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 local...
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 AD...
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

Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications
Publication date: Available online 22 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Anna Stroynowska-Czerwińska, Anna Piasecka, Matthias BochtlerAbstractCXXC domains have traditionally been considered as CpG specific DNA binding domains that are repelled by cytosine modifications. This view has recently been challenged by the demonstration that CXXC domain of TET3 has relaxed sequence specificity and binds with the highest affinity to symmetric DNA duplex containing 5caCpG. Here, we present a comparative analysis of the MLL1-CXXC and TET3-CXXC sequence specificity and toler...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 22, 2018 Category: Genetics & Stem Cells Source Type: research

Repression of yeast RNA polymerase III by stress leads to degradation of its largest subunit, C160
Publication date: Available online 19 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(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 biosy...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 20, 2018 Category: Genetics & Stem Cells Source Type: research

m6A-mediated translation regulation
Publication date: Available online 17 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Kate D. Meyer (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 18, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: November 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 11Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 18, 2018 Category: Genetics & Stem Cells Source Type: research

DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected Cells
In this study, we have used LC-MS/MS to track down the fate of the methyl group removed from 5mC on DNA by mouse DNMT3B in vitro and found that it becomes covalently linked to the DNA methylation catalytic cysteine of the enzyme. We also show that Ca2+ homeostasis-dependent but TET1/TET2/TET3/TDG-independent demethylation of methylated episomal DNA by mouse DNMT3A or DNMT3B can occur in transfected human HEK 293 and mouse embryonic stem (ES) cells. Based on these results, we present a tentative working model of Ca2+ and redox conditions-dependent active DNA demethylation by DNMTs. Our study substantiates the potential role...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 17, 2018 Category: Genetics & Stem Cells Source Type: research

Human ALKBH3-induced m1A demethylation increases the CSF-1 mRNA stability in breast and ovarian cancer cells
Publication date: Available online 17 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Ho-Hyung Woo, Setsuko K. ChambersAbstractIn ovarian and breast cancers, the actions of the cytokine CSF-1 lead to poor prognosis. CSF-1 expression can be regulated post-transcriptionally. RNA methylation is another layer of posttranscriptional regulation. The methylation of N1 atom of adenine (m1A) results in a conformational change of RNA which regulates translational efficiency. Our study indicates that the m1A is also involved in the CSF-1 mRNA decay. The alteration of ALKBH3 expression, a...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 17, 2018 Category: Genetics & Stem Cells Source Type: research

Regulation of ATM and ATR by SMARCAL1 and BRG1
Publication date: Available online 11 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Ramesh Sethy, Radhakrishnan Rakesh, Ketki Patne, Vijendra Arya, Tapan Sharma, Dominic Thangminlen Haokip, Reshma Kumari, Rohini MuthuswamiAbstractThe G2/M checkpoint is activated on DNA damage by the ATM and ATR kinases that are regulated by post-translational modifications. In this paper, the transcriptional co-regulation of ATM and ATR by SMARCAL1 and BRG1, both members of the ATP-dependent chromatin remodeling protein family, is described. SMARCAL1 and BRG1 co-localize on the promoters of ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 12, 2018 Category: Genetics & Stem Cells Source Type: research

Angiotensin II induced CSF1 transcription is mediated by a crosstalk between different epigenetic factors in vascular endothelial cells
In conclusion, our data unveil a novel epigenetic mechanism whereby a BRG1-centered complex mediates transcriptional activation of CSF1 by Ang II in vascular endothelial cells. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 12, 2018 Category: Genetics & Stem Cells Source Type: research

The expression of CKLFSF2B is regulated by GATA1 and CREB in the Leydig cells, which modulates testicular steroidogenesis
Publication date: Available online 12 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Sudeep Kumar, Hana Kang, Eunsook Park, Hee-Sae Park, Keesook LeeAbstractCKLFSF is a protein family that serves as a functional bridge between chemokines and members of the transmembrane 4 superfamily (TM4SF). In the course of evolution, CKLFSF2 has evolved as two isoforms, namely CKLFSF2A and CKLFSF2B, in mice. CKLFSF2A, also known as CMTM2A and ARR19, is expressed in the testis and is important for testicular steroidogenesis. CKLFSF2B is also known to be highly expressed in the testis. In th...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 12, 2018 Category: Genetics & Stem Cells Source Type: research

mRNA cap regulation in mammalian cell function and fate
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 - October 10, 2018 Category: Genetics & Stem Cells Source Type: research

