284 results match your criteria Biochimica et biophysica acta. Gene regulatory mechanisms[Journal]


Zbtb7c is a critical gluconeogenic transcription factor that induces glucose-6-phosphatase and phosphoenylpyruvate carboxykinase 1 genes expression during mice fasting.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 5. Epub 2019 Apr 5.

BK21 plus project of Medical Science, Department of Biochemistry and Molecular Biology, Yonsei University School of Medicine, 50-1 Yonsei-Ro, SeoDaeMoon-Ku, Seoul 03722, Republic of Korea. Electronic address:

Gluconeogenesis is essential for blood glucose homeostasis during fasting and is regulated by various enzymes, which are encoded by gluconeogenic genes. Those genes are controlled by various transcription factors. Zinc finger and BTB domain-containing 7c (Zbtb7c, also called Kr-pok) is a BTB-POZ family transcription factor with proto-oncogenic activity. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.04.001DOI Listing
April 2019
1 Read
6.332 Impact Factor

IsomiRs: Expanding the miRNA repression toolbox beyond the seed.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 4. Epub 2019 Apr 4.

RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States. Electronic address:

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play increasingly appreciated roles in gene regulation. In animals, miRNAs silence gene expression by binding to partially complementary sequences within target mRNAs. It is well-established that miRNAs recognize canonical target sites by base-pairing in the 5'region. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183053
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http://dx.doi.org/10.1016/j.bbagrm.2019.03.005DOI Listing
April 2019
4 Reads

Adaptor proteins in long noncoding RNA biology.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 2. Epub 2019 Apr 2.

Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. Electronic address:

Long noncoding RNAs (lncRNAs) are a heterogeneous class of noncoding RNAs that have gained increasing attention due to their vital roles in the regulation of diverse cellular processes. Because lncRNAs are generally expressed at low levels, are poorly conserved, and can act via diverse mechanisms, investigating the molecular mechanisms by which lncRNAs act is challenging. Similar to mRNAs, lncRNAs bind to RNA-binding proteins (RBPs) and in some cases, have been shown to regulate the activity of the RBP they bind to. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.03.003DOI Listing
April 2019
5 Reads

A non-autonomous role of MKL1 in the activation of hepatic stellate cells.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 2;1862(6):609-618. Epub 2019 Apr 2.

Institute of Biomedical Research, Liaocheng University, Liaocheng, China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China. Electronic address:

Although hepatic stellate cells (HSC) represent the major source of fibrogenesis in the liver under various pathological conditions, other cell types including hepatic parenchymal cells (hepatocytes) also contribute to HSC activation and hence liver fibrosis. The underlying mechanism, however, is poorly defined. Here we report that hepatocytes exposed to high concentrations of glucose (HG) emit a pro-fibrogenic cue as evidenced by the observation that primary HSCs cultured in conditioned media (CM) collected from hepatocytes exposed to HG up-regulated the production of extracellular matrix (ECM) proteins compared to CM collected from hepatocytes exposed to low glucose. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.03.001DOI Listing
April 2019
2 Reads

Inhibition of lysine-specific demethylase LSD1 induces senescence in Glioblastoma cells through a HIF-1α-dependent pathway.

Biochim Biophys Acta Gene Regul Mech 2019 May 2;1862(5):535-546. Epub 2019 Apr 2.

Department of Biology, University of Naples 'Federico II', Naples, Italy. Electronic address:

Senescence is a stress-responsive cellular program that leads to cell cycle arrest. In cancer cells, senescence has profound implications for tumor aggressiveness and clinical outcome, but the molecular events that provoke cancer cells to undergo senescence remain unclear. Herein, we provide evidence that the histone demethylase LSD1/KDM1A supports the growth of Glioblastoma tumor cells and its inhibition triggers senescence response. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.03.004DOI Listing
May 2019
2 Reads

Circular RNAs in myogenesis.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 1. Epub 2019 Apr 1.

Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India. Electronic address:

Skeletal muscles have an immense ability to regenerate from the muscle stem cells called satellite cells. The process of skeletal muscle regeneration is called myogenesis, which starts with activation of quiescent satellite cells immediately after muscle injury followed by proliferation and fusion of myoblasts into myotubes. Myogenesis is orchestrated through the expression of a specific set of genes which, at each step regulated by complex gene regulatory networks. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.011DOI Listing
April 2019
2 Reads

The chromatin remodeling protein BRM regulates the transcription of tight junction proteins: Implication in breast cancer metastasis.

Biochim Biophys Acta Gene Regul Mech 2019 May 2;1862(5):547-556. Epub 2019 Apr 2.

Institute of Biomedical Research, Liaocheng University, Liaocheng, China; Key Laboratory of Targeted Intervention of Cardiovascular Disease and Innovative Collaboration Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China. Electronic address:

Claudins are a group of cell tight junction proteins that play versatile roles in cancer biology. Recent studies have correlated down-regulation of Claudins with augmented breast cancer malignancy and poor prognosis. The mechanism underlying repression of Claudin transcription in breast cancer cells is not well understood. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.03.002DOI Listing
May 2019
1 Read

Dicer1 is required for pigment cell and craniofacial development in zebrafish.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 3;1862(4):472-485. Epub 2019 Mar 3.

Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina. Electronic address:

The multidomain RNase III endoribonuclease DICER is required for the generation of most functional microRNAs (miRNAs). Loss of Dicer affects developmental processes at different levels. Here, we characterized the zebrafish Dicer1 mutant, dicer1, which has a single point mutation induced by N-ethyl-N-nitrosourea mutagenesis. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.005DOI Listing
April 2019
1 Read

Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 2;1862(4):457-471. Epub 2019 Mar 2.

Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina-CSIC, Valencia, Spain. Electronic address:

Cells respond to external stimuli with transient gene expression changes in order to adapt to environmental alterations. However, the dose response profile of gene induction upon a given stress depends on many intrinsic and extrinsic factors. Here we show that the accurate quantification of dose dependent gene expression by live cell luciferase reporters reveals fundamental insights into stress signaling. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.009DOI Listing
April 2019
1 Read

RNA modifications in gene expression control.

Biochim Biophys Acta Gene Regul Mech 2019 Mar;1862(3):219-221

School of Life Science, Plant Science Division, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, United Kingdom.

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.010DOI Listing

Leukocyte integrin signaling regulates FOXP1 gene expression via FOXP1-IT1 long non-coding RNA-mediated IRAK1 pathway.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 2;1862(4):493-508. Epub 2019 Mar 2.

Harrington Heart & Vascular Institute, University Hospitals Cleveland Medical Center, Case Cardiovascular Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.

Leukocyte integrin-dependent downregulation of the transcription factor FOXP1 is required for monocyte differentiation and macrophage functions, but the precise gene regulatory mechanism is unknown. Here, we identify multi-promoter structure (P1, P2, and P3) of the human FOXP1 gene. Clustering of the β-leukocyte integrin Mac-1 downregulated transcription from these promoters. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.008DOI Listing
April 2019
16 Reads

The nuclear receptors PXR and LXR are regulators of the scaffold protein PDZK1.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 1;1862(4):447-456. Epub 2019 Mar 1.

Biopharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland. Electronic address:

PDZK1 (NHERF3) interacts with membrane proteins whereby modulating their spatial arrangement, membrane stability, and function. One of the membrane proteins shown to be stabilized by interaction with PDZK1 is the HDL-receptor SR-BI (SCARB1). Testing the influence of TO 901317, a known activator of liver X receptor alpha (LXRα, NR1H3) which is a central regulator of the lipid homeostasis, Grefhorst et al. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183028
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http://dx.doi.org/10.1016/j.bbagrm.2019.02.007DOI Listing
April 2019
3 Reads

The complex CBX7-PRMT1 has a critical role in regulating E-cadherin gene expression and cell migration.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 28;1862(4):509-521. Epub 2019 Feb 28.

