FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Abstract The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

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SorghumBase: a web-based portal for sorghum genetic information and community advancement

Planta ◽

10.1007/s00425-022-03821-6 ◽

2022 ◽

Vol 255 (2) ◽

Author(s):

Nicholas Gladman ◽

Andrew Olson ◽

Sharon Wei ◽

Kapeel Chougule ◽

Zhenyuan Lu ◽

...

Keyword(s):

Resource Sharing ◽

Content Management ◽

Research Community ◽

Data Types ◽

Training Materials ◽

Wide Range ◽

Variant Information ◽

Data Collation ◽

Genome Assemblies ◽

User Friendly

Abstract Main conclusion SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal (https://www.sorghumbase.org), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.

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Non-coding RNA: a new frontier in regulatory biology

National Science Review ◽

10.1093/nsr/nwu008 ◽

2014 ◽

Vol 1 (2) ◽

pp. 190-204 ◽

Cited By ~ 80

Author(s):

Xiang-Dong Fu

Keyword(s):

Rna World ◽

Large Fraction ◽

Biochemical Processes ◽

Non Coding Rna ◽

Genomics And Proteomics ◽

New Frontier ◽

Mammalian Genomes ◽

Non Coding Rnas ◽

World Hypothesis ◽

Rna World Hypothesis

Abstract A striking finding in the past decade is the production of numerous non-coding RNAs (ncRNAs) from mammalian genomes. While it is entirely possible that many of those ncRNAs are transcription noises or by-products of RNA processing, increasing evidence suggests that a large fraction of them are functional and provide various regulatory activities in the cell. Thus, functional genomics and proteomics are incomplete without understanding functional ribonomics. As has been long suggested by the ‘RNA world’ hypothesis, many ncRNAs have the capacity to act like proteins in diverse biochemical processes. The enormous amount of information residing in the primary sequences and secondary structures of ncRNAs makes them particularly suited to function as scaffolds for molecular interactions. In addition, their functions appear to be stringently controlled by default via abundant nucleases when not engaged in specific interactions. This review focuses on the functional properties of regulatory ncRNAs in comparison with proteins and emphasizes both the opportunities and challenges in future ncRNA research.

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Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

10.1101/700864 ◽

2019 ◽

Cited By ~ 5

Author(s):

Jordan A Ramilowski ◽

Chi Wai Yip ◽

Saumya Agrawal ◽

Jen-Chien Chang ◽

Yari Ciani ◽

...

Keyword(s):

Antisense Oligonucleotides ◽

Morphological Changes ◽

Dermal Fibroblasts ◽

Cellular Growth ◽

Molecular Phenotype ◽

Functional Roles ◽

Mammalian Genomes ◽

Non Coding Rnas ◽

Cellular Phenotypes ◽

Molecular Phenotyping

AbstractLong non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression 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 lncRNA 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 dataset with molecular phenotyping (over 1,000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

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TreeGenes: A Forest Tree Genome Database

International Journal of Plant Genomics ◽

10.1155/2008/412875 ◽

2008 ◽

Vol 2008 ◽

pp. 1-7 ◽

Cited By ~ 59

Author(s):

Jill L. Wegrzyn ◽

Jennifer M. Lee ◽

Brandon R. Tearse ◽

David B. Neale

Keyword(s):

Data Retrieval ◽

Forest Tree ◽

Research Community ◽

Genetic Maps ◽

Data Types ◽

Genome Database ◽

Access Points ◽

Web Resource ◽

Wide Range ◽

Visualization Tools

The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.

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Lantern: an integrative repository of functional annotations for lncRNAs in the human genome

BMC Bioinformatics ◽

10.1186/s12859-021-04207-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Swapna Vidhur Daulatabad ◽

Rajneesh Srivastava ◽

Sarath Chandra Janga

Keyword(s):

Human Genome ◽

Cellular Localization ◽

Expression Profiles ◽

Free Text ◽

Dynamic Visualization ◽

Specific Expression ◽

Web Resource ◽

Functional Dynamics ◽

Non Coding Rnas ◽

Retrieval Engine

Abstract Background With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. Results We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed’s abstract retrieval engine and NCBO’s recommender annotation system. Lantern’s annotations were benchmarked against lncRNAdb’s manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. Conclusions Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.

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Form and function of eukaryotic unstable non-coding RNAs

Biochemical Society Transactions ◽

10.1042/bst20120040 ◽

2012 ◽

Vol 40 (4) ◽

pp. 836-841 ◽

Cited By ~ 6

Author(s):

Jonathan Houseley

Keyword(s):

Unknown Function ◽

Budding Yeast ◽

Rna Degradation ◽

Present Review ◽

Form And Function ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Higher Eukaryotes ◽

And Function

Unstable non-coding RNAs are produced from thousands of loci in all studied eukaryotes (and also prokaryotes), but remain of largely unknown function. The present review summarizes the mechanisms of eukaryotic non-coding RNA degradation and highlights recent findings regarding function. The focus is primarily on budding yeast where the bulk of this research has been performed, but includes results from higher eukaryotes where available.