Myt1 and Myt1l transcription factors limit proliferation in GBM cells by repressing YAP1 expression
Publication date: Available online 10 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Tiffany A. Melhuish, Izabela Kowalczyk, Arkadi Manukyan, Ying Zhang, Anant Shah, Roger Abounader, David WottonAbstractMyelin transcription factor 1 (Myt1) and Myt1l (Myt1-like) are zinc finger transcription factors that regulate neuronal differentiation. Reduced Myt1l expression has been implicated in glioblastoma (GBM), and the related St18 was originally identified as a potential tumor suppressor for breast cancer. We previously analyzed changes in gene expression in a human GBM cell line w...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 10, 2018 Category: Genetics & Stem Cells Source Type: research

Heterogeneous ribonucleoprotein F regulates YAP expression via a G-tract in 3′UTR
Publication date: Available online 10 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Wing-Keung Chu, Li-Man Hung, Chun-Wei Hou, Jan-Kan ChenAbstractThe Yes-associated protein (YAP) is a transcription coactivator that plays crucial roles in organ size control and tumorigenesis, and was demonstrated to be inhibited by the Hippo signaling pathway. To date, the molecular mechanisms regulating the expression of YAP in human cells remain unknown. In the present study, we found that hnRNP F and hnRNP U negatively regulate YAP expression. We also showed that downregulation of YAP exp...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 10, 2018 Category: Genetics & Stem Cells Source Type: research

Active DNA demethylation by DNMT3A and DNMT3B in vitro and of methylated episomal DNA in transiently transfected cells
In this study, we have used LC-MS/MS to track down the fate of the methyl group removed from 5mC on DNA by mouse DNMT3B in vitro and found that it becomes covalently linked to the DNA methylation catalytic cysteine of the enzyme. We also show that Ca2+ homeostasis-dependent but TET1/TET2/TET3/TDG-independent demethylation of methylated episomal DNA by mouse DNMT3A or DNMT3B can occur in transfected human HEK 293 and mouse embryonic stem (ES) cells. Based on these results, we present a tentative working model of Ca2+ and redox conditions-dependent active DNA demethylation by DNMTs. Our study substantiates the potential role...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 9, 2018 Category: Genetics & Stem Cells Source Type: research

It's complicated… m6A-dependent regulation of gene expression in cancer
Publication date: Available online 5 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Christina M. Fitzsimmons, Pedro J. BatistaAbstractCellular function relies on multiple pathways that are coordinated to ensure the proper execution of gene expression networks. Failure to coordinate the multiple programs active in the cell can have catastrophic consequences and lead to diseases such as cancer. At the post-transcriptional level, RNA modifications play important roles in the regulation of gene expression. N6-methyladenosine (m6A) is the most abundant internal messenger RNA (mRNA...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 6, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 10Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 5, 2018 Category: Genetics & Stem Cells Source Type: research

The m6A‑methylase complex and mRNA export
Publication date: Available online 2 October 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Simon Lesbirel, Stuart A. WilsonAbstractDuring synthesis, mRNA undergoes a number of modifications such as capping, splicing and polyadenylation. These processes are coupled with the orderly deposition of the TREX complex on the mRNA and subsequent recruitment of the NXF1-P15 heterodimer which stimulates the nuclear export of mature mRNAs. mRNAs also undergo a number of internal modifications, the most common of which is the N6‑methyladenosine (m6A) modification. In this review we discuss th...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 5, 2018 Category: Genetics & Stem Cells Source Type: research

