A5064012145- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Mitochondrial Function and Pathology
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Endoplasmic Reticulum Stress and Disease
- Genetic Neurodegenerative Diseases
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Plant and Fungal Interactions Research
- ATP Synthase and ATPases Research
- Plant Disease Resistance and Genetics
- Neurological diseases and metabolism
- Metabolism and Genetic Disorders
- Birth, Development, and Health
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Neuroinflammation and Neurodegeneration Mechanisms
- Bioinformatics and Genomic Networks
- Acute Myeloid Leukemia Research
- Plant Pathogenic Bacteria Studies
- Plant Virus Research Studies
- S100 Proteins and Annexins
University of Warsaw
2018-2024
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2017-2024
Centre for Genomic Regulation
2016-2023
International Institute of Molecular and Cell Biology
2020-2022
Universitat Pompeu Fabra
2017-2019
Transition Technologies (Poland)
2017
The accurate identification and description of the genes in human mouse genomes is a fundamental requirement for high quality analysis data informing both genome biology clinical genomics. Over last 15 years, GENCODE consortium has been producing reference gene annotations to provide this foundational resource. includes experimental computational groups who work together improve extend annotation. Specifically, we generate primary data, create bioinformatics tools support expert manual...
Abstract The GENCODE project annotates human and mouse genes transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology clinical genomics. annotation processes make use of primary bioinformatic tools analysis generated both within the consortium externally to support creation transcript structures determination their function. Here, we present improvements our infrastructure, bioinformatics tools, analysis, advances they in...
GENCODE produces high quality gene and transcript annotation for the human mouse genomes. All is supported by experimental data serves as a reference genome biology clinical genomics. The consortium generates targeted data, develops bioinformatic tools carries out analyses that, along with externally produced methods, support identification of structures determination their function. Here, we present an update on genes, including developments in tools, major collaborations which underpin...
Mitochondria are organelles with their own genomes, but they rely on the import of nuclear-encoded proteins that translated by cytosolic ribosomes. Therefore, it is important to understand whether failures in mitochondrial uptake these can cause proteotoxic stress and identify response mechanisms may counteract it. Here, we report upon impairments protein import, high-risk precursor immature forms form aberrant deposits cytosol. These then further accumulation consequently aggregation other...
Abstract Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput accuracy, achieving reliable end-to-end identification transcripts remains a challenge for long-read methods. To address this limitation, we develop CapTrap-seq, cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming detect 5’ capped, full-length transcripts. In our study, evaluate performance...
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies methodologies allow us to catalog genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables identify large numbers of missing transcripts substantially improve existing models, our long non-coding RNA catalogs have undergone a dramatic expansion reconfiguration result. Meanwhile, we are...
Acute myeloid leukemia (AML) is the most common and severe form of acute diagnosed in adults. Owing to its heterogeneity, AML divided into classes associated with different treatment outcomes specific gene expression profiles. Based on previous studies AML, this study, we designed generated an AML-array containing 900 oligonucleotide probes complementary human genes implicated hematopoietic cell differentiation maturation, proliferation, apoptosis leukemic transformation. The was used...
Abstract Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires comprehensive, high-quality annotation their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification cDNA ends) long-read RNA sequencing. We apply RACE-Seq 398 human lncRNA genes in seven tissues, leading discovery 2,556...
Abstract Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference human mouse genomes, becoming a foundation biomedical genomics communities worldwide. Nevertheless, collections of important yet poorly-understood classes like long non-coding RNAs (lncRNAs) remain incomplete scattered across multiple, uncoordinated catalogs, slowing down progress in field. To...
Abstract The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60–65% patients without molecular diagnosis. Here, we explore incompleteness transcript models used for exome genome analysis as one potential explanation lack current diagnoses. Therefore, have updated GENCODE gene annotation 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries other data...
Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput accuracy, achieving reliable end-to-end identification transcripts remains a challenge for long-read methods. To address this limitation, we developed CapTrap-seq, cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming detect 5'capped, full-length transcripts, together data processing pipeline LyRic. We...
The molecular complexity of human breast cancer (BC) renders the clinical management disease challenging. Long non-coding RNAs (lncRNAs) are promising biomarkers for BC patient stratification, early detection, and monitoring. Here, we identified involvement long intergenic RNA 01087 (LINC01087) in oncogenesis. LINC01087 appeared significantly downregulated triple-negative BCs (TNBCs) upregulated luminal subtypes comparison to mammary samples from cancer-free women matched normal pairs....
Abstract In a 2018 paper posted to bioRxiv, Pertea et al. presented the CHESS database, new catalog of human gene annotations that includes 1,178 protein-coding predictions. These are based on evidence transcription in tissues and homology earlier other mammals. Here, we reanalyze used by CHESS, find nearly all predictions false positives. We 86% overlap transposons marked RepeatMasker known frequently result positive More than half homologous only nine Alu -derived primate sequences...
Development and function of tissues organs are powered by the activity mitochondria. In humans, inherited genetic mutations that lead to progressive mitochondrial pathology often manifest during infancy can death, reflecting indispensable nature biogenesis function. Here, we describe a zebrafish mutant for gene mia40a (chchd4a), life-essential homologue evolutionarily conserved Mia40 oxidoreductase which drives cysteine-rich proteins. We report animals undergo cellular respiration defects...
Abstract Accurate annotations of genes and their transcripts is a foundation genomics, but no annotation technique presently combines throughput accuracy. As result, reference gene collections remain incomplete: many models are fragmentary, while thousands more uncatalogued–particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted capture with third-generation long-read sequencing. We...
DATA REPORT article Front. Aging Neurosci., 20 March 2017Sec. Alzheimer's Disease and Related Dementias Volume 9 - 2017 | https://doi.org/10.3389/fnagi.2017.00064
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into organelle. To characterize spatial organization of gene products zebrafish ( Danio rerio ), we sequenced RNA from different cellular fractions. Our results confirmed presence nuclear-encoded mRNAs fraction, which unperturbed conditions, mainly transcripts encoding large with specific properties, like transmembrane domains. further explore principles protein compartmentalization zebrafish,...
Abstract Mitochondria are organelles with their own genomes, but they rely on the import of nuclear-encoded proteins that translated by cytosolic ribosomes. Therefore, it is important to understand whether failures in mitochondrial uptake these can cause proteotoxic stress and identify response mechanisms may counteract it. Here, we report upon impairments protein import, high-risk precursor immature forms form aberrant deposits cytosol. These then further accumulation consequently...