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Editorial Board
Publication date: December 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 12Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 23, 2018 Category: Genetics & Stem Cells Source Type: research

Deletion of an intronic HIF-2α binding site suppresses hypoxia-induced WT1 expression
Publication date: Available online 20 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Katharina Krueger, Lorenzo Catanese, Lina K. Sciesielski, Karin M. Kirschner, Holger ScholzAbstractHypoxia-inducible factors (HIFs) play a key role in the adaptation to low oxygen by interacting with hypoxia response elements (HREs) in the genome. Cellular levels of the HIF-2α transcription factor subunit influence the histopathology and clinical outcome of neuroblastoma, a malignant childhood tumor of the sympathetic ganglia. Expression of the Wilms tumor gene, WT1, marks a group of high-r...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 21, 2018 Category: Genetics & Stem Cells Source Type: research

Changes in Fluorescence Recovery After Photobleaching (FRAP) as an indicator of SOX9 transcription factor activity
Publication date: Available online 20 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Kannan Govindaraj, Jan Hendriks, Diane S. Lidke, Marcel Karperien, Janine N. PostAbstractCells respond to their environment via an intricate cellular signaling network, directing cell fate. Changes in cell fate are characterized by changes in gene transcription, dictated by (master) transcription factor activity. SOX9 is the master transcription factor for chondrocyte development. Its impaired function is implicated in osteoarthritis and growth disorders, such as dwarfism. However, the facto...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 21, 2018 Category: Genetics & Stem Cells Source Type: research

Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry
Publication date: Available online 7 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Manasses Jora, Peter A. Lobue, Robert L. Ross, Brittney Williams, Balasubrahmanyam AddepalliAbstractA small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information abo...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 8, 2018 Category: Genetics & Stem Cells Source Type: research

EP300-HDAC1-SWI/SNF functional unit defines transcription of some DNA repair enzymes during differentiation of human macrophages
Publication date: Available online 8 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Julita Pietrzak, Tomasz Płoszaj, Łukasz Pułaski, Agnieszka RobaszkiewiczAbstractDifferentiation of human macrophages predisposes these cells to numerous tasks, i.e. killing invading pathogens, and this entails the need for enhanced intracellular defences against stress, including conditions that may increase DNA damage. Our study shows that expression of DNA repair enzymes, such as PARP1, BRCA1 and XRCC1, are activated during macrophage development by the SWI/SNF chromatin remodelling comp...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 8, 2018 Category: Genetics & Stem Cells Source Type: research

Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs
This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 8, 2018 Category: Genetics & Stem Cells Source Type: research

Steering pluripotency and differentiation with N6-methyladenosine RNA modification
This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 7, 2018 Category: Genetics & Stem Cells Source Type: research

m6A: Widespread regulatory control in virus replication
This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 7, 2018 Category: Genetics & Stem Cells Source Type: research

Transcriptional regulation of Translocator protein (18 kDa) (TSPO) in microglia requires Pu.1, Ap1 and Sp factors
Publication date: Available online 6 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Khalid Rashid, Lea Geissl, Anne Wolf, Marcus Karlstetter, Thomas LangmannAbstractMitochondrial Translocator protein (18 kDa) (TSPO) is strongly expressed in reactive microglia and serves as a therapeutic target for alleviation of neuronal degeneration. However, little is known about TSPO's transcriptional regulation in microglia. The aim of this study was to identify genetic elements and transcription factors required for basal and inducible TSPO expression in microglia. Murine Tspo promote...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 6, 2018 Category: Genetics & Stem Cells Source Type: research

m6A mRNA modification regulates mammalian spermatogenesis
Publication date: Available online 2 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Ming-Han Tong, Zhen LinAbstractMammalian spermatogenesis is a highly specialized differentiation process involving precise regulatory mechanisms at the transcriptional, posttranscriptional, and translational levels. Emerging evidence has shown that N6-methyladenosine (m6A), an epitranscriptomic regulator of gene expression, can influence pre-mRNA splicing, mRNA export, turnover, and translation, which are controlled in the male germline to ensure coordinated gene expression. In this review, w...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 3, 2018 Category: Genetics & Stem Cells Source Type: research

Mechanistic insights into m6A RNA enzymes
Publication date: Available online 3 November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Tina Lence, Chiara Paolantoni, Lina Worpenberg, Jean-Yves RoignantSummaryThe field of RNA modifications, so-called epitranscriptomics, has flourished over the past years owing to improvements of detection methods and the identification of important regulatory players. N6-methyladenosine (m6A) is the most abundant internal modification in messenger (mRNA) and long non-coding (lncRNA), and controls most steps of RNA metabolism. Its physiological roles range from gametogenesis, stem cell differe...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 3, 2018 Category: Genetics & Stem Cells Source Type: research

The 3′UTR of human MAVS mRNA contains multiple regulatory elements for the control of protein expression and subcellular localization
In this study, we aimed to characterize the role of the MAVS 3′UTR during MAVS expression by truncating the 3′UTR into different fragments so as to identify the regulatory elements. We found that the different fragments (H1–H5) of the MAVS 3′UTR play different roles in regulating the subcellular localization and function of MAVS. Three AU-rich elements (AREs) in the MAVS 3′UTR H1 fragment (region 1-3445 in the 3′UTR) repressed MAVS expression by interacting with HuR to destabilize its mRNA. The MAVS 3′UTR H5 fragment (region 5955-7687 in the 3′UTR) affected the cellular localization of MAVS in mitochondria ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 2, 2018 Category: Genetics & Stem Cells Source Type: research

ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep
Publication date: Available online 31 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Ketty Sinigaglia, Dagmara Wiatrek, Anzer Khan, David Michalik, Nagraj Sambrani, Jiří Sedmík, Dragana Vukić, Mary A. O'Connell, Liam P. KeeganAbstractAdenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in dsRNA. ADAR editing in pre-mRNAs recodes open reading frames and alters splicing, mRNA structure and interactions with miRNAs. Here, we review ADAR gene expression, splice forms, posttranslational modifications, subcellular localizations and functions of ADAR protein i...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 1, 2018 Category: Genetics & Stem Cells Source Type: research

Functional validation of miRNAs targeting genes of DNA double-strand break repair to radiosensitize non-small lung cancer cells
In this study, we analyzed the combination of ionizing radiation (IR) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells. MicroRNAs are natural occurring modulators of gene expression and therefore represent an attractive strategy to affect the expression of DSB repair genes. As possible IR-sensitizing targets genes we selected genes of homologous recombination (HR) and non-homologous end joining (NHEJ) pathway (i.e. RAD51, BRCA2, PRKDC, XRCC5, LIG1). We examined these genes to determine whether they may be real targets of selected miRNAs by fu...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 31, 2018 Category: Genetics & Stem Cells Source Type: research

Repression of yeast RNA polymerase III by stress leads to ubiquitylation and proteasomal degradation of its largest subunit, C160
Publication date: January 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 1Author(s): Ewa Leśniewska, Małgorzata Cieśla, Magdalena BogutaAbstractRespiratory growth and various stress conditions repress RNA polymerase III (Pol III) transcription in Saccharomyces cerevisiae. Here we report a degradation of the largest Pol III catalytic subunit, C160 as a consequence of Pol III transcription repression. We observed C160 degradation in response to transfer of yeast from fermentation to respiration conditions, as well as treatment with rapamycin or inhibition of nucleotide bio...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 25, 2018 Category: Genetics & Stem Cells Source Type: research