The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.
The relationship between non‐protein‐coding DNA and eukaryotic complexity
Abstract
There are two intriguing paradoxes in molecular biology—the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein‐coding genes—referred to as the C‐value and G‐value paradoxes, respectively. The C‐value paradox may be largely explained by varying ploidy. The G‐value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount of non‐protein‐coding sequence increases consistently with complexity. We also show that the distribution of introns in complex organisms is non‐random. Genes composed of large amounts of intronic sequence are significantly overrepresented amongst genes that are highly expressed in the nervous system, and amongst genes downregulated in embryonic stem cells and cancers. We suggest that the informational paradox in complex organisms may be explained by the expansion of cis‐acting regulatory elements and genes specifying trans‐acting non‐protein‐coding RNAs. BioEssays 29: 288–299, 2007. © 2007 Wiley Periodicals, Inc.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750
Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. (2004) · Nature · doi:10.1038/nature03025 · Cited by 1,966
A germline-specific class of small RNAs binds mammalian Piwi proteins
Girard, A., Sachidanandam, R., Hannon, G. J., & Carmell, M. A. (2006) · Nature · doi:10.1038/nature04917 · Cited by 1,762
A novel class of small RNAs bind to MILI protein in mouse testes
Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J., Kuramochi-Miyagawa, S., Nakano, T., et al. (2006) · Nature · doi:10.1038/nature04916 · Cited by 1,516
The genome of the social amoeba Dictyostelium discoideum
Eichinger, L., Pachebat, J. A., Glöckner, G., Rajandream, M.-A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., et al. (2005) · Nature · doi:10.1038/nature03481 · Cited by 1,351
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165
An RNA gene expressed during cortical development evolved rapidly in humans
Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., et al. (2006) · Nature · doi:10.1038/nature05113 · Cited by 1,005
Cited by
Long non-coding RNAs: insights into functions
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2521 · Cited by 5,654
Self-citationLong non-coding RNAs: new players in cell differentiation and development
Fatica, A., & Bozzoni, I. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3606 · Cited by 2,980
Long noncoding RNAs: past, present, and future
Kung, J. T. Y., Colognori, D., & Lee, J. T. (2013) · Genetics · doi:10.1534/genetics.112.146704 · Cited by 1,874
The Emergence of lncRNAs in Cancer Biology
Prensner, J. R., & Chinnaiyan, A. M. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0209 · Cited by 1,770
Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,371
Self-citationSpecific expression of long noncoding RNAs in the mouse brain
Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F., & Mattick, J. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706729105 · Cited by 1,103
Self-citationEvolution of microRNA diversity and regulation in animals
Berezikov, E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3079 · Cited by 712
Long non-coding RNAs and complex diseases: from experimental results to computational models
Chen, X., Yan, C. C., Zhang, X., & You, Z.-H. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw060 · Cited by 567
Fromm, B., Billipp, T., Peck, L. E., Johansen, M., Tarver, J. E., King, B. L., Newcomb, J. M., Sempere, L. F., Flatmark, K., Hovig, E., et al. (2015) · Annual Review of Genetics · doi:10.1146/annurev-genet-120213-092023 · Cited by 537
Targeting long non-coding RNA to therapeutically upregulate gene expression
Wahlestedt, C. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd4018 · Cited by 532
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
Quek, X. C., Thomson, D. W., Maag, J. L. V., Bartonicek, N., Signal, B., Clark, M. B., Gloss, B. S., & Dinger, M. E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku988 · Cited by 527
Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells
Luo, S., Lu, J. Y., Liu, L., Yin, Y., Chen, C., Han, X., Wu, B., Xu, R., Liu, W., Yan, P., et al. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.01.024 · Cited by 409
MicroRNAs and the advent of vertebrate morphological complexity
Heimberg, A. M., Sempere, L. F., Moy, V. N., Donoghue, P. C. J., & Peterson, K. J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712259105 · Cited by 406
Vienberg, S., Geiger, J., Madsen, S., & Dalgaard, L. T. (2017) · Acta Physiologica · doi:10.1111/apha.12681 · Cited by 373
The functional role of long non-coding RNAs and epigenetics
Cao, J. (2014) · Biological Procedures Online · doi:10.1186/1480-9222-16-11 · Cited by 357
Non-coding RNAs, epigenetics and complexity
Costa, F. F. (2008) · Gene · doi:10.1016/j.gene.2007.12.008 · Cited by 317
Selection, breeding and engineering of microalgae for bioenergy and biofuel production
Larkum, A. W. D., Ross, I. L., Kruse, O., & Hankamer, B. (2012) · Trends in Biotechnology · doi:10.1016/j.tibtech.2011.11.003 · Cited by 310
Regulation of mammalian cell differentiation by long non‐coding RNAs
Hu, W., Alvarez‐Dominguez, J. R., & Lodish, H. F. (2012) · EMBO reports · doi:10.1038/embor.2012.145 · Cited by 309
The central role of RNA in human development and cognition
Mattick, J. S. (2011) · FEBS Letters · doi:10.1016/j.febslet.2011.05.001 · Cited by 274
Self-citationLekka, E., & Hall, J. (2018) · FEBS Letters · doi:10.1002/1873-3468.13182 · Cited by 251
Noncoding RNAs in neurodegeneration
Salta, E., & De Strooper, B. (2017) · Nature Reviews Neuroscience · doi:10.1038/nrn.2017.90 · Cited by 183
RNA oxidation in Alzheimer disease and related neurodegenerative disorders
Nunomura, A., Hofer, T., Moreira, P. I., Castellani, R. J., Smith, M. A., & Perry, G. (2009) · Acta Neuropathologica · doi:10.1007/s00401-009-0508-1 · Cited by 148
Deciphering the functions and regulation of brain-enriched A-to-I RNA editing
Li, J. B., & Church, G. M. (2013) · Nature Neuroscience · doi:10.1038/nn.3539 · Cited by 141
Promotion of embryonic cortico-cerebral neuronogenesis by miR-124
Maiorano, N. A., & Mallamaci, A. (2009) · Neural Development · doi:10.1186/1749-8104-4-40 · Cited by 95
PETERSON, K. J., SUMMONS, R. E., & DONOGHUE, P. C. J. (2007) · Palaeontology · doi:10.1111/j.1475-4983.2007.00692.x · Cited by 93
Genetic Networks Governing Heart Development
Waardenberg, A. J., Ramialison, M., Bouveret, R., & Harvey, R. P. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a013839 · Cited by 59
The mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37
Genomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Bliim, N., Leshchyns'ka, I., Keable, R., Chen, B. J., Curry-Hyde, A., Gray, L., Sytnyk, V., & Janitz, M. (2019) · Genomics · doi:10.1016/j.ygeno.2018.11.019 · Cited by 17
Epigenetic and experimental approaches influencing non-coding RNAs
(2025) · Progress in Molecular Biology and Translational Science · doi:10.1016/bs.pmbts.2025.05.001 · Cited by 3
Noncoding RNAs in Retrovirus Replication
Duchon, A. A., & Musier-Forsyth, K. (2018) · Retrovirus-Cell Interactions · doi:10.1016/b978-0-12-811185-7.00012-1 · Cited by 1
Metadata
- Authors
- Taft, R. J., Pheasant, M., & Mattick, J. S.
- Venue
- BioEssays
- Publisher
- Wiley
- Published
- 2007-02-12
- Volume
- 29
- Issue
- 3
- Pages
- 288-299
- ISSN
- 0265-9247 (ISSN-L)
- 1521-1878
- OpenAlex
- W2128731054
- Cited by
- 700
- References
- 16
- FWCI
- 4.33
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.