson, Per-Henrik Holmqvist, Yonit Tsatskis, Ilaria Nisoli, Damian B Yap, Alireza Lorzadeh, Michelle Moksa, Martin Hirst, Samuel Aparicio, Manolis Fanto, Per Stenberg, Mattias Mannervik, Helen McNeill
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways...
March 22, 2017: ELife
https://www.readbyqxmd.com/read/28325764/the-vitamin-b12-dependent-photoreceptor-aerr-relieves-photosystem-gene-repression-by-extending-the-interaction-of-crtj-with-photosystem-promoters
#7
Mingxu Fang, Carl E Bauer
Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear...
March 21, 2017: MBio
https://www.readbyqxmd.com/read/28324065/neurod-factors-discriminate-mineralocorticoid-from-glucocorticoid-receptor-dna-binding-in-the-male-rat-brain
#8
Lisa T C M van Weert, Jacobus C Buurstede, Ahmed Mahfouz, Pamela S M Braakhuis, J Annelies E Polman, Hetty C M Sips, Benno Roozendaal, Judit Balog, E Ronald de Kloet, Nicole A Datson, Onno C Meijer
In the limbic brain, mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) both function as receptors for the naturally occurring glucocorticoids (corticosterone/cortisol), but mediate distinct effects on cellular physiology via transcriptional mechanisms. The transcriptional basis for specificity of these MR- versus GR-mediated effects is unknown. To address this conundrum we have identified the extent of MR/GR DNA binding selectivity in the rat hippocampus using chromatin immunoprecipitation followed by sequencing (ChIP-seq)...
January 24, 2017: Endocrinology
https://www.readbyqxmd.com/read/28315703/molecular-endocrinology-of-vitamin-d-on-the-epigenome-level
#9
REVIEW
Carsten Carlberg
The molecular endocrinology of vitamin D is based on the facts that i) its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) is the high affinity ligand of the nuclear receptor vitamin D receptor (VDR) and ii) the transcription factor VDR is the unique target of 1,25(OH)2D3 in the nucleus. Short-term alterations of the epigenome are primarily changes in the post-translational modification status of nucleosome-forming histone proteins, the consequences of which are i) a local increase or decrease in chromatin accessibility and ii) the activation or repression of gene transcription...
March 16, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28300060/h3-ubiquitination-by-nedd4-regulates-h3-acetylation-and-tumorigenesis
#10
Xian Zhang, Binkui Li, Abdol Hossein Rezaeian, Xiaohong Xu, Ping-Chieh Chou, Guoxiang Jin, Fei Han, Bo-Syong Pan, Chi-Yun Wang, Jie Long, Anmei Zhang, Chih-Yang Huang, Fuu-Jen Tsai, Chang-Hai Tsai, Christopher Logothetis, Hui-Kuan Lin
Dynamic changes in histone modifications under various physiological cues play important roles in gene transcription and cancer. Identification of new histone marks critical for cancer development is of particular importance. Here we show that, in a glucose-dependent manner, E3 ubiquitin ligase NEDD4 ubiquitinates histone H3 on lysine 23/36/37 residues, which specifically recruits histone acetyltransferase GCN5 for subsequent H3 acetylation. Genome-wide analysis of chromatin immunoprecipitation followed by sequencing reveals that NEDD4 regulates glucose-induced H3 K9 acetylation at transcription starting site and enhancer regions...
March 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28299657/runx1-eto-leukemia
#11
Shan Lin, James C Mulloy, Susumu Goyama
AML1-ETO leukemia is the most common cytogenetic subtype of acute myeloid leukemia, defined by the presence of t(8;21). Remarkable progress has been achieved in understanding the molecular pathogenesis of AML1-ETO leukemia. Proteomic surveies have shown that AML-ETO forms a stable complex with several transcription factors, including E proteins. Genome-wide transcriptome and ChIP-seq analyses have revealed the genes directly regulated by AML1-ETO, such as CEBPA. Several lines of evidence suggest that AML1-ETO suppresses endogenous DNA repair in cells to promote mutagenesis, which facilitates acquisition of cooperating secondary events...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28298643/mkl1-defines-the-h3k4me3-landscape-for-nf-%C3%AE%C2%BAb-dependent-inflammatory-response
#12
Liming Yu, Fei Fang, Xin Dai, Huihui Xu, Xiaohong Qi, Mingming Fang, Yong Xu
Macrophage-dependent inflammatory response is considered a pivotal biological process that contributes to a host of diseases when aberrantly activated. The underlying epigenetic mechanism is not completely understood. We report here that MKL1 was both sufficient and necessary for p65-dependent pro-inflammatory transcriptional program in immortalized macrophages, in primary human and mouse macrophages, and in an animal model of systemic inflammation (endotoxic shock). Extensive chromatin immunoprecipitation (ChIP) profiling and ChIP-seq analyses revealed that MKL1 deficiency erased key histone modifications synonymous with transactivation on p65 target promoters...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28295289/long-non-coding-rna-neat1-is-a-transcriptional-target-of-p53-and-modulates-p53-induced-transactivation-and-tumor-suppressor-function
#13
Masashi Idogawa, Tomoko Ohashi, Yasushi Sasaki, Hiroshi Nakase, Takashi Tokino
p53 is one of the most important tumor suppressor genes and the direct transcriptional targets of p53 must be explored to elucidate its functional mechanisms. Thus far, the p53 targets that have been primarily studied are protein-coding genes. Our previous study revealed that several long non-coding RNAs (lncRNAs) are direct transcriptional targets of p53, and knockdown of specific lncRNAs modulates p53-induced apoptosis. In this study, analysis of next-generation chromatin immunoprecipitation-sequencing (ChIP-seq) data for p53 revealed that the lncRNA NEAT1 is a direct transcriptional target of p53...
