A5067140129- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Genetic factors in colorectal cancer
- Histone Deacetylase Inhibitors Research
- Estrogen and related hormone effects
- RNA modifications and cancer
- RNA Research and Splicing
- NF-κB Signaling Pathways
- Neuroblastoma Research and Treatments
- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- Cancer-related molecular mechanisms research
- DNA Repair Mechanisms
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Reproductive Biology and Fertility
- Hypothalamic control of reproductive hormones
- Peroxisome Proliferator-Activated Receptors
- Growth Hormone and Insulin-like Growth Factors
- Reproductive System and Pregnancy
- Protein Kinase Regulation and GTPase Signaling
- Epigenetics and DNA Methylation
Université de Sherbrooke
2011-2023
PROTEO
2017-2022
Université de Lille
2018
Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion one coding sequence (CDS) per transcript, leading to a substantial underestimation the potential eukaryotes. Here, we present OpenProt, first database fully endorsing polycistronic model genomes...
Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) addition to annotated protein coding sequences (CDSs). We show that a large number small proteins could fact be coded by these altORFs. The putative translated from altORFs orthologs many species contain functional domains. Evolutionary analyses indicate often more extreme conservation patterns than their CDSs. Thousands are...
Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate genome-wide approaches that is present at a subset of active bound the estrogen receptor alpha (ERα). We also determine does not influence local nucleosome positioning around ERα using ChIP...
Proteogenomics and ribosome profiling concurrently show that genes may code for both a large one or more small proteins translated from annotated coding sequences (CDSs) unannotated alternative open reading frames (named ORFs altORFs), respectively, but the stoichiometry between same gene is unknown. MIEF1, recently identified as dual-coding gene, harbors CDS newly actively altORF located in 5'UTR. Here, we use absolute quantification with stable isotope-labeled peptides parallel reaction...
Abstract Tumor characteristics are decisive in the determination of treatment strategy for patients with breast cancer. Patients estrogen receptor α (ERα)–positive cancer can benefit from long-term hormonal treatment. Nonetheless, majority will develop resistance to these therapies. Here, we investigated role nuclear liver homolog-1 (LRH-1, NR5A2) antiestrogen-sensitive and -resistant cells. We identified genome-wide LRH-1–binding sites using ChIP-seq (chromatin immunoprecipitation...
Pseudogenes are mutated copies of protein-coding genes that cannot be translated into proteins, but a small subset pseudogenes has been detected at the protein level. Although ubiquitin represent one most abundant pseudogene families in many organisms, little is known about their expression and signaling potential. By re-analyzing public RNA-sequencing proteomics datasets, we here provide evidence for several including UBB 4 (UBBP4), which encodes UbKEKS (Q2K, K33E, Q49K, N60S). The...
The ovarian follicle reserve, formed pre- or perinatally, comprises all oocytes for lifetime reproduction. Depletion of this reserve results in infertility. Steroidogenic factor 1 (SF-1; Nr5a1 ) and liver receptor homolog (LRH-1; Nr5a2 are two orphan nuclear receptors that regulate adult endocrine function, but their role formation is unknown. We developed models conditional depletion SF-1 LRH-1 from prenatal ovaries. SF-1, not LRH-1, resulted dramatically smaller ovaries fewer primordial...
The degradation of many nuclear receptors is controlled by ligand-binding and mediated the ubiquitin-proteasome pathway. However, mechanisms implicated in thyroid hormone receptor (TR) remain unclear. Our objective was to define kinetics, mechanisms, sub-cellular fractions involved TRs degradation.We used pulse-chase analyses, time-course experiments carried out presence cycloheximide (to inhibit new protein synthesis), biochemical fractionation with Western blot analyses determine kinetics...
Abstract Recent proteogenomic approaches have led to the discovery that regions of transcriptome previously annotated as non-coding (i.e. UTRs, open reading frames overlapping coding sequences in a different frame, and RNAs) frequently encode proteins (termed alternative proteins). This suggests identified protein-protein interaction networks are partially incomplete since not present conventional protein databases. Here we used resource OpenProt combined spectrum- peptide-centric analysis...
Abstract Recent studies in eukaryotes have demonstrated the translation of alternative open reading frames (altORFs) addition to annotated protein coding sequences (CDSs). We show that a large number small proteins could fact be coded by altORFs. The putative translated from altORFs orthologs many species and evolutionary patterns indicate are particularly constrained CDSs evolve slowly. Thousands predicted detected proteomic datasets reanalysis using database containing proteins. Protein...
<p>PDF file - 1103KB, Figure S1. ERalpha expression in HMEC, MCF7, LCC2 and LCC9 cells. S2. LRH-1 depletion using shRNA MCF7 AE-resistant cell lines. S3. ChIP-seq validation. S4. Med12 signal associated with binding events presenting low FAIRE H3K27ac signal. S5. Integration of ChIA-PET profile target genes. S6. S7. inhibition decreases cellular growth. S8. CCND1 following anti-estrogen treatment. Table List against LRH-1. primers used for mRNA analysis. antibodies ChIP WB....
<div>Abstract<p>Tumor characteristics are decisive in the determination of treatment strategy for patients with breast cancer. Patients estrogen receptor α (ERα)–positive cancer can benefit from long-term hormonal treatment. Nonetheless, majority will develop resistance to these therapies. Here, we investigated role nuclear liver homolog-1 (LRH-1, <i>NR5A2</i>) antiestrogen-sensitive and -resistant cells. We identified genome-wide LRH-1–binding sites using ChIP-seq...
<div>Abstract<p>Tumor characteristics are decisive in the determination of treatment strategy for patients with breast cancer. Patients estrogen receptor α (ERα)–positive cancer can benefit from long-term hormonal treatment. Nonetheless, majority will develop resistance to these therapies. Here, we investigated role nuclear liver homolog-1 (LRH-1, <i>NR5A2</i>) antiestrogen-sensitive and -resistant cells. We identified genome-wide LRH-1–binding sites using ChIP-seq...
<p>PDF file - 1103KB, Figure S1. ERalpha expression in HMEC, MCF7, LCC2 and LCC9 cells. S2. LRH-1 depletion using shRNA MCF7 AE-resistant cell lines. S3. ChIP-seq validation. S4. Med12 signal associated with binding events presenting low FAIRE H3K27ac signal. S5. Integration of ChIA-PET profile target genes. S6. S7. inhibition decreases cellular growth. S8. CCND1 following anti-estrogen treatment. Table List against LRH-1. primers used for mRNA analysis. antibodies ChIP WB....