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https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#1
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28627735/genetic-alterations-in-adult-t-cell-leukemia-lymphoma
#2
REVIEW
Yasunori Kogure, Keisuke Kataoka
Adult T-cell leukemia/lymphoma (ATL) is a peripheral T-cell neoplasm with a dismal prognosis, caused by human T-cell leukemia virus type-1 (HTLV-1) retrovirus. A long latency period from HTLV-1 infection to ATL onset suggests that not only HTLV-1 proteins, such as Tax and HBZ, but also additional genetic and/or epigenetic events are required for ATL development. Although many studies have demonstrated the biological functions of viral genes, alterations of cellular genes associated with ATL have not been fully investigated...
June 19, 2017: Cancer Science
https://www.readbyqxmd.com/read/28624690/toward-a-genetic-tool-development-pipeline-for-host-associated-bacteria
#3
REVIEW
Matthew C Waller, Josef R Bober, Nikhil U Nair, Chase L Beisel
Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host's health, behavior, and development, yet the causative mediators of host-microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host...
June 15, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28623094/structural-and-functional-relationships-of-fan1
#4
REVIEW
Hyeonseok Jin, Yunje Cho
FANCD2/FANCI-associated nuclease (FAN1) is a 5' flap structure-specific endonuclease and 5' to 3' exonuclease. This nuclease can resolve interstrand cross-links (ICLs) independently of the Fanconi anemia (FA) pathway and controls the progression of stalled replication forks in an FA-dependent manner, thereby maintaining chromosomal stability. Several FAN1 mutations are observed in various cancers and degenerative diseases. Recently, several crystal structures of the FAN1-DNA complexes have been reported, and to date, these represent the only structures for a DNA bound ICL-repair nuclease...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28621802/glypican-3-a-promising-biomarker-for-hepatocellular-carcinoma-diagnosis-and-treatment
#5
REVIEW
Fubo Zhou, Wenting Shang, Xiaoling Yu, Jie Tian
Liver cancer is the second leading cause of cancer-related deaths, and hepatocellular carcinoma (HCC) is the most common type. Therefore, molecular targets are urgently required for the early detection of HCC and the development of novel therapeutic approaches. Glypican-3 (GPC3), an oncofetal proteoglycan anchored to the cell membrane, is normally detected in the fetal liver but not in the healthy adult liver. However, in HCC patients, GPC3 is overexpressed at both the gene and protein levels, and its expression predicts a poor prognosis...
June 16, 2017: Medicinal Research Reviews
https://www.readbyqxmd.com/read/28620358/the-transcriptional-regulators-of-the-crp-family-regulate-different-essential-bacterial-functions-and-can-be-inherited-vertically-and-horizontally
#6
REVIEW
Gloria Soberón-Chávez, Luis D Alcaraz, Estefanía Morales, Gabriel Y Ponce-Soto, Luis Servín-González
One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3'-5'-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28616799/dolichol-phosphate-mannose-synthase-a-glycosyltransferase-with-unity-in-molecular-diversities
#7
REVIEW
Dipak K Banerjee, Zhenbo Zhang, Krishna Baksi, Jesús E Serrano-Negrón
N-glycans provide structural and functional stability to asparagine-linked (N-linked) glycoproteins, and add flexibility. Glycan biosynthesis is elaborative, multi-compartmental and involves many glycosyltransferases. Failure to assemble N-glycans leads to phenotypic changes developing infection, cancer, congenital disorders of glycosylation (CDGs) among others. Biosynthesis of N-glycans begins at the endoplasmic reticulum (ER) with the assembly of dolichol-linked tetra-decasaccharide (Glc3Man9GlcNAc2-PP-Dol) where dolichol phosphate mannose synthase (DPMS) plays a central role...
