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Transcriptional regulation

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https://www.readbyqxmd.com/read/29036829/microrna-221-targets-adam10-mrna-and-is-downregulated-in-alzheimer-s-disease
#1
Patricia R Manzine, Silvia Pelucchi, Maria A Horst, Francisco A C Vale, Sofia C I Pavarini, Matteo Audano, Nico Mitro, Monica Di Luca, Elena Marcello, Marcia R Cominetti
ADAM10 is the α-secretase that cleaves amyloid-β protein precursor in the non-amyloidogenic pathway in Alzheimer's disease (AD) and is known to be regulated by different microRNAs (miRNAs), which are post-transcriptional regulators related to several biological and pathological processes, including AD. Here we proposed to explore and validate miRNAs that have direct or indirect relations to the AD pathophysiology and ADAM10 gene. Approximately 700 miRNAs were analyzed and 21 differentially expressed miRNAs were validated in a sample of 21 AD subjects and 17 cognitively healthy matched controls...
October 7, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29036788/knockdown-of-lncrna-ccat2-inhibits-endometrial-cancer-cells-growth-and-metastasis-via-sponging-mir-216b
#2
Pengmu Xie, Hongying Cao, Ying Li, Jianhua Wang, Zhumei Cui
OBJECTIVE: Colon cancer-associated transcript 2 (CCAT2), a novel lncRNA has been reported as an oncogene in several cancers. This study was aimed to explore whether CCAT2 also exerted oncogenic roles in endometrial cancer cells. MATERIALS AND METHODS: The expression of CCAT2 in 30 pairs of endometrial cancer and matched non-cancerous tissues were detected by qRT-PCR. Two endometrial cancer cell lines HEC-1-A and RL95-2 were used throughout this study. CCAT2 in cells was silenced by transfection with shRNA targeted CCAT2, then cell growth and metastasis were assessed by performing trypan blue staining, Transwell assay, and flow cytometry...
September 29, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/29036702/a-hyperdynamic-h3-3-nucleosome-marks-promoter-regions-in-pluripotent-embryonic-stem-cells
#3
Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D Aguilera, Divya M Sivaraman, Tommy Kaplan, Eran Meshorer
Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036684/yeastract-an-upgraded-database-for-the-analysis-of-transcription-regulatory-networks-in-saccharomyces-cerevisiae
#4
Miguel C Teixeira, Pedro T Monteiro, Margarida Palma, Catarina Costa, Cláudia P Godinho, Pedro Pais, Mafalda Cavalheiro, Miguel Antunes, Alexandre Lemos, Tiago Pedreira, Isabel Sá-Correia
The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT-www.yeastract.com) information system has been, for 11 years, a key tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in Saccharomyces cerevisiae. Since its last update in June 2017, YEASTRACT includes approximately 163000 regulatory associations between transcription factors (TF) and target genes in S. cerevisiae, based on more than 1600 bibliographic references; it also includes 247 specific DNA binding consensus recognized by 113 TFs...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036674/detecting-and-characterizing-micrornas-of-diverse-genomic-origins-via-mirvial
#5
Jing Xia, Lun Li, Tiantian Li, Zhiwei Fang, Kevin Zhang, Junfei Zhou, Hai Peng, Weixiong Zhang
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036646/de-novo-deleterious-sequence-variants-that-alter-the-transcriptional-activity-of-the-homeoprotein-pbx1-are-associated-with-intellectual-disability-and-pleiotropic-developmental-defects
#6
Anne Slavotinek, Maurizio Risolino, Marta Losa, Megan T Cho, Kristin G Monaghan, Dina Schneidman-Duhovny, Sarah Parisotto, Johanna C Herkert, Alexander P A Stegmann, Kathryn Miller, Natasha Shur, Jacqueline Chui, Eric Muller, Suzanne DeBrosse, Justin O Szot, Gavin Chapman, Nicholas S Pachter, David S Winlaw, Bryce A Mendelsohn, Joline Dalton, Kyriakie Sarafoglou, Peter I Karachunski, Jane M Lewis, Helio Pedro, Sally L Dunwoodie, Licia Selleri, Joseph Shieh
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads...
September 22, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036642/striking-a-balance-regulation-of-transposable-elements-by-zfp281-and-mll2-in-mouse-embryonic-stem-cells
#7
Qian Dai, Yang Shen, Yan Wang, Xin Wang, Joel Celio Francisco, Zhuojuan Luo, Chengqi Lin
Transposable elements (TEs) compose about 40% of the murine genome. Retrotransposition of active TEs such as LINE-1 (L1) tremendously impacts genetic diversification and genome stability. Therefore, transcription and transposition activities of retrotransposons are tightly controlled. Here, we show that the Krüppel-like zinc finger protein Zfp281 directly binds and suppresses a subset of retrotransposons, including the active young L1 repeat elements, in mouse embryonic stem (ES) cells. In addition, we find that Zfp281-regulated L1s are highly enriched for 5-hydroxymethylcytosine (5hmC) and H3K4me3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036636/genetic-reduction-of-nrf2-exacerbates-cognitive-deficits-in-a-mouse-model-of-alzheimer-s-disease
#8
Caterina Branca, Eric Ferreira, Thuy-Vi Nguyen, Kristian Doyle, Antonella Caccamo, Salvatore Oddo
Aging is the major risk factor for several neurodegenerative diseases, including Alzheimer's disease (AD). However, the mechanisms by which aging contributes to neurodegeneration remain elusive. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is a transcription factor that regulates expression of a vast number of genes by binding to the antioxidant response element. Nrf2 levels decrease as a function of age, and reduced Nrf2 levels have been reported in postmortem human brains and animal models of AD...
