Using ENCODE Data for Human-Chimp DNA Comparisons

In 2012, a variety of research papers associated with the ENCODE project (Encyclopedia Of DNA Elements) described how the human genome was pervasively copied—transcribed—into an amazing array of functional RNA molecules that regulate how genes and the genome function.1

Much of the pervasive transcription is based on long non-coding RNAs (lncRNAs) that have the same control features as protein-coding genes but with other functions.2 A large group of lncRNAs stay in the cell’s nucleus, where some directly regulate how genes are expressed while others help modify chromosome structure. Some lncRNAs are exported into the cell’s cytoplasm to regulate the production of proteins, and others interact with various proteins to participate in other functions. Still other lncRNAs are exported completely out of the cell and communicate with other cells.

By definition, an lncRNA region of the genome encodes a non-protein-coding RNA transcript longer than 200 bases, yet some actually produce small proteins as well. These lncRNA areas can be found all over the genome, including inside introns—the non-coding segments within protein-coding genes.

Several major subclasses of lncRNAs are the long and very long intergenic non-coding RNAs that exist outside protein-coding genes, known as lincRNAs and vlincRNAs respectively.1,3 These are decidedly more restricted in their expression, depending on the animal classification in which they are found, compared to protein-coding genes.4 Thus, they make ideal candidates for research in studying genetic discontinuity, particularly between humans and chimpanzees.

A common claim among evolutionists is that human and chimp DNA is between 96 and 98 percent similar—but only carefully selected data were used to arrive at this conclusion. However, evolutionists themselves have reported that only about two-thirds of chimpanzee DNA sequence can be unambiguously aligned, meaning precisely matched, to human DNA.5 This is because the algorithm used in the analysis stops matching the DNA sequence when the human and chimp segments become too dissimilar, which occurs after only a few hundred bases, on average.6

In 2013, I published a research paper in which chimpanzee chromosomes were sequentially sliced into different sets of small pieces so that the algorithm could optimally compare them to human chromosomes. In so doing, I found that the chimpanzee genome was only about 70 percent similar to the human genome overall.7

More research is needed to show specifically how the new wealth of publicly available ENCODE data can be used beyond basic studies of human-chimp DNA similarity—incorporating lincRNAs and vlincRNAs to further highlight human uniqueness. Research using three large datasets produced by the ENCODE project is now underway at ICR for the purpose of addressing these questions. In a concurrent study, I am also comparing human protein-coding regions to those in chimpanzees. In combination, these new analyses will provide a much more detailed picture of what makes humans unique and will further demonstrate we are not evolved apes.


  1. Djebali, S. et al. 2012. Landscape of Transcription in Human Cells. Nature. 489 (7414): 101-108.
  2. Geisler, S. and J. Coller. 2013. RNA in Unexpected Places: Long Non-Coding RNA Functions in Diverse Cellular Contexts. Nature Reviews Molecular Cell Biology. 14 (11): 699-712.
  3. Tomkins, J. 2013. VlincRNAs Provide Clues to Genomic Dark Matter. Creation Science Update. Posted on August 19, 2013, accessed November 13, 2013.
  4. Liu, G., J. S. Mattick, and R. J. Taft. 2013. A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle. 12 (13): 2061-2072.
  5. Ebersberger, I. et al. 2002. Genomewide Comparison of DNA Sequences between Humans and Chimpanzees. American Journal of Human Genetics. 70 (6): 1490-1497.
  6. Tomkins, J. 2011. Genome-Wide DNA Alignment Similarity (Identity) for 40,000 Chimpanzee DNA Sequences Queried against the Human Genome is 86-89%. Answers Research Journal. 4 (2011): 233-241.
  7. Tomkins, J. 2013. Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70%. Answers Research Journal. 6 (2013): 63-69.

* Dr. Tomkins is Research Associate at the Institute for Creation Research and received his Ph.D. in genetics from Clemson University.

Cite this article: Jeffrey P. Tomkins, Ph.D. 2014. Using ENCODE Data for Human-Chimp DNA Comparisons. Acts & Facts. 43 (1).

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