June 14, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28611593/autophagy-and-its-impact-on-neurodegenerative-diseases-new-roles-for-tdp-43-and-c9orf72
#8
REVIEW
Mauricio Budini, Emanuele Buratti, Eugenia Morselli, Alfredo Criollo
Autophagy is a catabolic mechanism where intracellular material is degraded by vesicular structures called autophagolysosomes. Autophagy is necessary to maintain the normal function of the central nervous system (CNS), avoiding the accumulation of misfolded and aggregated proteins. Consistently, impaired autophagy has been associated with the pathogenesis of various neurodegenerative diseases. The proteins TAR DNA-binding protein-43 (TDP-43), which regulates RNA processing at different levels, and chromosome 9 open reading frame 72 (C9orf72), probably involved in membrane trafficking, are crucial in the development of neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD)...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28610839/fly-fishing-for-histones-catch-and-release-by-histone-chaperone-intrinsically-disordered-regions-and-acidic-stretches
#9
REVIEW
Christopher Warren, David Shechter
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly two-meter long human genome into a roughly ten-micron diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly, and thus the fluidity of the ever-changing chromatin landscape...
June 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28608630/precisely-tailored-dna-nanostructures-and-their-theranostic-applications
#10
REVIEW
Bing Zhu, Lihua Wang, Jiang Li, Chunhai Fan
A critical challenge in nanotechnology is the limited precision and controllability of the structural parameters, which brings about concerns in uniformity, reproducibility and performance. Self-assembled DNA nanostructures, as a newly emerged type of nano-biomaterials, possess low-nanometer precision, excellent programmability and addressability. They can precisely arrange various molecules and materials to form spatially ordered complex, resulting in unambiguous physical or chemical properties. Because of these, DNA nanostructures have shown great promise in numerous biomedical theranostic applications...
June 13, 2017: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/28608608/multiple-functions-of-long-non-coding-rnas-in-oxidative-stress-dna-damage-response-and-cancer-progression
#11
Sadra Samavarchi Tehrani, Ansar Karimian, Hadi Parsian, Maryam Majidinia, Bahman Yousefi
In addition to aberrant alternation of transcriptome, it is now suggested that dysregulation of the non-coding transcripts, particularly long non-coding RNAs (lncRNAs), which comprise the majority of the genome, is contributed to cancer initiation and progression. As the result of recent huge efforts, the possible roles of numerous lncRNAs in the human cancers were characterized, as well as various strategies with inhibitory effects to target these transcripts on the transformed cells. Moreover, DNA damage response (DDR) pathway is a complex regulatory network responsible for the identification of disruptions in DNA structure, integrity and stability- it is reported to be associated with the up-regulation and down-regulation of lncRNAs...
June 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28607505/predictive-genetic-markers-in-neoadjuvant-chemoradiotherapy-for-locally-advanced-esophageal-cancer-a-long-way-to-go-review-of-the-literature
#12
REVIEW
M Gusella, E Pezzolo, Y Modena, C Barile, D Menon, G Crepaldi, F La Russa, A P Fraccon, F Pasini
The role of genetic molecular markers in neoadjuvant treatment for locally advanced esophageal cancer has been reviewed, focusing strictly on concurrent chemoradiation protocols followed by surgery. Eleven studies evaluated the role of mRNA expression profile; the end point was overall survival (OS) in two studies and different definitions of histological response in nine. Genes reported as significant were involved in cell cycle control (30), apoptosis (7), structural molecules (9), cell metabolism (6) and DNA repair (1)...
June 13, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28605177/dna-origami-scaffolds-for-creating-higher-order-structures
#13
Fan Hong, Fei Zhang, Yan Liu, Hao Yan
DNA has become one of the most extensively used molecular building blocks for engineering self-assembling materials. DNA origami is a technique that uses hundreds of short DNA oligonucleotides, called staple strands, to fold a long single-stranded DNA, which is called a scaffold strand, into various designer nanoscale architectures. DNA origami has dramatically improved the complexity and scalability of DNA nanostructures. Due to its high degree of customization and spatial addressability, DNA origami provides a versatile platform with which to engineer nanoscale structures and devices that can sense, compute, and actuate...
June 12, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28604947/-application-of-snp-array-technology-in-the-genetic-analysis-of-pediatric-patients-with-growth-retardation
#14
Shiyu Luo, Chunyun Fu, Shujie Zhang, Jin Wang, Xin Fan, Jingsi Luo, Rongyu Chen, Xuyun Hu, Haisong Qin, Chuan Li, Shan Ou, Qifei Li, Shaoke Chen
OBJECTIVE: To explore the value of single nucleotide polymorphism array (SNP-array) for the analysis of pediatric patients with growth retardation. METHODS: One hundred eighty one children with growth retardation were enrolled. DNA was extracted from peripheral samples from the patients, and whole genome copy number variations (CNVs) were detected using Illumina Human Cyto SNP-12. All identified CNVs were further analyzed with reference to databases including ClinGen, ClinVar, DECIPHER, OMIM and DGV as well as comprehensive review of literature from PubMed to determine their pathogenicity...
