Marina Lizio
A5038594088- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Immunotherapy and Immune Responses
- Medical Imaging Techniques and Applications
- Medical and Biological Sciences
- Cell Adhesion Molecules Research
- Genomics and Phylogenetic Studies
- Protein Degradation and Inhibitors
- Bioinformatics and Genomic Networks
- MicroRNA in disease regulation
- RNA Interference and Gene Delivery
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Chromatin Remodeling and Cancer
- Histone Deacetylase Inhibitors Research
- Advanced biosensing and bioanalysis techniques
- Virus-based gene therapy research
- Cell Image Analysis Techniques
- Neuroinflammation and Neurodegeneration Mechanisms
- Vascular Malformations and Hemangiomas
- Plant and Fungal Interactions Research
- Genetic Associations and Epidemiology
Covance (United Kingdom)
2022-2024
RIKEN Center for Integrative Medical Sciences
2012-2023
RIKEN
2023
RIKEN Center for Brain Science
2016
CE Technologies (United Kingdom)
2015
The University of Queensland
2010
Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets genes has not been previously studied en masse. Exploiting the fact active are transcribed, we simultaneously measured their activity in 19 human 14 mouse time courses covering a wide range cell types biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated earliest responses....
The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access the data produced by project. It contains most complete and comprehensive sets of actively transcribed enhancers promoters in human mouse genomes. We determined transcription activities these regulatory elements CAGE (Cap Analysis Gene Expression) for both steady dynamic cellular states all major some rare cell types, consecutive stages differentiation responses stimuli. have expanded employing...
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes, and yet, their functions remain largely unknown. As part FANTOM6 project, we systematically knocked down expression 285 lncRNAs human dermal fibroblasts quantified cellular growth, morphological changes, transcriptomic responses using Capped Analysis Gene Expression (CAGE). Antisense oligonucleotides targeting same exhibited global concordance, molecular phenotype, measured by CAGE, recapitulated...
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found mature miR-21, the most widely researched miRNA because of its importance human disease, produced two prevalent isomiR forms differ by 1 nt at their 3' end, and moreover end miR-21 posttranscriptionally adenylated noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase expression level, suggesting...
Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that hypomethylated regions closely Treg up-regulated clusters, whereas had no significant correlation...
CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well structures. They measure expression by sequencing from either the 5′ end of capped molecules (CAGE) or tags randomly distributed along length a (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation platforms typically employ PCR preamplification prior clonal amplification, while third-generation,...
Upon the first publication of fifth iteration Functional Annotation Mammalian Genomes collaborative project, FANTOM5, we gathered a series primary data and database systems into FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers explore transcriptional regulation cellular states. In course collaboration, analysis results have been expanded, functionalities enhanced. We believe that our are invaluable resources, think scientific community will benefit for this recent...
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in pursuit of understanding transcriptome, and transcriptional regulation, mammalian genomes for last 20 years. To share these with research community, FANTOM web-interfaces databases are being regularly updated, enhanced expanded new data types. In recent years, Consortium's efforts have been mainly focused on creating non-coding RNA datasets resources. existing FANTOM5 human...
Abstract The FANTOM5 consortium described the promoter-level expression atlas of human and mouse by using CAGE (Cap Analysis Gene Expression) with single molecule sequencing. In original publications, GRCh37/hg19 NCBI37/mm9 assemblies were used as reference genomes respectively; later, Genome Reference Consortium released newer genome GRCh38/hg38 GRCm38/mm10. To increase utility in forthcoming researches, we reprocessed data to make them available on recent assemblies. include observed...
The Functional Annotation of the Mammalian Genome project (FANTOM5) mapped transcription start sites (TSSs) and measured their activities in a diverse range biological samples. FANTOM5 generated large data set; including detailed information about profiled samples, uncovered TSSs at high base-pair resolution on genome, transcriptional initiation activities, further regulation. Data sets to explore transcriptome individual cellular states encoded mammalian genomes have been enriched by series...