Istituto di Endocrinologia ed Oncologia Sperimentale - CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy. Electronic address:

The Chromobox protein homolog 7 (CBX7) belongs to the Polycomb Group (PcG) family, and, as part of the Polycomb repressive complex (PRC1), contributes to maintain transcriptional gene repression. Loss of CBX7 expression has been reported in several human malignant neoplasias, where it often correlates with an advanced cancer state and poor survival, proposing CBX7 as a candidate tumor-suppressor gene in cancer progression. Indeed, CBX7 is able to positively or negatively regulate the expression of genes involved in cell proliferation and cancer progression, such as E-cadherin, cyclin E, osteopontin, EGR1. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.006DOI Listing
April 2019
1 Read

The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 27;1862(4):486-492. Epub 2019 Feb 27.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America. Electronic address:

The bZIP homodimers CEBPB and CREB1 bind DNA containing methylated cytosines differently. CREB1 binds stronger to the C/EBP half-site GCAA when the cytosine is methylated. For CEBPB, methylation of the same cytosine does not affect DNA binding. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183040
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http://dx.doi.org/10.1016/j.bbagrm.2019.02.002DOI Listing
April 2019
6 Reads

Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription.

Biochim Biophys Acta Gene Regul Mech 2019 May 23;1862(5):598-607. Epub 2019 Feb 23.

Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address:

In eukaryotes, cytosine methylation of nuclear DNA at CpG sequences (CpG) regulates epigenetic inheritance through alterations in chromatin structure. However, mitochondria lack nucleosomal chromatin, therefore the molecular mechanisms by which CpG influences mitochondria must be different and are as yet unknown. Mitochondrial Transcription Factor A (TFAM) is both the primary DNA-compacting protein in the mitochondrial DNA (mtDNA) nucleoid and a transcription-initiation factor. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.01.006DOI Listing
May 2019
1 Read

Regulatory effect of host miR-101b-3p on parasitism of nematode Angiostrongylus cantonensis via superoxide dismutase 3.

Biochim Biophys Acta Gene Regul Mech 2019 May 11;1862(5):557-566. Epub 2019 Feb 11.

Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Tropical Diseases Control (SYSU), Ministry of Education, Guangzhou 510080, China; Provincial Engineering Technology Research Center for Diseases-vectors Control, Guangdong, Guangzhou 510080, China. Electronic address:

MicroRNA plays a vital role in the regulation of host-parasite interaction. In recent years, genomic and transcriptomic resources have become increasingly available for many helminths, but only a limited number of reports in this area are on the regulatory effects of host microRNAs on parasitic nematodes. In this work, we screened increased expression of host microRNAs after nematode infection from miRNA-seq data and predicted target genes by combined bioinformatics analysis and transcriptional profiling. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.004DOI Listing
May 2019
2 Reads

Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to "GAGAG" sequence motif present in Polycomb response elements.

Biochim Biophys Acta Gene Regul Mech 2019 May 10;1862(5):582-597. Epub 2019 Feb 10.

Division of Plant Biology, Bose Institute, Kolkata 700054, India. Electronic address:

Co-ordinated interplay between Polycomb group (PcG) and Trithorax group (TrxG) of proteins regulate chromatin state and maintain the transcription "off" and "on" state of a gene in higher eukaryotes. Targeting PcG complex to a specific locus is mediated by DNA sequences known as Polycomb response elements. Interestingly, these PREs are also recognized by TrxG proteins to antagonise PcG mediated gene repression. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.001DOI Listing
May 2019
1 Read

MiR-15/16 mediate crosstalk between the MAPK and Wnt/β-catenin pathways during hepatocyte differentiation from amniotic epithelial cells.

Biochim Biophys Acta Gene Regul Mech 2019 May 10;1862(5):567-581. Epub 2019 Feb 10.

Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of precision medicine, Jining Medical University, Jining, Shandong 272067, PR China; College of Basic Medicine, Jining Medical University, Jining, Shandong 272067, PR China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China. Electronic address:

MiR-15/16 play an important role in liver development and hepatocyte differentiation, but the mechanisms by which these miRNAs regulate their targets and downstream genes to influence cell fate are poorly understood. In this study, we showed up-regulation of miR-15/16 during HGF- and FGF4-induced hepatocyte differentiation from amniotic epithelial cells (AECs). To elucidate the role of miR-15/16 and their targets in hepatocyte differentiation, we investigated the roles of miR-15/16 in both the MAPK and Wnt/β-catenin pathways, which were predicted to be involved in miR-15/16 signaling. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.02.003DOI Listing
May 2019
1 Read

LPS promotes HBO1 stability via USP25 to modulate inflammatory gene transcription in THP-1 cells.

Biochim Biophys Acta Gene Regul Mech 2018 Sep 4;1861(9):773-782. Epub 2018 Aug 4.

Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213.

The 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. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368258PMC
September 2018
9 Reads

Epigenetic silencing of the synthesis of immunosuppressive Siglec ligand glycans by NF-κB/EZH2/YY1 axis in early-stage colon cancers.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 1;1862(2):173-183. Epub 2019 Feb 1.

Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. Electronic address:

Normal colonic epithelial cells express sialyl 6-sulfo Lewis and disialyl Lewis on their cell surface, which are ligands for the immunosuppressive molecule Siglec-7. Expression of these normal glycans is frequently lost upon malignant transformation by silencing DTDST and ST6GalNAc6 at the early stage of colorectal carcinogenesis, and leads to production of inflammatory mediators that facilitate carcinogenesis. Indeed, by querying The Cancer Genome Atlas datasets, we confirmed that the level of DTDST or ST6GalNAc6 mRNA is substantially decreased at the early stage of colorectal carcinogenesis. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.01.002DOI Listing
February 2019
3 Reads

Delineation of critical amino acids in activation function 1 of progesterone receptor for recruitment of transcription coregulators.

Biochim Biophys Acta Gene Regul Mech 2019 Apr 1;1862(4):522-533. Epub 2019 Feb 1.

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore. Electronic address:

The activation functions AF1 and AF2 of nuclear receptors mediate the recruitment of coregulators in gene regulation. AF1 is mapped to the highly variable and intrinsically unstructured N terminal domain and AF2 lies in the conserved ligand binding domain. The unstructured nature of AF1 offers structural plasticity and hence functional versatility in gene regulation. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183047
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http://dx.doi.org/10.1016/j.bbagrm.2019.01.004DOI Listing
April 2019
7 Reads

Class II transactivator (CIITA) mediates IFN-γ induced eNOS repression by enlisting SUV39H1.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 1;1862(2):163-172. Epub 2019 Feb 1.

Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China. Electronic address:

Endothelial nitric oxide synthase (eNOS), selectively expressed in vascular endothelial cells, plays important roles in a range of biological and pathological processes. eNOS levels can be altered by extrinsic and intrinsic cues at the transcriptional level. Here we examined the epigenetic mechanism whereby the pro-inflammatory cytokine interferon gamma (IFN-γ) represses eNOS transcription. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183037
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http://dx.doi.org/10.1016/j.bbagrm.2019.01.005DOI Listing
February 2019
7 Reads
6.332 Impact Factor

Hallmarks of HPV carcinogenesis: The role of E6, E7 and E5 oncoproteins in cellular malignancy.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 29;1862(2):153-162. Epub 2019 Jan 29.

Molecular Oncology and Viral Pathology Group, IPO-Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; FMUP, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; LPCC, Research Department Portuguese League Against Cancer (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), Estrada Interior da Circunvalação, no. 6657, 4200-177 Porto, Portugal; CEBIMED, Faculty of Health Sciences, Fernando Pessoa University, Porto, Portugal. Electronic address:

Human papillomavirus (HPV) is the most common sexually transmitted infectious agent worldwide, being also responsible for 5% of all human cancers. The integration and hypermethylation mechanisms of the HPV viral genome promote the unbalanced expression of the E6, E7 and E5 oncoproteins, which are crucial factors for the carcinogenic cascade in HPV-induced cancers. This review highlights the action of E6, E7 and E5 over key regulatory targets, promoting all known hallmarks of cancer. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2019.01.001DOI Listing
February 2019

Characterization of Toxoplasma gondii Spt5 like transcription elongation factor.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 29;1862(2):184-197. Epub 2019 Jan 29.