June 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28601075/mesoporous-silica-nanoparticles-as-a-carrier-platform-for-intracellular-delivery-of-nucleic-acids
#15
REVIEW
N A Keasberry, C W Yapp, A Idris
Virus-mediated gene delivery has been, to date, the most successful and efficient method for gene therapy. However, this method has been challenged because of serious safety concerns. Over the past decade, mesoporous silica nanoparticles (MSNs) have attracted much attention for intracellular delivery of nucleic acids. Delivery of cellular plasmid DNA (pDNA) is designed to replace the function of a defective gene and restore its normal function in the cell. Delivery of small interfering RNAs (siRNAs) can selectively knockdown genes by targeting specific mRNAs...
June 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28600336/diagnosis-and-classification-of-hematologic-malignancies-on-the-basis-of-genetics
#16
Justin Taylor, Wenbin Xiao, Omar Abdel-Wahab
Genomic analysis has greatly influenced the diagnosis and clinical management of patients affected by diverse forms of hematologic malignancies. Here we review how genetic alterations define subclasses of patients with acute leukemias, myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPNs), non-Hodgkin lymphomas and classical Hodgkin lymphoma. These include new subtypes of acute myeloid leukemia defined by mutations in RUNX1 or BCR-ABL1 translocations as well as a constellation of somatic structural DNA alterations in acute lymphoblastic leukemia...
June 9, 2017: Blood
https://www.readbyqxmd.com/read/28600135/human-dna-cytosine-5-methyltransferases-a-functional-and-structural-perspective-for-epigenetic-cancer-therapy
#17
REVIEW
Grégoire Rondelet, Johan Wouters
Epigenetic modifications modulate chromatin states to regulate gene expression. Among them, DNA methylation and histone modifications play a crucial role in the establishment of the epigenome. In cancer, these epigenetic events may act in concert to repress tumor suppressor genes or promote transcription of oncogenes and genes up-regulated by oncoproteins. In the context of cancer initiation and progression, recruitment of DNA (cytosine-5)-methyltransferases to specific genomic regions is mainly mediated by histone epigenetic marks, transcription factors and co-regulators as part of a dynamic process...
June 6, 2017: Biochimie
https://www.readbyqxmd.com/read/28598605/metal-sensing-by-dna
#18
Wenhu Zhou, Runjhun Saran, Juewen Liu
Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers...
June 9, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28596706/regulating-sting-in-health-and-disease
#19
REVIEW
Yang Li, Heather L Wilson, Endre Kiss-Toth
The presence of cytosolic double-stranded DNA molecules can trigger multiple innate immune signalling pathways which converge on the activation of an ER-resident innate immune adaptor named "STimulator of INterferon Genes (STING)". STING has been found to mediate type I interferon response downstream of cyclic dinucleotides and a number of DNA and RNA inducing signalling pathway. In addition to its physiological function, a rapidly increasing body of literature highlights the role for STING in human disease where variants of the STING proteins, as well as dysregulated STING signalling, have been implicated in a number of inflammatory diseases...
2017: Journal of Inflammation
https://www.readbyqxmd.com/read/28595554/sulphur-containing-amino-acids-protective-role-against-free-radicals-and-heavy-metals
#20
Mirjana B Čolović, Vesna M Vasić, Dragan M Djuric, Danijela Z Krstić
Sulphur is an abundant element in biological systems, which plays an important role in processes essential for life as a constituent of proteins, vitamins and other crucial biomolecules. The major source of sulphur for humans is plants being able to use inorganic sulphur in the purpose of sulphur-containing amino acids synthesis. Sulphur-containing amino acids include methionine, cysteine, homocysteine, and taurine. Among them, methionine and cysteine are classified as proteinogenic, canonic amino acids incorporated in proteins structure...
June 8, 2017: Current Medicinal Chemistry
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