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. 2014 May 8;10(5):e1004351.
doi: 10.1371/journal.pgen.1004351. eCollection 2014 May.

The case for junk DNA

Alexander F Palazzo  1 , T Ryan Gregory  2
Affiliations

The case for junk DNA

Alexander F Palazzo et al. PLoS Genet. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Summary of haploid nuclear DNA contents (“genome sizes”) for various groups of eukaryotes.
This graph is based on data for about 10,000 species , . There is a wide range in genome sizes even among developmentally similar species, and there is no correspondence between genome size and general organism complexity. Humans, which have an average-sized genome for a mammal, are indicated by a star. Note the logarithmic scale.
Figure 2
Figure 2. Levels of protein-coding and intergenic RNAs in mammalian cells.
(A) Analysis of nascent and total poly(A)+ RNA levels from mouse liver nuclei. Nascent (i.e., polymerase-associated) RNA and poly(A)+ RNA were isolated from mouse liver nuclei and analyzed by high-throughput sequencing. Individual reads were categorized by their source. Exonic and intronic are from known referenced genes (i.e., “RefSeq” genes), while intergenic originate from nonreferenced loci (i.e., “non-RefSeq”) in the mouse genome. Reproduced from . (B) Empirical Cumulative Distribution Function (ECDF) of transcript expression in each cell compartment as determined by the ENCODE consortia. Results for RNA that either contain (“polyA+”) or lack (“polyA−”) a poly(A)-tail in the nucleus and cytosolic fractions are shown. Each human cell line that was analyzed is represented by three lines, one for each pool of RNA (red for protein-coding RNAs, blue for lncRNAs [“noncoding”], and green for intergenic transcripts [“novel intergenic”]). The lines indicate the cumulative fraction of RNAs in a given pool (y-axis) that are expressed at levels that are equal or less than the reads per kilobase per million mapped reads (RPKM) on the x-axis. Total numbers in each pool are as follows: reference protein coding genes: 20,679, loci producing lncRNAs: 9,277, and regions producing intergenic transcripts: 41,204. Transcripts with expression levels of 0 RPKM were adjusted to an artificial value of 10−6 RPKM so that the onset of each graph represents the fraction of nonexpressed genes or loci. Note that 1–4 RPKM is approximately equivalent to one copy per tissue culture cell , . Using this figure, one can easily deduce that the vast majority of intergenic transcripts are present at levels less than one copy per cell. Reproduced with permission from .
See this image and copyright information in PMC

References

    1. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816 10.1038/nature05874 - DOI - PMC - PubMed
    1. ENCODE Project Consortium (2012) Bernstein BE, Birney E, Dunham I, Green ED, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57–74 10.1038/nature11247 - DOI - PMC - PubMed
    1. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, et al. (2012) Genomics: ENCODE explained. Nature 489: 52–55 10.1038/489052a - DOI - PubMed
    1. Pennisi E (2012) Genomics. ENCODE project writes eulogy for junk DNA. Science 337: 1159, 10.1126/science.337.6099.1159 - DOI - PubMed
    1. Eddy SR (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol CB 22: R898–899 10.1016/j.cub.2012.10.002 - DOI - PubMed

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