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Long Non-coding RNA FEZF1-AS1 Promotes Growth and Reduces Apoptosis Through Regulation of miR-363-3p/PAX6 Axis in Retinoblastoma

Biochemical Genetics ◽

10.1007/s10528-020-10026-7 ◽

2021 ◽

Author(s):

Xiuming Liu ◽

Xiaofeng Li ◽

Jianchang Li

Keyword(s):

Cell Viability ◽

Antisense Rna ◽

Tumor Formation ◽

Retinoblastoma Cell ◽

Non Coding Rna ◽

High Incidence ◽

Non Coding Rnas ◽

Long Non Coding Rna ◽

Common Malignancy

AbstractRetinoblastoma is the most common malignancy in children's eyes with high incidence. Long non-coding RNAs (lncRNAs) play important roles in the progression of retinoblastoma. LncRNA FEZF1 antisense RNA 1 (FEZF1-AS1) has been found to stimulate retinoblastoma. However, the mechanism of FEZF1-AS1 underlying progression of retinoblastoma is still unclear. In current study, FEZF1-AS1 was up-regulated in retinoblastoma tissues and cells. FEZF1-AS1 overexpression enhanced retinoblastoma cell viability, promoted cell cycle, and inhibited apoptosis. Conversely, FEZF1-AS1 knockdown reduced cell viability, cycle, and elevated apoptosis. The interaction between FEZF1-AS1 and microRNA-363-3p (miR-363-3p) was confirmed. FEZF1-AS1 down-regulated miR-363-3p and up-regulated PAX6. PAX6 was a target gene of miR-363-3p. EZF1-AS1 promoted retinoblastoma cell viability and suppressed apoptosis via PAX6. Further, we demonstrated that FEZF1-AS1 contribute to tumor formation in vivo. In conclusion, FEZF1-AS1 elevated growth and inhibited apoptosis by regulating miR-363-3p/PAX6 in retinoblastoma, which provide a new target for retinoblastoma treatment.

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Regulation of Metabolic Reprogramming by Long Non-Coding RNAs in Cancer

Cancers ◽

10.3390/cancers13143485 ◽

2021 ◽

Vol 13 (14) ◽

pp. 3485

Author(s):

Assunta Sellitto ◽

Giovanni Pecoraro ◽

Giorgio Giurato ◽

Giovanni Nassa ◽

Francesca Rizzo ◽

...

Keyword(s):

Lipid Metabolism ◽

Cancer Cells ◽

Metabolic Reprogramming ◽

Metabolic Phenotype ◽

Metabolic Alterations ◽

Cell Proliferation And Differentiation ◽

Non Coding Rna ◽

Proliferation And Differentiation ◽

Non Coding Rnas ◽

Additional Level

Metabolic reprogramming is a well described hallmark of cancer. Oncogenic stimuli and the microenvironment shape the metabolic phenotype of cancer cells, causing pathological modifications of carbohydrate, amino acid and lipid metabolism that support the uncontrolled growth and proliferation of cancer cells. Conversely, metabolic alterations in cancer can drive changes in genetic programs affecting cell proliferation and differentiation. In recent years, the role of non-coding RNAs in metabolic reprogramming in cancer has been extensively studied. Here, we review this topic, with a focus on glucose, glutamine, and lipid metabolism and point to some evidence that metabolic alterations occurring in cancer can drive changes in non-coding RNA expression, thus adding an additional level of complexity in the relationship between metabolism and genetic programs in cancer cells.

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Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽

10.3390/ani11072006 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2006

Author(s):

Hongyu Liu ◽

Ibrar Muhammad Khan ◽

Huiqun Yin ◽

Xinqi Zhou ◽

Muhammad Rizwan ◽

...

Keyword(s):

Target Genes ◽

Expression Profiles ◽

Age Groups ◽

Adherens Junction ◽

Integrated Analysis ◽

Sequencing Data ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Rna Interaction ◽

Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

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MiR-29a: a potential therapeutic target and promising biomarker in tumors

Bioscience Reports ◽

10.1042/bsr20171265 ◽

2018 ◽

Vol 38 (1) ◽

Cited By ~ 10

Author(s):

Jin-yan Wang ◽

Qian Zhang ◽

Dan-dan Wang ◽

Wei Yan ◽

Huan-huan Sha ◽

...

Keyword(s):

Cell Proliferation ◽

Therapeutic Target ◽

Therapeutic Strategy ◽

Transcriptional Level ◽

Additional Insight ◽

Potential Therapeutic Target ◽

Rna Molecules ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Novel Therapeutic

MiRNAs, small non-coding RNA molecules, were recognized to be associated with the incidence and development of diverse neoplasms. MiRNAs were small non-coding RNAs that could regulate post-transcriptional level by binding to 3′-UTR of target mRNAs. Amongst which, miR-29a was demonstrated that it had significant impact on oncogenicity in various neoplasms through binding to critical genes which enhanced or inhibited the progression of cancers. MiR-29a participated in kinds of physiological and pathological processes, including virus replication, cell proliferation, differentiation, apoptosis, fibrosis, angiogenesis, tumorigenicity, metastasis, drug-resistance, and so on. According to its sufficient sensitivity and specificity, many studies showed that miR-29a might serve as a potential therapeutic target and promising biomarker in various tumors. In this review, we discussed the functions of miR-29a and its potential application in the diagnosis, treatment and stages of carcinoma, which could provide additional insight to develop a novel therapeutic strategy.

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