National Institute of Animal Biotechnology, Hyderabad, India.

Elongation has emerged as a highly regulated step in the multistage process of transcription. Control of gene expression mediated through transcription elongation remains an unexplored area of study in Toxoplasma gondii where the demands of complex lifecycle necessitate a regulated transcription program. Here, we elucidate the central role of Spt5 homolog in T. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183043
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http://dx.doi.org/10.1016/j.bbagrm.2019.01.003DOI Listing
February 2019
9 Reads

Readers of the mA epitranscriptomic code.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 17;1862(3):329-342. Epub 2019 Jan 17.

LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France. Electronic address:

N-methyl adenosine (mA) is the most prevalent and evolutionarily conserved, modification of polymerase II transcribed RNAs. By post-transcriptionally controlling patterns of gene expression, mA deposition is crucial for organism reproduction, development and likely stress responses. mA mostly mediates its effect by recruiting reader proteins that either directly accommodate the modified residue in a hydrophobic pocket formed by their YTH domain, or otherwise have their affinity positively influenced by the presence of mA. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.12.008DOI Listing
March 2019
4 Reads

The adaptive potential of RNA editing-mediated miRNA-retargeting in cancer.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 31;1862(3):291-300. Epub 2018 Dec 31.

RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy. Electronic address:

A-to-I RNA editing is a post-transcriptional mechanism that converts the genomically coded Adenosine (A) into Inosine (I) at the RNA level. This type of RNA editing is the most frequent in humans and is mediated by the ADAR enzymes. RNA editing can alter the genetic code of mRNAs, but also affect the functions of noncoding RNAs such as miRNAs. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183047
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http://dx.doi.org/10.1016/j.bbagrm.2018.12.007DOI Listing
March 2019
12 Reads

Epigenetic regulation of carnitine palmitoyltransferase 1 (Cpt1a) by high fat diet.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 31;1862(2):141-152. Epub 2018 Dec 31.

Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America; Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States of America. Electronic address:

Carnitine palmitoyltransferase 1 (Cpt1a) is a rate-limiting enzyme that mediates the transport of fatty acids into the mitochondria for subsequent beta-oxidation. The objective of this study was to uncover how diet mediates the transcriptional regulation of Cpt1a. Pregnant Sprague Dawley rats were exposed to either a high-fat (HF) or low-fat control diet during gestation and lactation. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183034
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http://dx.doi.org/10.1016/j.bbagrm.2018.12.009DOI Listing
February 2019
10 Reads

Role of long non-coding RNAs in metabolic control.

Biochim Biophys Acta Gene Regul Mech 2018 Dec 27. Epub 2018 Dec 27.

Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea. Electronic address:

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression by influencing various biological processes including proliferation, apoptosis, differentiation, and senescence. Accumulating evidence implicates lncRNAs in the maintenance of metabolic homeostasis; dysregulation of certain lncRNAs promotes the progression of metabolic disorders such as diabetes, obesity, and cardiovascular diseases. In this review, we discuss our understanding of lncRNAs implicated in metabolic control, focusing on in particular diseases arising from chronic inflammation, insulin resistance, and lipid homeostasis. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.12.006DOI Listing
December 2018
1 Read

Post-transcriptional regulation by cytosine-5 methylation of RNA.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 27;1862(3):240-252. Epub 2018 Dec 27.

CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain.. Electronic address:

The recent advent of high-throughput sequencing technologies coupled with RNA modifications detection methods has allowed the detection of RNA modifications at single nucleotide resolution giving a more comprehensive landscape of post-transcriptional gene regulation pathways. In this review, we focus on the occurrence of 5-methylcytosine (mC) in the transcriptome. We summarise the main findings of the molecular role in post-transcriptional regulation that governs mC deposition in RNAs. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183034
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http://dx.doi.org/10.1016/j.bbagrm.2018.12.003DOI Listing
March 2019
17 Reads

The synergy between RSC, Nap1 and adjacent nucleosome in nucleosome remodeling.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 26;1862(2):129-140. Epub 2018 Dec 26.

Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan. Electronic address:

Eukaryotes have evolved a specific strategy to package DNA. The nucleosome is a 147-base-pair DNA segment wrapped around histone core proteins that plays important roles regulating DNA-dependent biosynthesis and gene expression. Chromatin remodeling complexes (RSC, Remodel the Structure of Chromatin) hydrolyze ATP to perturb DNA-histone contacts, leading to nucleosome sliding and ejection. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.11.008DOI Listing
February 2019

RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 17;1862(3):253-269. Epub 2018 Dec 17.

UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France. Electronic address:

Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.11.009DOI Listing
March 2019
1 Read

Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 14;1862(2):119-128. Epub 2018 Dec 14.

Laboratory of Biosystem Dynamics, BioMediTech Institute and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, 33101 Tampere, Finland. Electronic address:

Genetic circuits change the status quo of cellular processes when their protein numbers cross thresholds. We investigate the regulation of RNA and protein threshold crossing propensities in Escherichia coli. From in vivo single RNA time-lapse microscopy data from multiple promoters, mutants, induction schemes and media, we study the asymmetry and tailedness (quantified by the skewness and kurtosis, respectively) of the distributions of time intervals between transcription events. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.12.005DOI Listing
February 2019
2 Reads

The role of RNA adenosine demethylases in the control of gene expression.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 11;1862(3):343-355. Epub 2018 Dec 11.

Central European Institute of Technology (CEITEC), Masaryk University, Brno 625 00, Czech Republic. Electronic address:

RNA modifications are being recognized as an essential factor in gene expression regulation. They play essential roles in germ line development, differentiation and disease. In eukaryotic mRNAs, N-adenosine methylation (mA) is the most prevalent internal chemical modification identified to date. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.12.001DOI Listing
March 2019
1 Read

m6A modification of non-coding RNA and the control of mammalian gene expression.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 11;1862(3):310-318. Epub 2018 Dec 11.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

The biology of non-coding RNA (ncRNA) and the regulation of mammalian gene expression is a rapidly expanding field. In this review, we consider how recent advances in technology, enabling the precise mapping of modifications to RNA transcripts, has provided new opportunities to dissect post-transcriptional gene regulation. With this has come the realisation that in the absence of translation, the modification of ncRNAs may play a fundamental role in their regulation, protein interactome and subsequent downstream effector functions. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.12.002DOI Listing
March 2019
3 Reads

Modulation of vitamin D signaling by the pioneer factor CEBPA.

Biochim Biophys Acta Gene Regul Mech 2019 Jan 11;1862(1):96-106. Epub 2018 Dec 11.

School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland. Electronic address:

The myeloid master regulator CCAAT enhancer-binding protein alpha (CEBPA) is known as a pioneer factor. In this study, we report the CEBPA cistrome of THP-1 human monocytes after stimulation with the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D (1,25(OH)D) for 2, 8 and 24 h. About a third of the genomic VDR binding sites co-located with those of CEBPA. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183041
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http://dx.doi.org/10.1016/j.bbagrm.2018.12.004DOI Listing
January 2019
13 Reads
6.332 Impact Factor

The mammalian mitochondrial epitranscriptome.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 4;1862(3):429-446. Epub 2018 Dec 4.

MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK. Electronic address:

Correct expression of the mitochondrially-encoded genes is critical for the production of the components of the oxidative phosphorylation machinery. Post-transcriptional modifications of mitochondrial transcripts have been emerging as an important regulatory feature of mitochondrial gene expression. Here we review the current knowledge on how the mammalian mitochondrial epitranscriptome participates in regulating mitochondrial homeostasis. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414753PMC
March 2019
1 Read
6.332 Impact Factor

The emerging impact of tRNA modifications in the brain and nervous system.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 5;1862(3):412-428. Epub 2018 Dec 5.

Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA. Electronic address:

A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.11.007DOI Listing
March 2019
6.332 Impact Factor

A positive feedback regulation of Heme oxygenase 1 by CELF1 in cardiac myoblast cells.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 30;1862(2):209-218. Epub 2018 Nov 30.

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

As an RNA binding protein, CUG-BP Elav-like family (CELF) has been shown to be critical for heart biological functions. However, no reports have revealed the function of CELF1 in hypertrophic cardiomyopathy (HCM). Hinted by RNA immunoprecipitation-sequencing (RIP-seq) data, the influence of the CELF protein on heme oxygenase-1 (HO-1) expression was tested by modulating CELF1 levels. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183027
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http://dx.doi.org/10.1016/j.bbagrm.2018.11.006DOI Listing
February 2019
14 Reads
6.332 Impact Factor

Coregulatory long non-coding RNA and protein-coding genes in serum starved cells.

Biochim Biophys Acta Gene Regul Mech 2019 Jan 29;1862(1):84-95. Epub 2018 Nov 29.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, United States of America. Electronic address:

Serum starvation is widely used in cell biology to trigger cell cycle arrest, apoptosis, autophagy, and metabolic adaptations. Serum starvation-related molecular events have been well characterized at protein level but not at transcript level: how long non-coding RNAs contribute to the regulation of protein-coding genes is largely unknown. Here, we captured the lncRNA transcriptome in serum starved mouse embryonic fibroblasts and identified three main modes of action: cis-acting/coregulatory, trans-acting, and "miRNA-carrier". Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183043
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http://dx.doi.org/10.1016/j.bbagrm.2018.11.004DOI Listing
January 2019
5 Reads

Interaction of positive coactivator 4 with histone 3.3 protein is essential for transcriptional activation of the luteinizing hormone receptor gene.

Biochim Biophys Acta Gene Regul Mech 2018 Oct 13;1861(10):971-981. Epub 2018 Sep 13.

Section on Molecular Endocrinology, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

The luteinizing hormone receptor (LHR) is essential for sexual development and reproduction in mammals. We have established that Sp1 has a central role in derepression of LHR gene transcription induced by Trichostatin A (TSA) in MCF7 cells. Moreover, the co-activator PC4 which associates directly with Sp1 at the LHR promoter is essential for TSA-mediated LHR transcription. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.09.002DOI Listing
October 2018
1 Read
6.332 Impact Factor

HDAC1 interacts with the p50 NF-?B subunit via its nuclear localization sequence to constrain inflammatory gene expression.

Biochim Biophys Acta Gene Regul Mech 2018 Oct 10;1861(10):962-970. Epub 2018 Sep 10.

Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, UK. Electronic address:

The NF-?B 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-?B subunit to activate inflammatory genes. However, p50 also forms homodimers which actively repress NF-?B-dependent inflammatory gene expression and exert an important brake on the inflammatory process. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.09.001DOI Listing
October 2018

Sensory domain of the cell cycle kinase CckA regulates the differential DNA binding of the master regulator CtrA in Caulobacter crescentus.

Biochim Biophys Acta Gene Regul Mech 2018 Oct 31;1861(10):952-961. Epub 2018 Aug 31.

School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, Kerala, India. Electronic address:

Sophisticated 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. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.08.006DOI Listing
October 2018
1 Read

RNA localization and transport.

Authors:
Beat Suter

Biochim Biophys Acta Gene Regul Mech 2018 Oct 29;1861(10):938-951. Epub 2018 Aug 29.

Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland. Electronic address:

RNA 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 been documented to accumulate in specific subcellular compartments. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.08.004DOI Listing
October 2018
10 Reads

CIRCE element evolved for the coordinated transcriptional regulation of bacterial duplicate groELs.

