keyword
MENU ▼
Read by QxMD icon Read
search

Histone code

keyword
https://www.readbyqxmd.com/read/28918100/transcriptomic-and-epigenomic-biomarkers-of-antidepressant-response
#1
REVIEW
Raoul Belzeaux, Rixing Lin, Chelsey Ju, Marc-Aurele Chay, Laura M Fiori, Pierre-Eric Lutz, Gustavo Turecki
BACKGROUND: Antidepressant treatment is associated with a high rate of poor response, and thus, biomarker development is warranted. METHODS: We aimed to synthesize studies investigating gene expression, small RNAs, and epigenomic biomarkers of antidepressant response. We conducted a narrative review of the literature. RESULTS: Firstly, we detailed the challenges involved, in terms of biological tissues, relevant study time frames, and mandatory statistical tools...
September 8, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28912063/differential-expression-by-chromatin-modifications-of-alcohol-dehydrogenase-1-of-chorispora-bungeana-in-cold-stress
#2
Lijun Liu, Yuan Song, Jun Xu, Dongming Li, Gaopeng Li, Lizhe An
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28906248/transcription-of-a-5-extended-mrna-isoform-directs-dynamic-chromatin-changes-and-interference-of-a-downstream-promoter
#3
Minghao Chia, Amy Tresenrider, Jingxun Chen, Gianpiero Spedale, Victoria Jorgensen, Elçin Ünal, Folkert Jacobus van Werven
Cell differentiation programs require dynamic regulation of gene expression. During meiotic prophase in Saccharomyces cerevisiae, expression of the kinetochore complex subunit Ndc80 is downregulated by a 5' extended long undecoded NDC80 transcript isoform. Here we demonstrate a transcriptional interference mechanism that is responsible for inhibiting expression of the coding NDC80 mRNA isoform. Transcription from a distal NDC80 promoter directs Set1-dependent histone H3K4 dimethylation and Set2-dependent H3K36 trimethylation to establish a repressive chromatin state in the downstream canonical NDC80 promoter...
September 14, 2017: ELife
https://www.readbyqxmd.com/read/28904641/histone-code-and-long-non-coding-rnas-lncrnas-aberrations-in-lung-cancer-implications-in-the-therapy-response
#4
REVIEW
Abril Marcela Herrera-Solorio, Leonel Armas-López, Oscar Arrieta, Joaquín Zúñiga, Patricia Piña-Sánchez, Federico Ávila-Moreno
Respiratory diseases hold several genome, epigenome, and transcriptional aberrations as a cause of the accumulated damage promoted by, among others, environmental risk factors. Such aberrations can also come about as an adaptive response when faced with therapeutic oncological drugs. In epigenetic terms, aberrations in DNA methylation patterns, histone code marks balance, and/or chromatin-remodeling complexes recruitment, among Polycomb Repressive Complex-2 (PRC2) versus Trithorax (TRX) Activator Complex, have been proposed to be affected by several previously characterized functional long non-coding RNAs (lncRNAs)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28899740/histone-3-3-mutations-in-giant-cell-tumor-and-giant-cell-rich-sarcomas-of-bone
#5
Alberto Righi, Irene Mancini, Marco Gambarotti, Piero Picci, Gabriella Gamberi, Cristina Marraccini, Angelo Paolo Dei Tos, Lisa Simi, Pamela Pinzani, Alessandro Franchi
Mutually exclusive histone 3.3 gene mutations have been recognized in chondroblastoma and giant cell tumor of bone (GCTB), which may be useful for differential diagnostic purposes in morphologically ambiguous cases. While over 90% of GCTB presents histone 3.3 variants exclusively in the H3F3A gene, chondroblastoma is mutated mainly in H3F3B. In this study we examined a series of giant cell rich primary bone tumors, aiming to evaluate the possible diagnostic role of histone 3.3 mutations in the differential diagnosis between GCTB and giant cell rich sarcomas...
September 9, 2017: Human Pathology
https://www.readbyqxmd.com/read/28899360/biological-networks-in-parkinson-s-disease-an-insight-into-the-epigenetic-mechanisms-associated-with-this-disease
#6
Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
BACKGROUND: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT: We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28893800/vhl-deficiency-drives-enhancer-activation-of-oncogenes-in-clear-cell-renal-cell-carcinoma
#7
Xiaosai Yao, Jing Tan, Kevin Junliang Lim, Joanna Koh, Wen Fong Ooi, Zhimei Li, Dachuan Huang, Manjie Xing, Yang Sun Chan, James Zhengzhong Qu, Su Ting Tay, Giovani Wijaya, Yue Ning Lam, Jing Han Hong, Ai Ping Lee-Lim, Peiyong Guan, Michelle Shu Wen Ng, Cassandra Zhengxuan He, Joyce Suling Lin, Tannistha Nandi, Aditi Qamra, Chang Xu, Swe Swe Myint, James O J Davies, Jian Yuan Goh, Gary Loh, Bryan C Tan, Steven G Rozen, Qiang Yu, Iain Bee Huat Tan, Christopher Wai Sam Cheng, Shang Li, Kenneth Tou En Chang, Puay Hoon Tan, David Lawrence Silver, Alexander Lezhava, Gertrud Steger, Jim R Hughes, Bin Tean Teh, Patrick Tan
Protein-coding mutations in clear cell renal cell carcinoma (ccRCC) have been extensively characterized, frequently involving inactivation of the von Hippel Lindau (VHL) tumor suppressor. Roles for non-coding cis-regulatory aberrations in ccRCC tumorigenesis, however, remain unclear. Analyzing 10 primary tumor/normal pairs and 9 cell lines across 79 chromatin profiles, we observed pervasive enhancer malfunction in ccRCC, with cognate enhancer-target genes associated with tissue-specific aspects of malignancy...
