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

Structure and function of the histone chaperone FACT – Resolving FACTual issues
We describe FACT structure and nucleosomal interactions, and their roles in FACT-dependent transcription, replication and repair. The variable requirements for FACT among different tumor and non-tumor cells suggest that various FACT-dependent processes have significantly different levels of relative importance in different eukaryotic cells. We propose that the stability of chromatin, which might vary among different cell types, dictates these diverse requirements for FACT to support cell viability. Since tumor cells are among the most sensitive to FACT inhibition, this vulnerability could be exploited for cancer treatment....
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 25, 2018 Category: Genetics & Stem Cells Source Type: research

Real-time observation of nucleoplasmin-mediated DNA decondensation and condensation reveals its specific functions as a chaperone
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 8Author(s): Xin-Mei Huo, Li-feng Meng, Tao Jiang, Ming Li, Fang-Zhen Sun, Bo Sun, Jian-Ke LiAbstractFertilization requires decondensation of promatine-condensed sperm chromatin, a dynamic process serving as an attractive system for the study of chromatin reprogramming. Nucleoplasmin is a key factor in regulating nucleosome assembly as a chaperone during fertilization process. However, knowledge on nucleoplasmin in chromatin formation remains elusive. Herein, magnetic tweezers (MT) and a chromatin assemb...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 21, 2018 Category: Genetics & Stem Cells Source Type: research

KRAB-containing zinc finger protein ZNF496 inhibits breast cancer cell proliferation by selectively repressing ERα activity
Publication date: Available online 20 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Jinlong Wang, Xiuyuan Zhang, Jiming Ling, Yun Wang, Xiaolin Xu, Yuchen Liu, Chaozhi Jin, Jiyu Ju, Yanzhi Yuan, Fuchu He, Chunling Zhao, Jian Wang, Chunyan TianAbstractKRAB-containing zinc finger proteins (KZNF) constitute the largest family of transcriptional regulators in humans and play critical roles in normal development and tumorigenesis. However, the function and mechanism of most KZNFs remain unclear. Here, we report that ZNF496, a KZNF family member, interacts with the DNA binding domain...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 20, 2018 Category: Genetics & Stem Cells Source Type: research

Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 8Author(s): Bożena Bruhn-Olszewska, Vadim Molodtsov, Michał Sobala, Maciej Dylewski, Katsuhiko S. Murakami, Michael Cashel, Katarzyna PotrykusAbstractPrecise regulation of gene expression is crucial for bacteria to respond to changing environmental conditions. In addition to protein factors affecting RNA polymerase (RNAP) activity, second messengers play an important role in transcription regulation, such as well-known effectors of the stringent response: guanosine 5′triphosphate-3′diphosp...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 19, 2018 Category: Genetics & Stem Cells Source Type: research

YAP transcriptionally regulates ErbB2 to promote liver cell proliferation
We examined the liver transcriptome in response to YAP overexpression and identify the ErbB signaling pathway as a mediator of cell growth downstream of YAP. ErbB2 is transcriptionally regulated by YAP in both the mouse liver and in HepG2 human hepatoma cells. Knockdown of YAP or pharmacological inhibition with verteporfin reduced ERBB2 levels in HepG2 cells. Analysis of ChIP-seq data revealed enrichment of the transcription factor TEAD4 at the ERBB2 promoter. Using luciferase reporter and chromatin immunoprecipitation assays, we show that YAP and TEAD4 directly bind to and activate a regulatory element in the ErbB2 promot...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2018 Category: Genetics & Stem Cells Source Type: research

Egr-1 transactivates WNT5A gene expression to inhibit glucose-induced β-cell proliferation
In this study, we found palmitate, a saturated fatty acid, inhibited the β-cell proliferation induced by high glucose through the induction of Wnt5a expression in vitro and in vivo. We also found that Wnt5a was both sufficient and necessary for inhibition of β-cell proliferation. Additionally, Egr-1, but not NF-κB, FOXO1, Smad2, Smad3, SP1 or SP3 mediated the expression of Wnt5a. Deletion and site-directed mutagenesis of the WNT5A promoter revealed that activation of WNT5A gene transcription depends primarily on a putative Egr-binding sequence between nucleotides −52 to −44, upstream of the tran...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2018 Category: Genetics & Stem Cells Source Type: research

