Publications associées à Dinucléotide CpG

DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

Background Puberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early and late pubertal onset are both associated with various diseases developing later in life, and epigenetic c ...

BMC2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

John Maddocks, Rahul Sharma, Alessandro Samuele Patelli, Lennart de Bruin

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

Elsevier2023

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

Didier Trono, Evaristo Jose Planet Letschert, Shaoline Sheppard, Christopher James Playfoot

Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional co ...

2022

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Jacques Fellay, Konstantin Popadin, Dmitrii Iliushchenko, Stepan Denisov

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are ...

OXFORD UNIV PRESS2022

High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites

Ludovica Vanzan

Binding of mammalian transcription factors (TFs) to regulatory regions is hindered by chromatin compaction and DNA methylation of their binding sites. Nevertheless, pioneer transcription factors (PFs), a distinct class of TFs, have the ability to access nu ...

Nature Research2021

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation

Ludovica Vanzan

Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated geno ...

OXFORD UNIV PRESS2021

Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer

Gerard Llimos Aubach

This study addresses the roles of nuclear receptor corepressor 2 (NCOR2) in prostate cancer (PC) progression in response to androgen deprivation therapy (ADT). Reduced NCOR2 expression significantly associates with shorter disease-free survival in patients ...

CELL PRESS2021

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Giovanna Ambrosini, Philipp Bucher, Romain Fernand Pietro Groux, René Dreos, Patrick Meylan

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases

Kristina Makasheva

Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) st ...

2020

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer

Didier Trono, Bart Deplancke, Julien Léonard Duc, Julie Marie Russeil, Riccardo Dainese, Marco Cassano, Michaël Imbeault, Sunil Kumar Raghav, Petra Catalina Schwalie, Suk Min Jang, Wanze Chen, Carine Delattre-Gubelmann, Evgeniia Pankevich

Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revea ...

Nature Research2019

Expression and differential regulation of human TERRA at several chromosome ends

Joachim Lingner, Marianna Feretzaki, Patricia Renck Nunes

The telomeric long noncoding RNA TERRA has been implicated in regulating telomere maintenance by telomerase and homologous recombination, and in influencing telomeric protein composition during the cell cycle and the telomeric DNA damage response. TERRA tr ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2019

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

Didier Trono, Priscilla Turelli, Christian Axel Wandall Thorball, Julien Léonard Duc, Michaël Imbeault, Andrea Coluccio, Julien Paul André Pontis, Pierre-Yves Joseph Laurent Helleboid, Cécile Piot, Ruedi Aebersold

Krüppel‐associated box (KRAB)‐containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin‐inducing KAP1 as repressors of transposable elements (TEs) during early embryogene ...

2019

Beyond silence : a functional and evolutionary study of KRAB zinc finger proteins

Pierre-Yves Joseph Laurent Helleboid

Transposable elements (TEs) are genetic units capable of spreading within the genomes of their host. TEs contribute a readily recognizable 45% of the human DNA, reflecting in part their co-option for some as source of protein-coding sequences, for others a ...

EPFL2019

Infrared nanospectroscopic mapping of a single metaphase chromosome

Giovanni Dietler, Andrzej Kulik, Francesco Simone Ruggeri, Ewelina Wioletta Lipiec

The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy ...

Oxford University Press (OUP)2019

Psychotropic drug-induced genetic-epigenetic modulation of CRTC1 gene is associated with early weight gain in a prospective study of psychiatric patients

Johannes Gräff, Jose Vicente Sanchez Mut, Aurélie Delacrétaz, Céline Dubath

Background: Metabolic side effects induced by psychotropic drugs represent a major health issue in psychiatry. CREB-regulated transcription coactivator 1 (CRTC1) gene plays a major role in the regulation of energy homeostasis and epigenetic mechanisms may ...

2019

Opposing chromatin remodelers control transcription initiation frequency and start site selection

Philipp Bucher, René Dreos

Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy fol ...

NATURE PUBLISHING GROUP2019

Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells

Didier Trono, Priscilla Turelli, Sandra Eloise Kjeldsen, Gabriela Ecco, Julien Léonard Duc, Andrea Coluccio

BACKGROUND: The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in repressing transposable elements (TEs) and maintaining parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of g ...

2018

Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each

Lukas Kühn, Giovanna Ambrosini, Philipp Bucher, Barbara Grisoni-Neupert, Ramona Pauchard-Batschulat, Otto Hagenbüchle

Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse N ...

2018