September 11, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28891741/erna-binding-produces-tailored-cbp-activity-profiles-to-regulate-gene-expression
#8
Daniel A Bose, Shelley L Berger
Enhancers are cis- regulatory genetic elements crucial for controlling temporal and cell-type specific patterns of gene expression. Active enhancers generate bi-directional non-coding RNA transcripts called enhancer RNAs (eRNAs). eRNAs are important for stimulating gene expression, but precise mechanisms for this ability remain unclear. Here we highlight recent findings that demonstrate a direct interaction between RNAs and the transcriptional co-activator Creb-binding protein (CBP). Notably, RNA binding could stimulate the core histone acetyltransferase activity of the enzyme, observable in cells as a link between eRNA production, CBP-dependent histone acetylation and expression of genes regulated by specific enhancers...
September 11, 2017: RNA Biology
https://www.readbyqxmd.com/read/28889823/epigenetics-and-dohad-from-basics-to-birth-and-beyond
#9
T Bianco-Miotto, J M Craig, Y P Gasser, S J van Dijk, S E Ozanne
Developmental origins of health and disease (DOHaD) is the study of how the early life environment can impact the risk of chronic diseases from childhood to adulthood and the mechanisms involved. Epigenetic modifications such as DNA methylation, histone modifications and non-coding RNAs are involved in mediating how early life environment impacts later health. This review is a summary of the Epigenetics and DOHaD workshop held at the 2016 DOHaD Society of Australia and New Zealand Conference. Our extensive knowledge of how the early life environment impacts later risk for chronic disease would not have been possible without animal models...
September 11, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28886306/lncrna-h19-contributes-to-rh2-mediated-mc3t3-e1cell-proliferation-by-regulation-of-osteopontin
#10
B Dong, T-T Pang
20(R)-ginsenoside Rh2 (Rh2) is one of the most active components of red ginseng, possessing the beneficial effects in cancer prevention and metabolic diseases. However, the detailed mechanisms that contribute to Rh2-mediated bone formation remain largely unknown. In this study, we assessed the expression of 17 long non-coding RNAs (lncRNAs) in cultured MC3T3-E1 cells under Rh2 treatments. We found that lncRNA H19 was significantly increased in Rh2-treated MC3T3-E1 cells. Expression of lncRNA H19 was promoted in a dose- and time-dependent manner after Rh2 treatments...
August 30, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28882223/micrornas-and-epigenetics
#11
Catia Moutinho, Manel Esteller
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression mainly at the posttranscriptional level. Similar to protein-coding genes, their expression is also controlled by genetic and epigenetic mechanisms. Disruption of these control processes leads to abnormal expression of miRNAs in cancer. In this chapter, we discuss the supportive links between miRNAs and epigenetics in the context of carcinogenesis. miRNAs can be epigenetically regulated by DNA methylation and/or specific histone modifications...
2017: Advances in Cancer Research
https://www.readbyqxmd.com/read/28881702/the-epigenetic-integrator-uhrf1-on-the-road-to-become-a-universal-biomarker-for-cancer
#12
REVIEW
Waseem Ashraf, Abdulkhaleg Ibrahim, Mahmoud Alhosin, Liliyana Zaayter, Khalid Ouararhni, Christophe Papin, Tanveer Ahmad, Ali Hamiche, Yves Mély, Christian Bronner, Marc Mousli
Cancer is one of the deadliest diseases in the world causing record number of mortalities in both developed and undeveloped countries. Despite a lot of advances and breakthroughs in the field of oncology still, it is very hard to diagnose and treat the cancers at early stages. Here in this review we analyze the potential of Ubiquitin-like containing PHD and Ring Finger domain 1 (UHRF1) as a universal biomarker for cancers. UHRF1 is an important epigenetic regulator maintaining DNA methylation and histone code in the cell...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28881218/downregulated-expression-of-mir-223-promotes-toll-like-receptor-activated-inflammatory-responses-in-macrophages-by-targeting-rhob
#13
Ningjie Zhang, Liyao Fu, Yanhong Bu, Yao Yao, Yongjun Wang
Toll-like receptors (TLRs) induced-inflammatory response must be tightly regulated to avoid impairment in host itself. Numerous factors have been identified in regulation of TLR-triggered inflammatory response. Among these, microRNAs (miRNAs) are small non-coding RNA molecules which have got much attention. MiR-223, which highly expresses in myeloid cells of the bone marrow, has reported to participate in kinds of inflammatory responses by targeting inflammasome sensor-NLRP3 to repress production of IL-6 and IL-1β, and thus attenuate inflammatory response...