Transcription factor Zbtb38 downregulates the expression of anti-inflammatory IL1r2 in mouse model of rheumatoid arthritis
Publication date: Available online 15 September 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Tímea Ocskó, Dániel M. Tóth, Gyula Hoffmann, Vilmos Tubak, Tibor T. Glant, Tibor A. RauchAbstractDNA methylation is a decisive regulator of gene expression. Differentially methylated promoters were described in rheumatoid arthritis (RA), but we do not know how these epimutations can trigger a proinflammatory cytokine milieu. B cell-focused DNA methylome studies identified a group of genes that had undergone disease-associated changes in a murine model of RA. An a...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 17, 2018 Category: Genetics & Stem Cells Source Type: research

G-quadruplex structures at the promoter of HOXC10 regulate its expression
In this report, we revealed that the HOXC10 promoter contains multiple G-tracts in its negative strand and has high potential of forming G-quadruplex structures. In circular dichroism studies, synthesized oligonucleotides based on the G-rich region of 241–297 base pairs upstream of the HOXC10 transcription start site showed molar ellipticity at specific wavelengths characteristic of G-quadruplex structures. Analyses of these oligonucleotides by native polyacrylamide gel electrophoresis, gel-shift assay, immunostaining and replication stop assay revealed formation of multiple types of G-quadruplex structures in presen...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 15, 2018 Category: Genetics & Stem Cells Source Type: research

Pro-inflammatory cytokines IL-6 and CCL2 suppress expression of circadian gene Period2 in mammary epithelial cells
Publication date: Available online 13 September 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Chan-Wei Yu, Kuo-Chih Cheng, Ling-Chih Chen, Meng-Xuan Lin, Yi-Cheng Chang, Wendy W. Hwang-VersluesAbstractChronic inflammation is known to contribute to tumor initiation and cancer progression. In breast tissue, the core circadian gene Period (PER)2 plays a critical role in mammary gland development and possesses tumor suppressor function. Interleukin (IL)-6 and C-C motif chemokine ligand (CCL) 2 are among the most abundant cytokines in the inflammatory microenvironment. We found that acut...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 15, 2018 Category: Genetics & Stem Cells Source Type: research

Comprehensive analysis of chromatin signature and transcriptome uncovers functional lncRNAs expressed in nephron progenitor cells
In conclusion, we identified a lncRNA, Gm29418, in nephron progenitor cells that has an enhancer-like function on a key regulatory gene, Six2. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 15, 2018 Category: Genetics & Stem Cells Source Type: research

Slt2 MAPK association with chromatin is required for transcriptional activation of Rlm1 dependent genes upon cell wall stress
Publication date: Available online 14 September 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Ana Belén Sanz, Raúl García, José Manuel Rodríguez-Peña, César Nombela, Javier ArroyoAbstractThe regulation of gene expression through the cell wall integrity (CWI) pathway in yeast is mainly coordinated by the MAPK Slt2 and the transcription factor Rlm1. In this work, we elucidate a new role for Slt2 as a part of the transcriptional activation machinery that regulates CWI gene expression in response to cell wall stress. We show that Slt2 is ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 15, 2018 Category: Genetics & Stem Cells Source Type: research

Interaction of positive coactivator 4 with histone 3.3 protein is essential for transcriptional activation of the luteinizing hormone receptor gene
This study explores interactions of PC4 with histone proteins, which presumably triggers chromatin modifications during LHR transcriptional activation. TSA treatment of MCF7 cells expressing PC4-Flag protein induces acetylation of histone 3 (H3) and immunoprecipitation (IP) studies revealed its interaction with PC4-Flag protein. MS/MS analysis of the protein complex obtained after IP from TSA treated samples detected H3.3 acetylated at K9, K14, K18, K23 and K27 as a PC4 interacting protein. The association of PC4 with H3.3 was corroborated by IP and re-ChIP using H3.3 antibody. Similarly, IP and reChIP showed association o...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 14, 2018 Category: Genetics & Stem Cells Source Type: research