An exon three-way junction structure modulates splicing and degradation of the SUS1 yeast pre-mRNA
Publication date: August 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 8Author(s): Ali AbuQattam, Joan Serrano-Quílez, Susana Rodríguez-Navarro, José GallegoAbstractThe SUS1 gene of Saccharomyces cerevisiae is unusual as it contains two introns and undergoes alternative splicing, retaining one or both introns depending on growth conditions. The exon located between the two introns can be skipped during splicing and has been detected in circular form. This exon (E2) has also been found to influence the splicing of the flanking introns, an unusual situat...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 14, 2018 Category: Genetics & Stem Cells Source Type: research

Regulation of the replication initiator DnaA in Caulobacter crescentus
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 10, 2018 Category: Genetics & Stem Cells Source Type: research

Bistability and phase variation in Salmonella enterica
Publication date: Available online 31 January 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Lucía García-Pastor, Elena Puerta-Fernández, Josep CasadesúsAbstractCell-to-cell differences in bacterial gene expression can merely reflect the occurrence of noise. In certain cases, however, heterogeneous gene expression is a programmed event that results in bistable expression. If bistability is heritable, bacterial lineages are formed. When programmed bistability is reversible, the phenomenon is known as phase variation. In certain cases, bistability is control...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Pseudomonas aeruginosa zinc homeostasis: Key issues for an opportunistic pathogen
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 10, 2018 Category: Genetics & Stem Cells Source Type: research

Post-transcriptional control of virulence gene expression in Staphylococcus aureus
Publication date: Available online 27 April 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Alexandre Le Scornet, Peter RedderAbstractOpportunistic pathogens have to be ready to change life-style whenever the occasion arises, and therefore need to keep tight control over the expression of their virulence factors. Doubly so for commensal bacteria, such as Staphylococcus aureus, which should avoid harming their hosts when they are in a state of peaceful co-existence. S. aureus carries very few sigma factors to help define the transcriptional programs, but instead uses a plethora of smal...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Cell division control in Caulobacter crescentus
Publication date: Available online 30 April 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Justine CollierAbstractCaulobacter crescentus is a free-living Alphaproteobacterium that thrives in oligotrophic environments. This review focuses on the regulatory network used by this bacterium to control the levels of cell division proteins, their organization inside the cell and their activity as a function of the cell cycle. Strikingly, C. crescentus makes frequent use of master transcriptional regulators and epigenetic signals, most likely to synchronize cell division with other events of...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Transcriptional regulation of development in heterocyst-forming cyanobacteria
Publication date: Available online 30 April 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Enrique Flores, Silvia Picossi, Ana Valladares, Antonia HerreroAbstractFilamentous, heterocyst-forming cyanobacteria are among the simplest multicellular systems in Nature. In the absence of combined nitrogen, the filaments consist of vegetative cells that fix CO2 through oxygenic photosynthesis and micro-oxic heterocysts specialized for the fixation of N2 in a proportion of about 10 to 1. The development of a heterocyst-containing filament involves differentiation of vegetative cells into hete...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Extracytoplasmic function sigma factors in Pseudomonas aeruginosa
Publication date: Available online 2 May 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Sylvie Chevalier, Emeline Bouffartigues, Alexis Bazire, Ali Tahrioui, Rachel Duchesne, Damien Tortuel, Olivier Maillot, Thomas Clamens, Nicole Orange, Marc G.J. Feuilloley, Olivier Lesouhaitier, Alain Dufour, Pierre CornelisAbstractThe opportunistic pathogen Pseudomonas aeruginosa, like all members of the genus Pseudomonas, has the capacity to thrive in very different environments, ranging from water, plant roots, to animals, including humans to whom it can cause severe infections. This remarkable...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Coordination of symbiosis and cell cycle functions in Sinorhizobium meliloti
Publication date: Available online 19 May 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Shuanghong Xue, Emanuele G. BiondiAbstractThe symbiotic nitrogen fixing species Sinorhizobium meliloti represents a remarkable model system for the class Alphaproteobacteria, which includes genera such as Caulobacter, Agrobacterium and Brucella. It is capable of living free in the soil, and is also able to establish a complex symbiosis with leguminous plants, during which its cell cycle program is completely rewired presumably due, at least in part, to the action of peptides secreted by the plant...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