September 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036620/fe-controls-the-transcription-of-downstream-flowering-regulators-through-two-distinct-mechanisms-in-leaf-phloem-companion-cells
#9
Mio Shibuta, Mitsutomo Abe
In facultative long-day plant, Arabidopsis thaliana, FLOWERING LOCUS T (FT) encoding a mobile hormone florigen plays an essential role in modulating the optimal timing of flowering to ensure reproductive success. Under inductive long-day conditions, the transcription of FT is activated by the CONSTANS (CO)/NUCLEAR FACTOR-Y (NF-Y) protein complex in leaf phloem companion cells. FT is transported to the shoot apical meristem through interaction with florigen transporters, such as SODIUM POTASSIUM ROOT DEFECTIVE 1 (NaKR1)...
September 25, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29036481/identification-of-the-direct-regulon-of-ntca-during-early-acclimation-to-nitrogen-starvation-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#10
Joaquín Giner-Lamia, Rocío Robles-Rengel, Miguel A Hernández-Prieto, M Isabel Muro-Pastor, Francisco J Florencio, Matthias E Futschik
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036458/metabolic-syndrome-induces-over-expression-of-the-human-at1r-a-haplotype-dependent-effect-with-implications-on-cardio-renal-function
#11
Sudhir Jain, Nitin Puri, Anita Rana, Natalie Sirianni, Brahmaraju Mopidevi, Ashok Kumar
Background: The transcriptional regulation of the human AT1R gene in pathophysiologies, like the metabolic syndrome, is poorly understood. The human AT1R gene has polymorphisms in its promoter that can be arranged in two haplotypes. Variants -810T, -713T, -214A, and -153A always occur together (Hap-I) and variants -810A, -713G, -214C, and -153G form Hap-II. We have hypothesized that high fat diet will alter cellular transcriptional milieu and increase hAT1R gene expression in a haplotype-dependent manner...
October 5, 2017: American Journal of Hypertension
https://www.readbyqxmd.com/read/29036442/global-inhibition-of-transcription-causes-an-increase-in-histone-h2a-z-incorporation-within-gene-bodies
#12
Anahita Lashgari, Jean-François Millau, Pierre-Étienne Jacques, Luc Gaudreau
H2A.Z histone variant is an important regulator of gene transcription, which is enriched at regulatory regions but is also found within gene bodies. Recent evidence suggests that active recruitment of H2A.Z within gene bodies is required to induce gene repression. In contrast to this view, we show that global inhibition of transcription results in H2A.Z accumulation at gene transcription start sites, as well as within gene bodies. Our results indicate that accumulation of H2A.Z within repressed genes can also be a consequence of the repression of gene transcription rather than an active mechanism required to establish the repression...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036435/the-wuschel-related-homeobox-5a-ptowox5a-is-involved-in-adventitious-root-development-in-poplar
#13
Jianbo Li, Jin Zhang, Huixia Jia, Bobin Liu, Pei Sun, Jianjun Hu, Lijuan Wang, Mengzhu Lu
Adventitious rooting is an essential step in vegetative propagation. Currently, the mechanism that regulates adventitious root (AR) development in woody plants is poorly understood. This work demonstrates that Populus tomentosa WUSCHEL-related homeobox 5a (PtoWOX5a) transcription factor is involved in AR development in poplar. PtoWOX5a was specifically expressed in the AR tip and lateral root tip during AR and lateral root regeneration from the stem segment. Phenotypic complementation experiments indicated that the PtoWOX5a can functionally complement AtWOX5 in quiescent center (QC) cells...
