Cited by 1,000Cancer-related molecular mechanisms researchChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

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The evolution of lncRNA repertoires and expression patterns in tetrapods

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Necsulea, Anamaria, Soumillon, Magali, Warnefors, Maria, Liechti, Angélica, Daish, Tasman, Zeller, Ulrich, Baker, Julie C., Grützner, Frank, Kaessmann, Henrik·2014·Nature

DOI 10.1038/nature12943

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Abstract

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
The Pfam Protein Families Database
Bateman, A. G. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,075
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expressionPreprint
Derrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,135
Cytoscape 2.8: new features for data integration and network visualization
Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., & Ideker, T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq675 · Cited by 4,770
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398

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Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915–1927 (2011) · DOI

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Additional file 4 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
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Additional file 10 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
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Additional file 12 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
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Additional file 4 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053254
Additional file 4 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Sang, S., Chen, W., Zhang, D., Zhang, X., Yang, W., & Liu, C. (2021) · Figshare · doi:10.6084/m9.figshare.16815930
Additional file 5 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
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Additional file 3 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053251
Additional file 8 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031294
Additional file 10 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776526
Additional file 1 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053245
Additional file 2 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031276
Additional file 2 of Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
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Additional file 5 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031285
Additional file 3 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Sang, S., Chen, W., Zhang, D., Zhang, X., Yang, W., & Liu, C. (2021) · Figshare · doi:10.6084/m9.figshare.16815927
Additional file 2 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Sang, S., Chen, W., Zhang, D., Zhang, X., Yang, W., & Liu, C. (2021) · Figshare · doi:10.6084/m9.figshare.16815924
Additional file 3 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031279
Additional file 6 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Sang, S., Chen, W., Zhang, D., Zhang, X., Yang, W., & Liu, C. (2021) · Figshare · doi:10.6084/m9.figshare.16815936
Additional file 9 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J. R., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Xue, C., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776565
Additional file 7 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776559
Additional file 5 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053257
Additional file 5 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776553
Additional file 11 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776529
Additional file 9 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053269
Additional file 1 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031273
Additional file 2 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053248
Additional file 1 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Sang, S., Chen, W., Zhang, D., Zhang, X., Yang, W., & Liu, C. (2021) · Figshare · doi:10.6084/m9.figshare.16815921
Additional file 6 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031288
Additional file 11 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053239
Additional file 13 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J. R., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Xue, C., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776535
Additional file 8 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053266
Additional file 4 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031282
Additional file 3 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776547
Additional file 12 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J. R., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Xue, C., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776532
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Additional file 5 of Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
Zhu, Y., Chen, L., Hong, X., Shi, H., & Li, X. (2022) · Figshare · doi:10.6084/m9.figshare.19799873