The brassinosteroid-regulated transcription factors BZR1/BES1 function as a coordinator in multisignal-regulated plant growth
Publication date: June 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6Author(s): Qian-Feng Li, Jun Lu, Jia-Wen Yu, Chang-Quan Zhang, Jun-Xian He, Qiao-Quan LiuAbstractBZR1 and BES1 are key transcription factors of brassinosteroid (BR) signaling and represent the integration node of numerous signaling cascades. Their direct target genes have been identified, and BZR1/BES1-DNA interactions have been experimentally verified. Importantly, BZR1/BES1 also integrate different growth and development events via direct protein-protein interactions. For instance, DELLAs, PIFs, ARF6, ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: June 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

BmSUC1 is essential for glycometabolism modulation in the silkworm, Bombyx mori
In this study, we investigated sucrose hydrolysis activity in the larval midgut of B. mori by inhibition tests and found that sucrase activity mainly stemmed from β-FFase, not α-glucosidase. Next, we performed shRNA-mediated transgenic RNAi to analyze the growth characteristics of silkworm larvae and variations in glycometabolism in vivo in transgenic silkworms. The results showed that in the RNAi-BmSuc1 transgenic line, larval development was delayed, and their body size was markedly reduced. Finally, the activity of several disaccharidases alone in the midgut and the sugar distribution, total sugar and glycoge...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

A metadynamic approach to understand the recognition mechanism of the histone H3 tail with the ATRXADD domain
Publication date: June 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 6Author(s): Radha Charan Dash, Angela M. Zaino, M. Kyle HaddenAbstractThe binding affinity between the histone 3 (H3) tail and the ADD domain of ATRX (ATRXADD) increases with the subsequent addition of methyl groups on lysine 9 on H3. To improve our understanding of how the difference in methylation state affects binding between H3 and the ATRXADD, we adopted a metadynamic approach to explore the recognition mechanism between the two proteins and identify the key intermolecular interactions that mediate t...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Potential role for microRNA in regulating hypoxia-induced metabolic suppression in jumbo squids
We examined expression levels of 39 highly-conserved invertebrate microRNAs in D. gigas brain, mantle muscle, and branchial heart, comparing hypoxic and normoxic conditions. Hypoxia-inducible microRNAs are potentially involved in facilitating neuroprotection, anti-apoptosis, and regenerative mechanisms in brain; inhibiting apoptosis and cell proliferation while conserving energy in heart; and limiting damage by reactive oxygen species and apoptosis in muscle. Rather than orchestrate global metabolic rate depression, the majority of hypoxia-inducible microRNAs identified are involved in promoting cytoprotective mechanisms, ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Cdk-related kinase 9 regulates RNA polymerase II mediated transcription in Toxoplasma gondii
In this study, we functionally characterize T. gondii Cdk-related kinase 9 (TgCrk9) showing maximal homology to eukaryotic Cdk9. An uncanonical cyclin, TgCyclin L, colocalizes with TgCrk9 in the parasite nucleus and co-immunoprecipitate, could activate the kinase in-vitro. We identify two threonines in conserved T-loop domain of TgCrk9 that are important for its activity. The activated TgCrk9 phosphorylates C-terminal domain (CTD) of TgRpb1, the largest subunit of RNA polymerase II highlighting its role in transcription. Selective chemical inhibition of TgCrk9 affected serine 2 phosphorylation in the heptapeptide repeats o...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Conserved association of Argonaute 1 and 2 proteins with miRNA and siRNA pathways throughout insect evolution, from cockroaches to flies
Conclusions and general significanceThese basic associations are equivalent to those observed in D. melanogaster, implying that they have been evolutionary conserved from at least cockroach to flies, and possibly stem from the last common ancestor of extant insects. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

