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- Noguchi, S, et al.
(author)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Journal article (peer-reviewed)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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- Carninci, P, et al.
(author)
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The transcriptional landscape of the mammalian genome
- 2005
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In: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Journal article (peer-reviewed)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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- Ramilowski, JA, et al.
(author)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Journal article (peer-reviewed)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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- Grapotte, M, et al.
(author)
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- 2021
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 3297-
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Journal article (peer-reviewed)abstract
- Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
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- de Hoon, M, et al.
(author)
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Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- 2022
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 32:9, s. 1727-1735
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Journal article (peer-reviewed)abstract
- In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction have a strong preference to produce either long or short capped RNAs, with one out of six peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs have highly specific 3′ ends, typically overlapping splice sites. Enhancers also preferentially generate either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Enhancers producing either short or long capped RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.
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- Api, Anne Marie, et al.
(author)
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Quantitative Risk Assessment of Contact Sensitization: Clinical Data to Assess Utility of the Model
- 2010
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In: Dermatitis. - : Mary Ann Liebert Inc. - 1710-3568. ; 21:4, s. 207-213
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Journal article (peer-reviewed)abstract
- Background: Contact hypersensitivity quantitative risk assessment (QRA) for fragrance ingredients is being used to establish new international standards for all fragrance ingredients that are potential skin sensitizers. Objective: The objective was to evaluate the retrospective clinical data on three fragrance ingredients in order to provide a practical assessment of the predictive value of the QRA approach. It is important to have data to assess that the methodology provides a robust approach for primary prevention of contact sensitization induction for fragrance ingredients identified as potential sensitizers. Methods: This article reviews clinical data for three fragrance ingredients cinnamic aldehyde, citral, and isoeugenol to assess the utility of the QRA approach for fragrance ingredients. Results: This assessment suggests that had the QRA approach been available at the time standards were established for these fragrance ingredients, the clinical response might have been noticeably improved. Prospectively, with the establishment of QRA-derived standards, there should be a continued downward trend in patch test-positive rates for cinnamic aldehyde, citral, and isoeugenol over time. Conclusion: While it is recognized that the availability of retrospective data is limited, a longitudinal review of these data gives confidence that the QRA approach should be an effective tool for primary prevention. This study also highlights the importance of continued active monitoring of clinical patch-test data for fragrance ingredients.
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- Belsito, D., et al.
(author)
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A safety assessment of branched chain saturated alcohols when used as fragrance ingredients
- 2010
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In: Food and Chemical Toxicology. - : Elsevier BV. - 0278-6915. ; 48, s. 1-46
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Research review (peer-reviewed)abstract
- The Branched Chain Saturated Alcohol (BCSA) group of fragrance ingredients was evaluated for safety. In humans, no evidence of skin irritation was found at concentrations of 2-10%. Undiluted, 11 materials evaluated caused moderate to severe eye irritation. As current end product use levels are between 0.001% and 1.7%, eye irritation is not a concern. The materials have no or low sensitizing potential. For individuals who are already sensitized, an elicitation reaction is possible. Due to lack of UVA/UVB light-absorbing structures, and review of phototoxic/photoallergy data, the BCSA are not expected to elicit phototoxicity or photoallergy. The 15 materials tested have a low order of acute toxicity. Following repeated application, seven BCSA tested were of low systemic toxicity. Studies performed on eight BCSA and three metabolites show no in vivo or in vitro genotoxicity. A valid carcinogenicity study showed that 2-ethyl-1-hexanol is a weak inducer of liver tumors in female mice, however, the relevance of this effect and mode of action to humans is still a matter of debate. The Panel is of the opinion that there are no safety concerns regarding BCSA under the present levels of use and exposure. (C) 2010 Elsevier Ltd. All rights reserved.
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- Gioia, C., et al.
(author)
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Lignin-Based Epoxy Resins : Unravelling the Relationship between Structure and Material Properties
- 2020
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In: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 21:5, s. 1920-1928
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Journal article (peer-reviewed)abstract
- Here we investigate the relationship between thermomechanical properties and chemical structure of well-characterized lignin-based epoxy resins. For this purpose, technical lignins from eucalyptus and spruce, obtained from the Kraft process, were used. The choice of lignins was based on the expected differences in molecular structure. The lignins were then refined by solvent fractionation, and three fractions with comparable molecular weights were selected to reduce effects of molar mass on the properties of the final thermoset resins. Consequently, any differences in thermomechanical properties are expected to correlate with molecular structure differences between the lignins. Oxirane moieties were selectively introduced to the refined fractions, and the resulting lignin epoxides were subsequently cross-linked with two commercially available polyether diamines (Mn = 2000 and 400) to obtain lignin-based epoxy resins. Molecular-scale characterization of the refined lignins and their derivatives were performed by 31P NMR, 2D-NMR, and DSC methods to obtain the detailed chemical structure of original and derivatized lignins. The thermosets were studied by DSC, DMA, and tensile tests and demonstrated diverse thermomechanical properties attributed to structural components in lignin and selected amine cross-linker. An epoxy resin with a lignin content of 66% showed a Tg of 79 °C from DMA, Young's modulus of 1.7 GPa, tensile strength of 66 MPa, and strain to failure of 8%. The effect of molecular lignin structure on thermomechanical properties was analyzed, finding significant differences between the rigid guaiacyl units in spruce lignin compared with sinapyl units in eucalyptus lignin. The methodology points toward rational design of molecularly tailored lignin-based thermosets.
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