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Abstract Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) is a state-of-the-art technology to map the RNA interaction sites of an RNA-binding protein (RBP) across the transcriptome. Here, we present the new iCLIP2 protocol that allows to obtain high-quality iCLIP libraries in a fast and efficient manner. The new protocol comprises separate adapter ligations, two cDNA amplification steps and bead-based size selection. The full procedure can be completed within four...
#1Mowei Zhou (Environmental Molecular Sciences Laboratory)H-Index: 12
#2Neha Malhan (Environmental Molecular Sciences Laboratory)H-Index: 1
Last.Ljiljana Paša-Tolić (Environmental Molecular Sciences Laboratory)H-Index: 42
view all 14 authors...
Abstract Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. Herein, we present an analytical workflow to explore the changes in histone modifications through plant developmental stages and two drought stresses in two sorghum genotypes that differ in their response to drought. Top-down mass spectrometry (MS) is an ideal method to profile histone modifications and distinguish closely related histone proteoforms. We analyzed...
#1Joan M. Hevel (USU: Utah State University)H-Index: 17
#2Owen M. Price (USU: Utah State University)H-Index: 2
Abstract Protein arginine methylation is a widespread eukaryotic posttranslational modification that occurs to both histone and non-histone proteins. The S-adenosyl-L-methionine (AdoMet or SAM)-dependent modification is catalyzed by the protein arginine methyltransferase (PRMT) family of enzymes. In the last several years a series of both direct and indirect assay formats have been described that allow the rate of methylation to be measured. Here we provide a detailed protocol to directly measur...
#1Roberta Noberini (IEO: European Institute of Oncology)H-Index: 15
#2Camilla Restellini (IEO: European Institute of Oncology)H-Index: 1
Last.Tiziana Bonaldi (IEO: European Institute of Oncology)H-Index: 32
view all 4 authors...
Abstract Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more compreh...
#1Ruifeng Hu (University of Texas Health Science Center at Houston)H-Index: 1
#2Guangsheng Pei (University of Texas Health Science Center at Houston)H-Index: 2
Last.Zhen Zhen Zhao (VUMC: Vanderbilt University Medical Center)H-Index: 59
view all 4 authors...
Abstract The development of chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing (ChIP-seq) technologies has promoted generation of large-scale epigenomics data, providing us unprecedented opportunities to explore the landscape of epigenomic profiles at scales across both histone marks and tissue types. In addition to many tools directly for data analysis, advanced computational approaches, such as deep learning, have recently become promising to deeply mine the data struc...
#1Dan CapursoH-Index: 1
#2Zhonghui TangH-Index: 13
Last.Yijun Ruan (University of Connecticut Health Center)H-Index: 63
view all 3 authors...
Abstract The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review metho...
#1Jp Zambon (Wake Forest Institute for Regenerative Medicine)H-Index: 13
#2AtalaAnthony (Wake Forest Institute for Regenerative Medicine)H-Index: 104
Last.James J. Yoo (Wake Forest Institute for Regenerative Medicine)H-Index: 66
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Abstract The shortage of donor organs for transplantation remains a continued problem for patients with irreversible end-stage organ failure. Tissue engineering and regenerative medicine aims to develop therapies to provide viable solutions for these patients. Use of decellularized tissue scaffolds has emerged as an attractive approach to generate tissue constructs that mimic native tissue architecture and vascular networks. The process of decellularization which involves the removal of resident...
#2Shafaque ZahraH-Index: 2
Last.Shailesh KumarH-Index: 37
view all 3 authors...
Abstract Plants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to...
#1Wan Zhao (CAS: Chinese Academy of Sciences)H-Index: 4
#2Qiong Li (CAS: Chinese Academy of Sciences)H-Index: 1
Last.Feng Cui (CAS: Chinese Academy of Sciences)H-Index: 17
view all 3 authors...
Abstract During infection, RNA viruses can produce two types of virus-derived small RNAs (vsRNAs), small interfering RNA (siRNA) and microRNA (miRNA), that play a key role in RNA silencing-mediated antiviral mechanisms in various hosts by associating with different Argonaute (Ago) proteins. Ago1 has been widely identified as an essential part of the miRNA pathway, while Ago2 is required for the siRNA pathway. Thus, analysis of the interaction between vsRNAs and Ago proteins can provide a clue ab...
#1Hyejin Kim (SNU: Seoul National University)H-Index: 23
#2Dajeong Kim (SNU: Seoul National University)H-Index: 3
Last.Jong Bum Lee (SNU: Seoul National University)H-Index: 18
view all 6 authors...
Abstract Cells secrete extracellular vesicles (EVs) to external environments to achieve cellular homeostasis and cell-to-cell communication. Their therapeutic potential has been constantly spotlighted since they mirror both cytoplasmic and membranous components of parental cells. Meanwhile, growing evidence suggests that EV engineering could further promote EVs with a maximized capacity. In this review, a range of engineering techniques as well as upscaling approaches to exploit EVs and their mi...
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