The histone methyltransferase SETD1A regulates thrombomodulin transcription in vascular endothelial cells
Publication date: Available online 22 June 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Zilong Li, Baoyu Chen, Xinyu Weng, Liming Yu, Mingzi Song, Mingming Fang, Junli Guo, Yong XuAbstractThrombomodulin (TM, encoded by the THBD gene) expressed in vascular endothelial cells plays pivotal roles maintaining the equilibrium of coagulation and anti-coagulation. TM levels can be regulated at the transcriptional level although the epigenetic mechanism is underexplored. Here we report that transcriptional activation of TM in both immortalized vascular endothelial cells (EAhy926) and primar...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Enhancer-driven transcriptional regulation is a potential key determinant for human visceral and subcutaneous adipocytes
Publication date: Available online 30 June 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Robert Liefke, Kristin Bokelmann, B. Michael Ghadimi, Sebastian DangoAbstractObesity is characterized by the excess of body fat leading to impaired health. Abdominal fat is particularly harmful and is associated with cardiovascular and metabolic diseases and cancer. In contrast, subcutaneous fat is generally considered less detrimental. The mechanisms that establish the cellular characteristics of these distinct fat types in humans are not fully understood. Here, we explored whether differences ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Tau/DDX6 interaction increases microRNA activity
Publication date: Available online 30 June 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Alban Chauderlier, Melissa Gilles, Andrea Spolcova, Raphaelle Caillierez, Maggy Chwastyniak, Michel Kress, Herve Drobecq, Eliette Bonnefoy, Florence Pinet, Dominique Weil, Luc Buée, Marie-Christine Galas, Bruno LefebvreAbstractTauopathies, such as Alzheimer's disease, are characterized by intracellular aggregates of insoluble Tau proteins. Originally described as a microtubule binding protein, recent studies demonstrated additional physiological roles for Tau. The fact that a single prote...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Transfer RNA-derived fragments target and regulate ribosome-associated aminoacyl-transfer RNA synthetases
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): Anna M. Mleczko, Piotr Celichowski, Kamilla Bąkowska-ŻywickaAbstractRibosome-associated noncoding (ranc) RNAs are a novel class of short regulatory RNAs with functions and origins that have not been well studied. In this present study, we functionally characterized the molecular activity of Saccharomyces cerevisiae transfer RNA (tRNA)-derived fragments (tRFs) during protein biosynthesis. Our results indicate ribosome-associated tRFs derived from both 5′ (ranc-5′-tRFs) and 3&prime...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

A Trichostatin A (TSA)/Sp1-mediated mechanism for the regulation of SALL2 tumor suppressor in Jurkat T cells
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): Matías I. Hepp, David Escobar, Carlos Farkas, Viviana E. Hermosilla, Claudia Álvarez, Roberto Amigo, José L. Gutiérrez, Ariel F. Castro, Roxana PincheiraAbstractSALL2 is a transcription factor involved in development and disease. Deregulation of SALL2 has been associated with cancer, suggesting that it plays a role in the disease. However, how SALL2 is regulated and why is deregulated in cancer remain poorly understood. We previously showed that the p53 tumor suppre...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Histone variants H3.3 and H2A.Z are incorporated into the β-globin locus during transcription activation via different mechanisms
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): Jin Kang, Yea Woon Kim, AeRi KimAbstractHistone variants H3.3 and H2A.Z are often enriched in enhancers and transcriptionally active genes. However, the incorporation dynamics of these variants and the mechanisms of their incorporation are unclear. Here, we examined the distribution of H3.3 and H2A.Z in the human β-globin locus and analyzed their incorporation dynamics during transcription activation. Locus control region hypersensitive sites (LCR HSs), acting as enhancers, and active glo...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Retraction notice to Retraction notice to WRKY71 and TGA1a physically interact and synergistically regulate the activity of a novel promoter isolated from Petunia vein-clearing virus BBAGRM 1861/2 (2018) 133-146]
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): Ankita Shrestha, Ahamed Khan, Dipti Ranjan Mishra, Kashyap Bhuyan, Bhabani Sahoo, Indu B. Maiti, Nrisingha Dey (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Human PRDM2: Structure, function and pathophysiology
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): A. Sorrentino, M. Rienzo, A. Ciccodicola, A. Casamassimi, C. AbbondanzaAbstractPRDM2/RIZ is a member of a superfamily of histone/protein methyltransferases (PRDMs), which are characterized by the conserved N-terminal PR domain, with methyltransferase activity and zinc finger arrays at the C-terminus. Similar to other family members, two main protein types, known as RIZ1 and RIZ2, are produced from the PRDM2 locus differing by the presence or absence of the PR domain. The imbalance in their res...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

