Publications related to Bisulfite sequencing

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

Maria del Carmen Sandi Perez, Mandy Meijer

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

PERGAMON-ELSEVIER SCIENCE LTD2023

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

Markus Kirolos Youssef

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

Natural competence of the pathogen Acinetobacter baumannii: an elusive phenomenon

Nina Vesel

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

EPFL2022

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Mustafa Demir

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said meth ...

2022

Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

Martinus Gijs, Thomas Lehnert, Lin Sun

DNA fragmentation is an essential process in developing genetic sequencing strategies, genetic research, as well as for the diagnosis of diseases with a genetic signature like cancer. Efficient on-chip DNA fragmentation protocols would be beneficial to pro ...

ROYAL SOC CHEMISTRY2022

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

Hmx1 regulates urfh1 expression in the craniofacial region in zebrafish

H6 family homeobox 1 (HMX1) regulates multiple aspects of craniofacial development as it is widely expressed in the eye, peripheral ganglia and branchial arches. Mutations in HMX1 are linked to an ocular defect termed Oculo-auricular syndrome of Schorderet ...

2021

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

Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

Elisa Oricchio, Natalya Katanayeva, Daniele Tavernari, Stephanie Jocelyne Sungalee, Ruxandra-Andreea Lambuta, Giovanni Ciriello

In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increased deposition of acetylated histone H3 lysine 27 (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is a ...

2021

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Marion Leleu, Ludovica Vanzan, Flavia Marzetta, Ioannis Xenarios

Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation ...

2020

Comprehensive analysis of PM20D1 QTL in Alzheimer's disease

Johannes Gräff, Liliane Glauser, Jose Vicente Sanchez Mut

Background Alzheimer's disease (AD) is a complex disorder caused by a combination of genetic and non-genetic risk factors. In addition, an increasing evidence suggests that epigenetic mechanisms also accompany AD. Genetic and epigenetic factors are not ind ...

2020

Methylation of arsenic by single-species and soil-derived microbial cultures

Karen Elda Viacava Romo

Arsenic (As) is simultaneously a ubiquitous and a toxic element. Arsenic is subject to bio-transformations catalyzed by microorganisms constituting the As biogeochemical cycle. The primordial Earth was devoid of oxygen, exposing life to the highly mobile a ...

EPFL2020

Variability in arsenic methylation efficiency across aerobic and anaerobic microorganisms

Rizlan Bernier-Latmani, Karin Lederballe Meibom, Karen Elda Viacava Romo, Arnaud Michel Gelb, Leia Soraya Véronique Falquet, Shannon Eliot Dyer, Adrien Mestrot

Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) m ...

2020

Roles of Epigenetic Dysregulation in Cancer Progression and Metastasis

Mohammad Sadegh Saghafinia

Nearly all the cells of an organism share the same DNA sequence or genome, and yet they show different phenotypes and carry out different functions. This diversity is made possible by a verity of molecular modifications acting on the DNA sequence that coll ...

EPFL2020

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

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

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

Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders

Vincent Meyer

Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in similar to 260 genes. Albeit that many genes are implicated in IRD, for 30-50% of the cases, the gene defect ...

WILEY2019

Mitotic chromosome binding predicts transcription factor properties in interphase

Cédric Deluz, David Michael Suter, Torgil Elias Friman, Andrea Brigitta Alber, Mahé Cécile Raccaud

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The as ...

Nature Research2019

A Tale of Two Tumors: Unraveling the Complexities of Epigenetic Dysregulation in Cancer

Maria Christine Donaldson

Epigenetics plays an important role in cancer development and progression. Cancer cells hijack the epigenome by modifying the histone protein units responsible for packaging DNA, or by modifying the DNA itself, resulting in changes to chromatin topology an ...

EPFL2019