March 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28289232/transcriptional-landscape-of-the-human-cell-cycle
#14
Yin Liu, Sujun Chen, Su Wang, Fraser Soares, Martin Fischer, Feilong Meng, Zhou Du, Charles Lin, Clifford Meyer, James A DeCaprio, Myles Brown, X Shirley Liu, Housheng Hansen He
Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28288905/bioinformatic-approaches-to-interrogating-vitamin-d-receptor-signaling
#15
Moray J Campbell
Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity...
March 10, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28288683/chromatin-landscapes-and-genetic-risk-for-juvenile-idiopathic-arthritis
#16
Lisha Zhu, Kaiyu Jiang, Karstin Webber, Laiping Wong, Tao Liu, Yanmin Chen, James N Jarvis
BACKGROUND: The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci...
March 14, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28286326/genome-wide-analysis-of-chromatin-structures-in-trypanosoma-brucei-using-high-resolution-mnase-chip-seq
#17
Carolin Wedel, T Nicolai Siegel
Specific DNA-protein interactions are the basis for many important cellular mechanisms like the regulation of gene expression or replication. Knowledge about the precise genomic locations of DNA-protein interactions is important because it provides insight into the regulation of these processes. Recently, we have adapted an approach that combines micrococcal nuclease (MNase) digestion of chromatin with chromatin immunoprecipitation in Trypanosoma brucei. Here, we describe in detail how this method can be used to map the genome-wide distribution of nucleosomes or other DNA-binding proteins at high resolution in T...
March 9, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28286232/steroid-receptor-coactivator-1-can-regulate-osteoblastogenesis-independently-of-estrogen
#18
R J Watters, R J Hartmaier, H U Osmanbeyoglu, R M Gillihan, J Rae, L Liao, K Chen, W Li, X Lu, S Oesterreich
Steroid receptor coactivator-1 (SRC-1), a well-studied coactivator of estrogen receptor (ER), is known to play an important and functional role in the development and maintenance of bone tissue. Previous reports suggest SRC-1 maintains bone mineral density primarily through its interaction with ER. Here we demonstrate that SRC-1 can also affect bone development independent of estrogen signaling as ovariectomized SRC-1 knockout (SRC-1 KO) mouse had decreased bone mineral density. To identify estrogen-independent SRC-1 target genes in osteoblastogenesis, we undertook an integrated analysis utilizing ChIP-Seq and mRNA microarray in transformed osteoblast-like U2OS-ERα cells...
March 7, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28282965/hyper-and-hypo-nutrition-studies-of-the-hepatic-transcriptome-and-epigenome-suggest-that-ppar%C3%AE-regulates-anaerobic-glycolysis
#19
Anthony R Soltis, Shmulik Motola, Santiago Vernia, Christopher W Ng, Norman J Kennedy, Simona Dalin, Bryan J Matthews, Roger J Davis, Ernest Fraenkel
Diet plays a crucial role in shaping human health and disease. Diets promoting obesity and insulin resistance can lead to severe metabolic diseases, while calorie-restricted (CR) diets can improve health and extend lifespan. In this work, we fed mice either a chow diet (CD), a 16 week high-fat diet (HFD), or a CR diet to compare and contrast the effects of these diets on mouse liver biology. We collected transcriptomic and epigenomic datasets from these mice using RNA-Seq and DNase-Seq. We found that both CR and HFD induce extensive transcriptional changes, in some cases altering the same genes in the same direction...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28280365/downregulation-of-long-noncoding-rna-hotairm1-promotes-monocyte-dendritic-cell-differentiation-through-competitively-binding-to-endogenous-mir-3960
#20
Jiaxuan Xin, Jing Li, Yue Feng, Liyang Wang, Yuan Zhang, Rongcun Yang
Myeloid differentiation is controlled by a multilayered regulatory circuitry consisting of various elements, including histone modifications, transcription factors, and posttranscriptional regulators such as miRNAs, long noncoding RNAs, and circular RNAs. However, the molecular mechanism underlying this biological process remains unclear. In this study, through epigenetic profiling analysis using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq), we identified an lncRNA, HOTAIRM1, with a critical role in myeloid development...
2017: OncoTargets and Therapy
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