Additional file 7 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F. S., Hu, L., Khan, A. A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053263
Additional file 3 of Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
Zhu, Y., Chen, L., Hong, X., Shi, H., & Li, X. (2022) · Figshare · doi:10.6084/m9.figshare.19799867
Additional file 8 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776562
Additional file 7 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031291
Additional file 6 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J. R., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Xue, C., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776556
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(2025) · eLife · doi:10.7554/elife.94502.3.sa2
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Additional file 2 of LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3
Shu, G., Su, H., Wang, Z., Lai, S., Wang, Y., Liu, X., Dai, L., Bi, Y., Chen, W., Huang, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13646888
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Ramos, T. A. R., Maracaja‐Coutinho, V., Ortega, J. M., & do Rego, T. G. (2020) · Figshare · doi:10.6084/m9.figshare.12655193
Additional file 8 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695821
Additional file 1 of Long non-coding RNA LINC01116 acts as an oncogene in prostate cancer cells through regulation of miR-744-5p/UBE2L3 axis
Yu, S., Yu, H., Zhang, Y., Liu, C., Zhang, W., & Zhang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14227912
Additional file 9 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695824
Additional file 2 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776541
Additional file 2 of Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
Low, W. Y., Rosen, B. D., Ren, Y., Bickhart, D. M., To, T., Martin, F. J., Billis, K., Sonstegard, T. S., Sullivan, S. T., Hiendleder, S., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19711493
Additional file 12 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., ChunNian, L., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031270
Additional file 10 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695827
Additional file 6 of LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3
Shu, G., Su, H., Wang, Z., Lai, S., Wang, Y., Liu, X., Dai, L., Bi, Y., Chen, W., Huang, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13646900
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Additional file 1 of LncRNA MYLK-AS1 facilitates tumor progression and angiogenesis by targeting miR-424-5p/E2F7 axis and activating VEGFR-2 signaling pathway in hepatocellular carcinoma
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Additional file 1 of ortho2align: a sensitive approach for searching for orthologues of novel lncRNAs
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Additional file 1 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695800
Additional file 11 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., ChunNian, L., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031267
Additional file 1 of Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
Zhu, Y., Chen, L., Hong, X., Shi, H., & Li, X. (2022) · Figshare · doi:10.6084/m9.figshare.19799861
Additional file 5 of LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3
Shu, G., Su, H., Wang, Z., Lai, S., Wang, Y., Liu, X., Dai, L., Bi, Y., Chen, W., Huang, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13646897
Additional file 9 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., Liang, C., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031297
Additional file 1 of Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
Low, W. Y., Rosen, B. D., Ren, Y., Bickhart, D. M., To, T., Martin, F. J., Billis, K., Sonstegard, T. S., Sullivan, S. T., Hiendleder, S., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19711490
Additional file 3 of LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3
Shu, G., Su, H., Wang, Z., Lai, S., Wang, Y., Liu, X., Dai, L., Bi, Y., Chen, W., Huang, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13646891
Additional file 1 of LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3
Shu, G., Su, H., Wang, Z., Lai, S., Wang, Y., Liu, X., Dai, L., Bi, Y., Chen, W., Huang, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13646885
Additional file 6 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695815
Additional file 7 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695818
Additional file 1 of Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
Wang, L., Han, J., Lu, K., Li, M., Gao, M., Cao, Z., Zhao, T., Chen, X., Tao, X., Chen, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14776538
Additional file 3 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695806
Additional file 2 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695803
Additional file 4 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695809
Additional file 10 of Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Zhang, X., Bao, Q., Jia, C., Li, C., Chang, Y., Wu, X., ChunNian, L., Bao, P., & Yan, P. (2020) · Figshare · doi:10.6084/m9.figshare.13031264
Additional file 5 of Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis
Cardeillac, C. R., Trovero, M. F., Radío, S., Smircich, P., Rodríguez‐Casuriaga, R., Geisinger, A., & Sotelo-Silveira, J. (2024) · Figshare · doi:10.6084/m9.figshare.26695812
Additional file 4 of Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species
Zhu, Y., Chen, L., Hong, X., Shi, H., & Li, X. (2022) · Figshare · doi:10.6084/m9.figshare.19799870
Additional file 4 of LINC00680 enhances hepatocellular carcinoma stemness behavior and chemoresistance by sponging miR-568 to upregulate AKT3
Shu, G., Su, H., Wang, Z., Lai, S., Wang, Y., Liu, X., Dai, L., Bi, Y., Chen, W., Huang, W., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13646894
Additional file 6 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress
Dou, J., Schenkel, F., Hu, L., Khan, A., Khan, M. Z., Yu, Y., Wang, Y., & Wang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14053260
Population‐level analyses reveal contrasting landscapes of gene expression divergence and evolution between male and female transcriptome lineages in the house mouse
Wei, K., Xie, C., Zhang, X., Ahmad, A., Duan, L., Chu, M., Gao, Y., Tautz, D., & Zhang, W. (2026) · Journal of Systematics and Evolution · doi:10.1111/jse.70037
The Bivalent Chromatin and a Potential Silencer for Differential Expression of PRSS Genes in the Human Testis
Iijima, K., Shibayama, R., Fujimori, C., & Kimura, A. P. (2026) · Molecular Reproduction and Development · doi:10.1002/mrd.70091
Population-wide variation in connectopic organization of cerebral language hubsPreprint
Amelink, J. S., Ramoser, C., Soheili‐Nezhad, S., Schijven, D., Wang, M., Fisher, S. E., Beckmann, C. F., Haak, K. V., & Francks, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.12.711274
Genome-Wide Identification and Functional Characterization of LncRNA-mRNA Networks During Petal Opening and Senescence in Osmanthus fragrans
Yang, J., Cai, X., Chen, X., Zeng, X., Li, Z., Wu, Y., Chen, H., Zhang, Y., & Zou, J. (2026) · Horticulturae · doi:10.3390/horticulturae12030365
MiRNA degradation by a conserved target RNA regulates animal behavior
Bitetti, A. (2017) · theses.fr (ABES) · doi:10.70675/30bd04eczc40bz4791z8cffz311f59320c18
Evolution of the human & mouse X-chromosome inactivation regulatory network
Rosspopoff, O. (2018) · theses.fr (ABES) · doi:10.70675/969f9a3cz607bz4b1fzb38fzfb3fd338b65d
Discovery of the role of protein-RNA interactions in protein multifunctionality and cellular complexity
Ribeiro, D. M. (2018) · theses.fr (ABES) · doi:10.70675/7fc623a8z4c1dz4aefz8460zf6be1886d753
Nuclear organization and regulation of gene expression in mouse Embryonic Stem Cells by long non-coding RNAs
Tachtsidi, A. (2018) · theses.fr (ABES) · doi:10.70675/2ef58956zd619z4f59z94dbz6262d6448ed1
Functional characterization of long non-coding RNAs associated with the epithelial-to-mesenchymal transition
Jarroux, J. (2019) · theses.fr (ABES) · doi:10.70675/6004244ez8528z4704z9d6cz5dd43c9c2ba3
Annotation des ARN longs non-codants chez la poule et les espèces d’élevage : Focus sur les ARNlnc régulateurs du métabolisme des lipides
Muret, K. (2018) · theses.fr (ABES) · doi:10.70675/defce595z0f08z4947z894bzcac35e8d29e7
Dans les abysses du transcriptome : découverte de nouveaux biomarqueurs de cellules souches mésenchymateuses par analyse approfondie du RNAseq
Riquier, S. (2019) · theses.fr (ABES) · doi:10.70675/3d47a367z9d23z46f2za905z5bb80c2492b3
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Authors: Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J. C., Grützner, F., & Kaessmann, H.
Affiliations: Broad Institute (US)
SIB Swiss Institute of Bioinformatics (CH)
The University of Adelaide (AU)
Humboldt-Universität zu Berlin (DE)
Stanford Medicine (US)
Corresponding author: Kaessmann, Henrik
ORCID: Liechti, Angélica
Baker, Julie C.
Grützner, Frank
Kaessmann, Henrik
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2014-01-19
Volume: 505
Issue: 7485
Pages: 635-640
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature12943
OpenAlex: W2088069070
Cited by: 984
References: 58
Citations by year: 2026: 30 · 2025: 26 · 2024: 62 · 2023: 55 · 2022: 70 · 2021: 85 · 2020: 116 · 2019: 107 · 2018: 87 · 2017: 106 · 2016: 104 · 2015: 91 · 2014: 44
FWCI: 36.87
Type: journal article
Language: en
Open access: green
cnrs.hal.science
Licence: other-oa
www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
HAL (submittedVersion, other-oa)
RePEc: Research Papers in Economics (submittedVersion)
Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
IRIS (submittedVersion)
SERVAL (Université de Lausanne) (submittedVersion)
Funders: Wellcome Trust (099175/Z/12/Z)
Medical Research Council (MC_PC_15004)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: long non-coding RNA, lncRNA evolution, tetrapods, embryonic development, tissue-specific gene expression, co-expression network, spermatogenesis, synaptic transmission, placental development, non-model organisms
MeSH terms: Animals, Anura, Chickens, Multigene Family, Humans, Primates, Proteins, RNA Precursors, Conserved Sequence, Gene Expression Regulation, Developmental, Evolution, Molecular, Genomics, MicroRNAs, Mice, Transcriptome, RNA, Long Noncoding

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The evolution of lncRNA repertoires and expression patterns in tetrapods

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