Abstract Neuroinflammation is highly influenced by microglia, particularly through activation of the NLRP3 inflammasome and subsequent release IL-1β. Extracellular ATP a strong activator inducing K + efflux as key signaling event, suggesting that -permeable ion channels could have high therapeutic potential. In these include ATP-gated THIK-1 P2X7 receptors, but their interactions potential role in human brain are unknown. Using novel specific inhibitor combination with patch-clamp...
In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along differentiation time course the human THP-1 cell line under 52 systematic siRNA perturbations. addition, data regarding chromatin status derived from ChIP-chip to elucidate transcriptional regulatory interactions are included. Here present these community as integrated web resource.
Gene expression profiles in homologous tissues have been observed to be different between species, which may due differences species the gene program each cell type, but also reflect type composition of tissue species. Here, we compare matching primary cells human, mouse, rat, dog, and chicken using Cap Analysis Expression (CAGE) short RNA (sRNA) sequencing data from FANTOM5. While find that orthologous genes are highly correlated across types, many were differentially expressed with...
The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand transcriptional network that regulates macrophage differentiation and uncover novel components of transcriptome employing a series high-throughput experiments. primary unique technique is cap analysis gene expression (CAGE), sequencing mRNA 5′-ends with second-generation sequencer quantify promoter activities even in absence annotation. Additional genome-wide...
VEGF-C/VEGFR-3 signaling plays a central role in lymphatic development, regulating the budding of progenitor cells from embryonic veins and maintaining expression PROX1 during later developmental stages. However, how VEGFR-3 activation translates into target gene is still not completely understood. We used cap analysis (CAGE) RNA sequencing to characterize transcriptional changes invoked by VEGF-C LECs identify transcription factors (TFs) involved. found that MAFB, TF involved...
Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping transcription start sites (TSSs) and genome-wide capture promoter activities differentiated steady state cell populations. Much less is known about whether TSS profiling can characterize diverse non-steady populations, such as the approximately 400 transitory heterogeneous types that arise during ontogeny vertebrate animals. To gain insight, we used chick model performed...
The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, association to histone H4-hyperacetylated chromatin is not understood at genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses ChIP-seq transcriptome profiles human non-small cell lung (NSCLC) line H23. We show that...
Lung cancer is the leading cause of cancer-related deaths worldwide. The majority driver mutations have been identified; however, relevant epigenetic regulation involved in tumorigenesis has only fragmentarily analyzed. Epigenetically regulated genes a great theranostic potential, especially tumors with no apparent mutations. Here, epigenetically were identified lung by an integrative analysis promoter-level expression profiles from Cap Analysis Gene Expression (CAGE) 16 non-small cell...
Neuroinflammation, specifically the NLRP3 inflammasome cascade, is a common underlying pathological feature of many neurodegenerative diseases. Evidence suggests that activation involves changes in intracellular K+. Nuclear Enriched Transcript Sort Sequencing (NETSseq), which allows for deep sequencing purified cell types from human post-mortem brain tissue, demonstrated highly specific expression tandem pore domain halothane-inhibited K+ channel 1 (THIK-1) microglia compared to other glial...
Super-enhancers (SEs), which activate genes involved in cell-type specificity, have mainly been defined as genomic regions with top-ranked enrichment(s) of histone H3 acetylated K27 (H3K27ac) and/or transcription coactivator(s) including a bromodomain and extra-terminal domain (BET) family protein, BRD4. However, BRD4 preferentially binds to multi-acetylated H4, typically K5 K8 (H4K5acK8ac), leading us hypothesize that SEs should be by high H4K5acK8ac enrichment at least well H3K27ac.Here,...
Here we describe a method for constructing small RNA libraries highthroughput sequencing in which have made significant improvement to commonly available standard protocols. We added locked nucleic acid (LNA) oligonucleotide—named dimer eliminator—that is complementary the adapter-dimer ligation products during reverse transcription reaction. It reduces adapter-dimers, often contaminate and increase number of non-insert sequence reads. This simple technology can be used simultaneous...