MicroRNAs of miR-17-92 cluster increase gene expression by targeting mRNA-destabilization pathways
In this study, we globally analyzed AGO2-bound mRNAs and found that the miR-17-92 miRNAs coherently repress multiple targets involved in the destabilization of mRNA. While the miRNAs repress the expression of their targets, they increase stability and lengthen the poly-A tails of non-target mRNAs. Furthermore, the expression of BTG3, TOB1, CSNK1A1 and ANKRD52 is negatively correlated with the expression of the miR-17-92 cluster in cancer cell lines. Our results suggest that the miR-17-92 miRNAs promote tumorigenesis not only by repression of key regulators, but also by posttranscriptional increases of global gene expressio...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening
Publication date: July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1861, Issue 7Author(s): Chun-Bo Song, Wei Shan, Ying-Ying Yang, Xiao-Li Tan, Zhong-Qi Fan, Jian-Ye Chen, Wang-Jin Lu, Jian-Fei KuangAbstractThe biological processes involved in banana fruit ripening are extremely complex and modulated by a number of genes such as transcription factors (TFs). Although TFs like MADS, ERF and NAC are implicated in controlling banana ripening, little is known about other TFs such as TCP in this process. In this work, 25 MaTCPs named MaTCP1 to MaTCP25 were characterized from our previousl...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

The impact of the vitamin D-modulated epigenome on VDR target gene regulation
This study focuses on histone marks of active chromatin at promoter and enhancer regions and investigates, whether these genomic loci are sensitive to vitamin D. The epigenome of THP-1 human monocytes contains nearly 23,000 sites with H3K4me3 histone modifications, 550 of which sites are significantly (p 
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells
This study also issues an important cautionary note concerning the design and interpretation of any experiments using cells and tissues where CTCF180 may be present. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Transcription factor 21 regulates expression of ERβ and SF-1 via upstream stimulatory factor-2 in endometriotic tissues
Publication date: Available online 7 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Pei-Li Wu, Yan Zhou, Cheng Zeng, Xin Li, Zhao-Tong Dong, Ying-Fang Zhou, Serdar E. Bulun, Qing XueAbstractSteroidogenic factor-1 (SF-1, encoded by NR5A1) and estrogen receptor beta (ERβ, encoded by ESR2), which are highly expressed in endometriotic stromal cells (ESCs), contribute to the pathogenesis of endometriosis, but the regulation mechanism remains largely unknown. Transcription factor 21 (TCF21) belongs to the helix-loop-helix (bHLH) family characterized by regulating gene expression ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Mediator, known as a coactivator, can act in transcription initiation in an activator-independent manner in vivo
Publication date: Available online 7 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Hélène Jean-Jacques, Siew Lay Poh, Laurent KurasAbstractMediator is an evolutionarily conserved complex best known for its role as a coactivator responsible for transducing regulatory signals from DNA-bound activators to the basal RNA polymerase II (Pol II) machinery that initiates transcription from promoters of protein-encoding genes. By exploiting our in vivo activator-independent transcription assay in Saccharomyces cerevisiae, in combination with new temperature sensitive (ts) ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 10, 2018 Category: Genetics & Stem Cells Source Type: research

Transcription factor 21 regulates expression of ERβ and SF-1 via upstream stimulatory factor-2 in endometriotic tissues
Publication date: Available online 7 July 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Pei-Li Wu, Yan Zhou, Cheng Zeng, Xin Li, Zhao-Tong Dong, Ying-Fang Zhou, Serdar E. Bulun, Qing XueAbstractSteroidogenic factor-1 (SF-1, encoded by NR5A1) and estrogen receptor beta (ERβ, encoded by ESR2), which are highly expressed in endometriotic stromal cells (ESCs), contribute to the pathogenesis of endometriosis, but the regulation mechanism remains largely unknown. Transcription factor 21 (TCF21) belongs to the helix-loop-helix (bHLH) family characterized by regulating gene expression ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 7, 2018 Category: Genetics & Stem Cells Source Type: research

Regulation of the replication initiator DnaA in Caulobacter crescentus
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 5, 2018 Category: Genetics & Stem Cells Source Type: research

Bistability and phase variation in Salmonella enterica
Publication date: Available online 31 January 2018Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Lucía García-Pastor, Elena Puerta-Fernández, Josep CasadesúsAbstractCell-to-cell differences in bacterial gene expression can merely reflect the occurrence of noise. In certain cases, however, heterogeneous gene expression is a programmed event that results in bistable expression. If bistability is heritable, bacterial lineages are formed. When programmed bistability is reversible, the phenomenon is known as phase variation. In certain cases, bistability is control...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 5, 2018 Category: Genetics & Stem Cells Source Type: research