HDAC1 interacts with the p50 NF-κB subunit via its nuclear localization sequence to constrain inflammatory gene expression
Publication date: Available online 10 September 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Tyrell N. Cartwright, Julie C. Worrell, Letizia Marchetti, Catríona M. Dowling, Amber Knox, Patrick Kiely, Jelena Mann, Derek A. Mann, Caroline L. WilsonAbstractThe NF-κB p50 subunit is an important regulator of inflammation, with recent experimental evidence to support it also having a tumor suppressor role. Classically, p50 functions in heterodimeric form with the RelA (p65) NF-κB subunit to activate inflammatory genes. However, p50 also forms homodimers which actively ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 11, 2018 Category: Genetics & Stem Cells Source Type: research

MiR-19b non-canonical binding is directed by HuR and confers chemosensitivity through regulation of P-glycoprotein in breast cancer
This study suggests a novel therapeutic target to impair P-glycoprotein mediated drug efflux, and also indicates that current microRNA binding predictions that rely on seed regions alone may be too conservative. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 2, 2018 Category: Genetics & Stem Cells Source Type: research

Sensory domain of the cell cycle kinase CckA regulates the differential DNA binding of the master regulator CtrA in Caulobacter crescentus
Publication date: Available online 31 August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Sharath Narayanan, Lokesh Kumar, Sunish Kumar RadhakrishnanAbstractSophisticated signaling mechanisms allow bacterial cells to cope with environmental and intracellular challenges. Activation of specific pathways ameliorates these challenges and thereby warrants integrity. Here, we demonstrate the pliability of the CckA-CtrA two component signaling system in the freshwater bacterium Caulobacter crescentus. Our forward genetic screen to analyze suppressor mutations that can negate the chromosom...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 31, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: September 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 9Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 31, 2018 Category: Genetics & Stem Cells Source Type: research

RNA localization and transport
Publication date: Available online 29 August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Beat SuterAbstractRNA localization serves numerous purposes from controlling development and differentiation to supporting the physiological activities of cells and organisms. After a brief introduction into the history of the study of mRNA localization I will focus on animal systems, describing in which cellular compartments and in which cell types mRNA localization was observed and studied. In recent years numerous novel localization patterns have been described, and countless mRNAs have bee...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 29, 2018 Category: Genetics & Stem Cells Source Type: research

CIRCE element evolved for the coordinated transcriptional regulation of bacterial duplicate groELs
In this study, we reported that the controlling inverted repeat of chaperone expression (CIRCE) element (the HrcA-binding site located upstream of the promoter) evolved for the transcriptional regulation of duplicate groELs. CIRCE composition and locations were found to be phylogenetically conserved in bacterial taxa. Myxococcus xanthus DK1622 has two CIRCE elements (CIRCE1groESL1 and CIRCE2groESL1) in the promoter region of groESL1 and one CIRCE element (CIRCEgroEL2) before groEL2. We also found that negative HrcA and positive σ32 regulators coordinated the transcription of duplicate groELs, and that the double dele...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 26, 2018 Category: Genetics & Stem Cells Source Type: research

Hypermethylated in cancer 1 (HIC1) mediates high glucose induced ROS accumulation in renal tubular epithelial cells by epigenetically repressing SIRT1 transcription
In conclusion, our data suggest that epigenetic repression of SIRT1 by HIC1 may contribute to HG-induced elevation of ROS levels in renal tubular epithelial cells. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 25, 2018 Category: Genetics & Stem Cells Source Type: research

LPS promotes HBO1 stability via USP25 to modulate inflammatory gene transcription in THP-1 cells
Publication date: Available online 4 August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Chen Long, Yandong Lai, Jin Li, Jiangsheng Huang, Chunbin ZouAbstractThe histone acetyltransferase HBO1 (Histone acetyltransferase binding to origin recognition complex 1, Myst2/Kat7) participates in a range of life processes including DNA replication and tumorigenesis. Recent studies revealed that HBO1 is involved in gene transcriptional activation. However, the molecular behavior of HBO1 in inflammation is yet to be studied. Here we report that endotoxin lipopolysaccharide (LPS) elevates HBO1...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 4, 2018 Category: Genetics & Stem Cells Source Type: research