September 26, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29036403/cscd-a-database-for-cancer-specific-circular-rnas
#14
Siyu Xia, Jing Feng, Ke Chen, Yanbing Ma, Jing Gong, Fangfang Cai, Yuxuan Jin, Yang Gao, Linjian Xia, Hong Chang, Lei Wei, Leng Han, Chunjiang He
Circular RNA (circRNA) is a large group of RNA family extensively existed in cells and tissues. High-throughput sequencing provides a way to view circRNAs across different samples, especially in various diseases. However, there is still no comprehensive database for exploring the cancer-specific circRNAs. We collected 228 total RNA or polyA(-) RNA-seq samples from both cancer and normal cell lines, and identified 272 152 cancer-specific circRNAs. A total of 950 962 circRNAs were identified in normal samples only, and 170 909 circRNAs were identified in both tumor and normal samples, which could be further used as non-tumor background...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036396/the-fastk-family-of-proteins-emerging-regulators-of-mitochondrial-rna-biology
#15
Alexis A Jourdain, Johannes Popow, Miguel A de la Fuente, Jean-Claude Martinou, Paul Anderson, Maria Simarro
The FASTK family proteins have recently emerged as key post-transcriptional regulators of mitochondrial gene expression. FASTK, the founding member and its homologs FASTKD1-5 are architecturally related RNA-binding proteins, each having a different function in the regulation of mitochondrial RNA biology, from mRNA processing and maturation to ribosome assembly and translation. In this review, we outline the structure, evolution and function of these FASTK proteins and discuss the individual role that each has in mitochondrial RNA biology...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036329/m6avar-a-database-of-functional-variants-involved-in-m6a-modification
#16
Yueyuan Zheng, Peng Nie, Di Peng, Zhihao He, Mengni Liu, Yubin Xie, Yanyan Miao, Zhixiang Zuo, Jian Ren
Identifying disease-causing variants among a large number of single nucleotide variants (SNVs) is still a major challenge. Recently, N6-methyladenosine (m6A) has become a research hotspot because of its critical roles in many fundamental biological processes and a variety of diseases. Therefore, it is important to evaluate the effect of variants on m6A modification, in order to gain a better understanding of them. Here, we report m6AVar (http://m6avar.renlab.org), a comprehensive database of m6A-associated variants that potentially influence m6A modification, which will help to interpret variants by m6A function...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036198/the-homeodomain-interacting-protein-kinase-hpk-1-preserves-protein-homeostasis-and-longevity-through-master-regulatory-control-of-the-hsf-1-chaperone-network-and-torc1-restricted-autophagy-in-caenorhabditis-elegans
#17
Ritika Das, Justine A Melo, Manjunatha Thondamal, Elizabeth A Morton, Adam B Cornwell, Beresford Crick, Joung Heon Kim, Elliot W Swartz, Todd Lamitina, Peter M Douglas, Andrew V Samuelson
An extensive proteostatic network comprised of molecular chaperones and protein clearance mechanisms functions collectively to preserve the integrity and resiliency of the proteome. The efficacy of this network deteriorates during aging, coinciding with many clinical manifestations, including protein aggregation diseases of the nervous system. A decline in proteostasis can be delayed through the activation of cytoprotective transcriptional responses, which are sensitive to environmental stress and internal metabolic and physiological cues...
October 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29035972/hyperammonemia-and-proteostasis-in-cirrhosis
#18
Srinivasan Dasarathy, Maria Hatzoglou
PURPOSE OF REVIEW: Skeletal muscle loss or sarcopenia is a frequent complication of cirrhosis that adversely affects clinical outcomes. As skeletal muscle is the largest store of proteins in the body, proteostasis or protein homeostasis is required for maintenance of muscle mass. This review will focus on disordered skeletal muscle proteostasis in liver disease. RECENT FINDINGS: Increased skeletal muscle uptake of ammonia initiates responses that result in disordered proteostasis including impaired protein synthesis and increased autophagy...
October 14, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/29035884/protective-effects-of-pretreatment-with-quercetin-against-lipopolysaccharide-induced-apoptosis-and-the-inhibition-of-osteoblast-differentiation-via-the-mapk-and-wnt-%C3%AE-catenin-pathways-in-mc3t3-e1-cells
#19
Chun Guo, Rui-Juan Yang, Ke Jang, Xiao-Ling Zhou, Yu-Zhen Liu
BACKGROUND/AIMS: Quercetin, a flavonoid found in onions and other vegetables, has potential inhibitory effects on bone resorption in vivo and in vitro. In our previous study, we found that quercetin treatment reversed lipopolysaccharide (LPS)-induced inhibition of osteoblast differentiation through the mitogen-activated protein kinase (MAPK) pathway in MC3T3-E1 cells. In this study, we investigated the underlying mechanisms of pretreatment with quercetin on apoptosis and the inhibition of osteoblast differentiation in MC3T3-E1 cells induced by LPS...
October 16, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29035780/long-non-coding-rnas-in-the-atherosclerotic-plaque
#20
Serdal Arslan, Öcal Berkan, Torkia Lalem, Nil Özbilüm, Sabahattin Göksel, Özge Korkmaz, Nilgün Çetin, Yvan Devaux
BACKGROUND AND AIMS: Genetic and environmental factors are important components of the development of atherosclerosis. Long non-coding RNA (lncRNAs) have emerged as regulators of multiple pathophysiological pathways in the cardiovascular system. Here, we investigated potential associations between lncRNAs and atherosclerosis. METHODS: Tissue samples from atherosclerotic coronary artery plaques and non-atherosclerotic internal mammary artery were obtained from 20 patients during coronary artery bypass surgery...
October 7, 2017: Atherosclerosis
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