September 4, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28880717/bivalent-histone-codes-on-wnt5a-during-odontogenic-differentiation
#14
Y Zhou, L Zheng, F Li, M Wan, Y Fan, X Zhou, W Du, C Pi, D Cui, B Zhang, J Sun, X Zhou
Lineage-committed differentiation is an essential biological program during odontogenesis, which is tightly regulated by lineage-specific genes. Some of these genes are modified by colocalization of H3K4me3 and H3K27me3 marks at promoter regions in progenitors. These modifications, named "bivalent domains," maintain genes in a poised state and then resolve for later activation or repression during differentiation. Wnt5a has been reported to promote odontogenic differentiation in dental mesenchyme. However, relatively little is known about the epigenetic modulations on Wnt5a activation during tooth development...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28874875/the-role-of-histone-modification-and-a-regulatory-single-nucleotide-polymorphism-rs2071166-in-the-cx43-promoter-in-patients-with-tof
#15
Ruoyi Gu, Jun Xu, Yixiang Lin, Wei Sheng, Duan Ma, Xiaojing Ma, Guoying Huang
Abnormal level of Cx43 expression could result in CHD. Epigenetic modification and disease-associated, non-coding SNPs might influence gene transcription and expression. Our study aimed to determine the role of histone modification and an rSNP (rs2071166) in the Cx43 promoter in patients with TOF. Our results indicate that H3K18ac bind to Cx43 promoter and that their levels are reduced in TOF patients relative to controls. The relationship between the non-coding SNP in the Cx43 gene and TOF patients was evaluated in 158 patients and 300 controls...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28874519/a-histone-code-reader-and-a-transcriptional-activator-interact-to-regulate-genes-for-salt-tolerance
#16
Wei Wei, Jian-Jun Tao, Hao-Wei Chen, Qing-Tian Li, Wan-Ke Zhang, Biao Ma, Qing Lin, Jin-Song Zhang, Shou-Yi Chen
Plant homeodomain (PHD) finger proteins are involved in various developmental processes and stress responses. They recognize and bind to epigenetically modified histone H3 'tail' and function as 'histone code readers'. Here we report that GmPHD6 reads low methylated histone H3K4me0/1/2 but not H3K4me3 with its N-terminal domain instead of the PHD finger. GmPHD6 does not possess transcriptional regulatory ability but has DNA-binding ability. Through the PHD finger, GmPHD6 interacts with its co-activator, LHP1-1/2 to form a transcriptional activation complex...
September 5, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28872116/chromatin-immunoprecipitation-chip-protocol-for-low-abundance-embryonic-samples
#17
Rizwan Rehimi, Michaela Bartusel, Francesca Solinas, Janine Altmüller, Alvaro Rada-Iglesias
Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies...
August 29, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28864990/exploitation-of-non-mammalian-model-organisms-in-epigenetic-research
#18
William V Holt
Model organisms are widely used in research that is ultimately aimed at understanding the causes and consequences of human disease. It may seem counterintuitive to expect clinically useful information to be obtained from species as diverse as fishes and insects, but because fundamental biological mechanisms share evolutionary origins they transcend species barriers. Epigenetic mechanisms fulfil this expectation admirably as more and more is discovered about the basic operational rules of inheritance, which are much more elaborate than formerly thought...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28856239/histone-hypervariants-h2a-z-1-and-h2a-z-2-play-independent-and-context-specific-roles-in-neuronal-activity-induced-transcription-of-arc-arg3-1-and-other-immediate-early-genes
#19
Carissa J Dunn, Pushpita Sarkar, Emma R Bailey, Shannon Farris, Meilan Zhao, James M Ward, Serena M Dudek, Ramendra N Saha
The histone variant H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the transcriptional process remains perplexing. In vertebrates, H2A.Z has two hypervariants, H2A.Z.1 and H2A.Z.2, that have almost identical sequences except for three amino acid residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated rat cortical neurons, we asked if H2A...
July 2017: ENeuro
https://www.readbyqxmd.com/read/28855099/epigenetics-in-chronic-liver-disease
#20
REVIEW
Marie Boyle, Jelena Mann
Elucidation of the fundamental epigenetic mechanisms governing gene expression and cellular phenotype in the past decade has provided novel insights into the epigenetic modulation of chronic liver disease. While genetic factors are undoubtedly important, the opportunity afforded by exploitation of the "fine-tuning" epigenetic mechanisms promises to drive forward an unprecedented advance in precision medicine within hepatology. The current challenges remain to improve diagnostics, prognostics and develop personalised therapy...
August 27, 2017: Journal of Hepatology
keyword
keyword
6315
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"