MRGBP promotes AR-mediated transactivation of KLK3 and TMPRSS2 via acetylation of histone H2A.Z in prostate cancer cells
This study showed that MRG domain binding protein (MRGBP) accelerated AR-mediated transactivation. We first showed that MRGBP promoted growth of AR-positive prostate cancer cells. MRGBP increased the expression of certain AR target genes, including KLK3 and TMPRSS2, and it associated with AR binding regions of these genes during androgen treatment. Furthermore, MRGBP interacted with MRG15 and TIP60 in prostate cancer cells. Androgen-stimulated AR enhanced histone H3K4me1 or H3K4me3 levels at AR binding regions. MRGBP was recruited to active gene regions through its binding with H3K4me1/3 by MRG15. Then, MRGBP promoted recr...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 1, 2018 Category: Genetics & Stem Cells Source Type: research

Fine-tuning of fgf8a expression through alternative polyadenylation has a selective impact on Fgf-associated developmental processes
Publication date: Available online 31 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Sara F. Fernandes, Rita Fior, Francisco Pinto, Margarida Gama-Carvalho, Leonor SaúdeAbstractThe formation of distinct 3′UTRs through alternative polyadenylation is a mechanism of gene expression regulation that has been implicated in many physiological and pathological processes. However, its functions in the context of vertebrate embryonic development have been largely unaddressed, in particular with a gene-specific focus. Here we show that the most abundant 3′UTR for the zeb...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 31, 2018 Category: Genetics & Stem Cells Source Type: research

DNA methylation on N6-adenine in lepidopteran Bombyx mori
Publication date: Available online 30 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Xiaoyan Wang, Zhiqing Li, Quan Zhang, Bingqian Li, Chenchen Lu, Wanshun Li, Tingcai Cheng, Qingyou Xia, Ping ZhaoAbstractIncreasing knowledge of DNA methylation that occurs on the sixth position of adenine (N6-methyladenine, 6 mA) has emerged as a novel epigenetic mark in eukaryotes and plays an important role in regulating gene transcription, DNA replication and repair, transposable activities, and others. Here, we show DNA 6 mA methylation is present in Bombyx mori, a lepidopteran model in...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 30, 2018 Category: Genetics & Stem Cells Source Type: research

Linking toxin-antitoxin systems with phenotypes: A Staphylococcus aureus viewpoint
This article is part of a Special Issue entitled: Dynamic gene expression, edited by Prof. Patrick Viollier”. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 27, 2018 Category: Genetics & Stem Cells Source Type: research

Epigenetic activation of PERP transcription by MKL1 contributes to ROS-induced apoptosis in skeletal muscle cells
In conclusion, our data illustrate a novel epigenetic pathway that links PERP transcription to ROS-induced apoptosis in skeletal muscle cells. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 27, 2018 Category: Genetics & Stem Cells Source Type: research

Regulation of multiple abiotic stress tolerance by LexA in the cyanobacterium Anabaena sp. strain PCC7120
Publication date: Available online 26 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Arvind Kumar, Anurag Kirti, Hema RajaramAbstractThe paradigm of involvement of LexA in regulation of only SOS-response in bacteria through the down-regulation of DNA repair genes was challenged in the unicellular cyanobacterium, Synechocystis PCC6803, wherein it was originally shown not to be associated with DNA repair and later also involved in management of carbon-starvation through up-regulation of C-metabolism genes. In the filamentous cyanobacterium, Anabaena sp. strain PCC7120, global stre...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 26, 2018 Category: Genetics & Stem Cells Source Type: research

Cbt modulates Foxo activation by positively regulating insulin signaling in Drosophila embryos
In this study, we used genomic approaches to identify genes regulated by Cbt as well as its direct targets during late embryogenesis. Our results reveal a complex transcriptional circuit downstream of Cbt and evidence that it is functionally related with the Insulin/insulin-like growth factor signaling pathway. In this context, Cbt may act as a positive regulator of the pathway, leading to the repression of Foxo activity. Our results also suggest that the DC defects observed in cbt embryos could be partially due to Foxo overactivation and that a regulatory feedback loop between Foxo and Cbt may be operating in the DC conte...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 26, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 8Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 26, 2018 Category: Genetics & Stem Cells Source Type: research