Biochim Biophys Acta Gene Regul Mech 2018 Oct 26;1861(10):928-937. Epub 2018 Aug 26.

State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China. Electronic address:

Chaperonin groEL genes are duplicated in approximately 20% of bacteria, and the duplicates are differentially transcribed due to their divergent functions. The coordinated regulation of this differential transcription is as yet undetermined. 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. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183029
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http://dx.doi.org/10.1016/j.bbagrm.2018.08.003DOI Listing
October 2018
17 Reads

Hypermethylated in cancer 1 (HIC1) mediates high glucose induced ROS accumulation in renal tubular epithelial cells by epigenetically repressing SIRT1 transcription.

Biochim Biophys Acta Gene Regul Mech 2018 Oct 25;1861(10):917-927. Epub 2018 Aug 25.

Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, Nanjing Medical University, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China. Electronic address:

Reactive oxygen species (ROS) is a key regulator of an array of physiological and pathological processes. While essential for the host defense mechanism, excessive ROS generation and/or deficient clearance is blamed for the pathogenesis of human diseases. In the present study, we investigated the regulatory role of hypermethylated in cancer 1 (HIC1), a transcription factor, in high glucose-induced ROS accumulation in renal tubular epithelial cells (HK-2). Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.08.002DOI Listing
October 2018
2 Reads

Deletion of an intronic HIF-2α binding site suppresses hypoxia-induced WT1 expression.

Biochim Biophys Acta Gene Regul Mech 2019 Jan 20;1862(1):71-83. Epub 2018 Nov 20.

Institut für Vegetative Physiologie, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany. Electronic address:

Hypoxia-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-risk neuroblastoma. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.11.003DOI Listing
January 2019
12 Reads

Changes in Fluorescence Recovery After Photobleaching (FRAP) as an indicator of SOX9 transcription factor activity.

Biochim Biophys Acta Gene Regul Mech 2019 Jan 20;1862(1):107-117. Epub 2018 Nov 20.

Developmental BioEngineering, University of Twente, Drienerlolaan 5, 7522NB Enschede, the Netherlands. Electronic address:

Cells 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. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2018.11.001DOI Listing
January 2019
14 Reads

Comprehensive analysis of chromatin signature and transcriptome uncovers functional lncRNAs expressed in nephron progenitor cells.

Biochim Biophys Acta Gene Regul Mech 2019 Jan 14;1862(1):58-70. Epub 2018 Sep 14.

Medical and Research Services, Greater Los Angeles Veterans Affairs Healthcare System at Sepulveda, North Hills, CA, USA; University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA. Electronic address:

Emerging evidence from recent studies has unraveled the roles of long noncoding RNAs (lncRNAs) in the function of various tissues. However, little is known about the roles of lncRNAs in kidney development. In our present study, we aimed to identify functional lncRNAs in one of the three lineages of kidney progenitor cells, i. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183019
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http://dx.doi.org/10.1016/j.bbagrm.2018.09.006DOI Listing
January 2019
11 Reads

EP300-HDAC1-SWI/SNF functional unit defines transcription of some DNA repair enzymes during differentiation of human macrophages.

Biochim Biophys Acta Gene Regul Mech 2019 Feb 8;1862(2):198-208. Epub 2018 Nov 8.

Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland. Electronic address:

Differentiation 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. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183034
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http://dx.doi.org/10.1016/j.bbagrm.2018.10.019DOI Listing
February 2019
4 Reads

Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs.

Biochim Biophys Acta Gene Regul Mech 2019 Mar 8;1862(3):230-239. Epub 2018 Nov 8.

University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA. Electronic address:

Pseudouridylation is a post-transcriptional isomerization reaction that converts a uridine to a pseudouridine (Ψ) within an RNA chain. Ψ has chemical properties that are distinct from that of uridine and any other known nucleotides. Experimental data accumulated thus far have indicated that Ψ is present in many different types of RNAs, including coding and noncoding RNAs. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18749399183019
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http://dx.doi.org/10.1016/j.bbagrm.2018.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401265PMC
March 2019
17 Reads