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Chromatin states
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The liver X receptors (LXRs, NR1H2 and NR1H3) and peroxisome proliferator-activated receptor gamma (PPARG, NR1C3) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis. Intriguingly, recent studies suggest that these metabolic regulators also impact tumor cell proliferation.
16p
vioraclene
31-03-2024
5
2
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Ebook "Male infertility: Contemporary clinical approaches, andrology, ART & antioxidants" offers a comprehensive review of well-established, current diagnostic and treatment techniques for male infertility. This state-of-the-art, evidence-based resource incorporates new multidisciplinary and complementary medicine approaches to create a first-of-its-kind guide to treatment strategies involving antioxidants for male infertility.
511p
cotieubac1004
15-03-2024
7
0
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CTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains. Complete removal of CTCF from mammalian cells causes catastrophic genome dysregulation, likely due to widespread collapse of 3D chromatin looping and alterations to inter- and intra-TAD interactions within the nucleus.
17p
vigalileogalilei
27-02-2022
13
1
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Prediction of cell type-specific, in vivo transcription factor binding sites is one of the central challenges in regulatory genomics. Here, we present our approach that earned a shared first rank in the “ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge” in 2017. In post-challenge analyses, we benchmark the influence of different feature sets and find that chromatin accessibility and binding motifs are sufficient to yield state-of-the-art performance.
17p
vigalileogalilei
27-02-2022
19
1
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The mutational processes underlying non-coding cancer mutations and their biological significance in tumor evolution are poorly understood. To get better insights into the biological mechanisms of mutational processes in breast cancer, we integrate whole-genome level somatic mutations from breast cancer patients with chromatin states and transcription factor binding events.
15p
vigalileogalilei
27-02-2022
24
2
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Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phenotypic diversity beyond changes to nucleotide sequence. Previous research has looked at the rate at which spontaneous epialleles arise but it is currently unknown how they are maintained across generations.
16p
vialfrednobel
29-01-2022
11
0
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Genetic influence on DNA methylation is potentially an important mechanism affecting individual differences in humans. We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects.
16p
viaristotle
29-01-2022
10
0
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Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression.
18p
viaristotle
29-01-2022
13
0
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A recent super-resolution imaging study by Boettiger et al. elegantly demonstrates that three epigenetically defined, and functionally disparate, chromatin states have distinct folding characteristics in Drosophila nuclei.
3p
viaristotle
29-01-2022
8
1
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Embryonic stem cells are intrinsically unstable and differentiate spontaneously if they are not shielded from external stimuli. Although the nature of such instability is still controversial, growing evidence suggests that protein translation control may play a crucial role.
22p
viaristotle
29-01-2022
6
0
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We are entering an era of epigenome engineering. The precision manipulation of chromatin and epigenetic modifications provides new ways to interrogate their influence on genome and cell function and to harness these changes for applications. We review the design and state of epigenome editing tools, highlighting the unique regulatory properties afforded by these systems.
17p
viaristotle
29-01-2022
17
0
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Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of promoter G4s, transcription and chromatin state.
14p
viarchimedes
26-01-2022
10
0
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An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed.
44p
viarchimedes
26-01-2022
10
1
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Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging.
36p
viarchimedes
26-01-2022
8
0
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Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome.
30p
viarchimedes
26-01-2022
42
0
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Chromatin state provides a clear decipherable blueprint for maintenance of transcriptional patterns, exemplifying a mitotically stable form of cellular programming in dividing cells. In this regard, genomic studies of chromatin states within cancerous tissues have the potential to uncover novel aspects of tumor biology and unique mechanisms associated with disease phenotypes and outcomes.
15p
vielonmusk
21-01-2022
10
0
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Using chemicals known as inhibitors of chromatin remodeling enzymes is a useful approach in understanding the regulation machinery that contributes to the maintenance of or conversion to a pluri- and totipotent states of the cells in multicellular organisms. They can serve as tools to reveal the molecular and cellular mechanisms required for reprogramming. A deeper understanding of reprogramming pathways that drive the cell into a dedifferentiated state might help us enhance plant micropropagation and green biotechnology applications.
9p
tudichquannguyet
29-11-2021
10
1
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The role of histone modifications in the DNA damage response has been extensively studied in nonplant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response.
15p
vilarryellison
29-10-2021
10
2
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Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings.
12p
vibeauty
23-10-2021
13
0
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To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells.
11p
vibeauty
23-10-2021
13
0
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