publication . Other literature type . Preprint . 2019

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Lorenzi, Lucia; Chiu, Hua-Sheng; Cobos, Francisco Avila; Gross, Stephen; Volders, Pieter-Jan; Cannoodt, Robrecht; Nuytens, Justine; Vanderheyden, Katrien; Anckaert, Jasper; Lefever, Steve; ...
Open Access
  • Published: 17 Oct 2019
Abstract
AbstractThe human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines. We report on thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addit...
Persistent Identifiers
Subjects
free text keywords: Intron, Polyadenylation, Non-coding RNA, Transcriptome, RNA, Computational biology, Biology, Nucleotide, chemistry.chemical_classification, chemistry
Funded by
EC| iPC
Project
iPC
individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology
  • Funder: European Commission (EC)
  • Project Code: 826121
  • Funding stream: H2020 | RIA
Validated by funder
,
EC| PrECISE
Project
PrECISE
PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION
  • Funder: European Commission (EC)
  • Project Code: 668858
  • Funding stream: H2020 | RIA
36 references, page 1 of 3

1. Esteller M. Non-coding RNAs in human disease. 2011. doi:10.1038/nrg3074

2. Chen L-L. The Biogenesis and Emerging Roles of Circular RNAs. Vol 17.; 2016. doi:10.1038/nrm.2015.32

3. Lorenzi L, Avila Cobos F, Decock A, et al. Long noncoding RNA expression profiling in cancer: Challenges and opportunities. Genes, Chromosom Cancer. January 2019. doi:10.1002/gcc.22709

4. Ardlie KG, DeLuca DS, Segrè A V., et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (80- ). 2015;348(6235):648- 660. doi:10.1126/science.1262110

5. Barretina J, Caponigro G, Stransky N, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483. doi:10.1038/nature11003

6. Forrest ARR, Kawaji H, Rehli M, et al. A promoter-level mammalian expression atlas. Nature. 2014;507(7493):462-470. doi:10.1038/nature13182

7. Hon CC, Ramilowski JA, Harshbarger J, et al. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature. 2017;543(7644):199-204. doi:10.1038/nature21374

8. Derek de Rie, Imad Abugessaisa , Tanvir Alam3, Erik Arner1, 4, Peter Arner5, Haitham Ashoor3, Gaby Åström5, Magda Babina6, Nicolas Bertin1, 4, 7 , A Maxwell Burroughs1, 4, 8, Ailsa J Carlisle9, Carsten O Daub1, 4 , Michael Detmar10 , Ruslan Deviatiia 21 & Michiel J L de Hoon1. An integrated expression atlas of miRNAs and their promoters in human and mouse MicroRNAs. Nat Biotechnol. 2017.

9. Pertea M, Shumate A, Pertea G, et al. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biol. 2018;19(1):208. doi:10.1186/s13059-018-1590-2 [OpenAIRE]

10. Iyer M, Niknafs Y, Malik R, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47(3):199-208. doi:10.1038/ng.3192

11. Abstract G. The Landscape of Circular RNA in Cancer. 2019. doi:10.1016/j.cell.2018.12.021

12. Regev A, Teichmann SA, Lander ES, et al. The human cell atlas. Elife. 2017;6. doi:10.7554/eLife.27041

13. Melé M, Ferreira PG, Reverter F, et al. The human transcriptome across tissues and individuals. Science (80- ). 2015;348(6235). http://science.sciencemag.org/content/348/6235/660/tab-pdf. Accessed July 30, 2017.

14. Arun G, Diermeier SD, Spector DL. Therapeutic Targeting of Long Non-Coding RNAs in Cancer. 2018. doi:10.1016/j.molmed.2018.01.001

15. Leucci E, Vendramin R, Spinazzi M, et al. Melanoma addiction to the long non-coding RNA SAMMSON. 2016. doi:10.1038/nature17161

36 references, page 1 of 3
Abstract
AbstractThe human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines. We report on thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addit...
Persistent Identifiers
Subjects
free text keywords: Intron, Polyadenylation, Non-coding RNA, Transcriptome, RNA, Computational biology, Biology, Nucleotide, chemistry.chemical_classification, chemistry
Funded by
EC| iPC
Project
iPC
individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology
  • Funder: European Commission (EC)
  • Project Code: 826121
  • Funding stream: H2020 | RIA
Validated by funder
,
EC| PrECISE
Project
PrECISE
PERSONALIZED ENGINE FOR CANCER INTEGRATIVE STUDY AND EVALUATION
  • Funder: European Commission (EC)
  • Project Code: 668858
  • Funding stream: H2020 | RIA
36 references, page 1 of 3

1. Esteller M. Non-coding RNAs in human disease. 2011. doi:10.1038/nrg3074

2. Chen L-L. The Biogenesis and Emerging Roles of Circular RNAs. Vol 17.; 2016. doi:10.1038/nrm.2015.32

3. Lorenzi L, Avila Cobos F, Decock A, et al. Long noncoding RNA expression profiling in cancer: Challenges and opportunities. Genes, Chromosom Cancer. January 2019. doi:10.1002/gcc.22709

4. Ardlie KG, DeLuca DS, Segrè A V., et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (80- ). 2015;348(6235):648- 660. doi:10.1126/science.1262110

5. Barretina J, Caponigro G, Stransky N, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483. doi:10.1038/nature11003

6. Forrest ARR, Kawaji H, Rehli M, et al. A promoter-level mammalian expression atlas. Nature. 2014;507(7493):462-470. doi:10.1038/nature13182

7. Hon CC, Ramilowski JA, Harshbarger J, et al. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature. 2017;543(7644):199-204. doi:10.1038/nature21374

8. Derek de Rie, Imad Abugessaisa , Tanvir Alam3, Erik Arner1, 4, Peter Arner5, Haitham Ashoor3, Gaby Åström5, Magda Babina6, Nicolas Bertin1, 4, 7 , A Maxwell Burroughs1, 4, 8, Ailsa J Carlisle9, Carsten O Daub1, 4 , Michael Detmar10 , Ruslan Deviatiia 21 & Michiel J L de Hoon1. An integrated expression atlas of miRNAs and their promoters in human and mouse MicroRNAs. Nat Biotechnol. 2017.

9. Pertea M, Shumate A, Pertea G, et al. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biol. 2018;19(1):208. doi:10.1186/s13059-018-1590-2 [OpenAIRE]

10. Iyer M, Niknafs Y, Malik R, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47(3):199-208. doi:10.1038/ng.3192

11. Abstract G. The Landscape of Circular RNA in Cancer. 2019. doi:10.1016/j.cell.2018.12.021

12. Regev A, Teichmann SA, Lander ES, et al. The human cell atlas. Elife. 2017;6. doi:10.7554/eLife.27041

13. Melé M, Ferreira PG, Reverter F, et al. The human transcriptome across tissues and individuals. Science (80- ). 2015;348(6235). http://science.sciencemag.org/content/348/6235/660/tab-pdf. Accessed July 30, 2017.

14. Arun G, Diermeier SD, Spector DL. Therapeutic Targeting of Long Non-Coding RNAs in Cancer. 2018. doi:10.1016/j.molmed.2018.01.001

15. Leucci E, Vendramin R, Spinazzi M, et al. Melanoma addiction to the long non-coding RNA SAMMSON. 2016. doi:10.1038/nature17161

36 references, page 1 of 3
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