Intelligent Design

CTCF controls ~ 10,000 3D Chromatin Loops

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Erez Aiden’s team of Baylor researchers discover a CTCF protein controlling 3D formation of 10,000 loops. Only 1 of 4 orientations is found. Challenges for evolution:
1) How did this essential CTCF protein develop to loop DNA when the DNA is essential for its production.
2) How was the 1 orientation in 4 selected?
See: There’s a Mystery Machine That Sculpts the Human Genome

. . .In 2014, a team led by Erez Lieberman Aiden at Baylor College of Medicine took important steps towards this goal by creating an unprecedentedly detailed 3-D map of the human genome. These genetic cartographers used a technique called Hi-C to embalm the genome and identify regions that interact with one another. Using this method, they identified a grand total of 10,000 loops—far fewer than the millions that were thought to exist. . . .
But when Aiden’s team looked at CTCF more closely, they found a huge surprise. The protein recognizes and sticks to specific DNA sequences, which act as its landing pads. These sequences point in a particular direction, which means that a pair of them can line up in four possible ways. They don’t. In reality, they almost always line up in just one of the four orientations, pointing towards each other in what study co-leader Eric Lander described as “a genomic yin and yang.”

They also showed that the loops obey certain rules. Most tend to be short. They occur in the same places whether you’re looking at a neuron or a skin cell, or a human cell or mouse cell. And they almost always associate with a protein called CTCF, which acts as a fastener. In theory, two CTCF proteins will bind to separate stretches of DNA and then lock together, creating a loop and holding it in place. . . .
The big mystery, he says, is how the loops actually grow. Is there some kind of ratcheting system that stops the DNA from sliding back? . . .
There’s a growing appreciation that some diseases are related to how the genome is oriented rather than just a mutation,” adds Rao. . . .

Rao et al., A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping, Cell (2014),

Already cited by 151 papers.

Curiouser and curioser for stochastic theoriests.
Obvious design components for ID.

6 Replies to “CTCF controls ~ 10,000 3D Chromatin Loops

  1. 1
    DLH says:

    One citing article: Chromatin architecture reorganization during stem cell differentiation Dixon et al. Nature 518, 331–336 (19 February 2015) doi:10.1038/nature14222

    Higher-order chromatin structure is emerging as an important regulator of gene expression. . . .
    although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. . . .
    we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.

    I predict this further differentiation applied to founder analysis will provide dramatic evidence contrary to conventional evolutionary wisdom.

  2. 2
    ppolish says:

    Unlocking the secrets of design. Unlocking secrets of the Design. Great Bio School down there in Texas.

  3. 3
    tjguy says:

    I wonder if Materialists ever find themselves in the position of fearing the results of scientific research. The more we find, the more the evidence piles up against them and stretches their faith even more.

    So, in this case, we need to learn more. I wonder if they are happy for this kind of research.

    You hear all the time that they are open to whatever is found. And that even if they don’t have answers, saying “I don’t know” is a good answer because it presents an exciting new field of research. But it also provides more data that fit nicely into the ID worldview as well. In fact the data fit better there than in the Materialist worldview.

    But, worldview is something we all simply take by faith so the Materialist just assumes that somehow it happened and sometime they will hopefully be able to explain it.

    Again, it seems there is no evidence at all that will convince them they could be wrong. They just ratchet up their faith in the powers of evolution and put off the problem to future research.

  4. 4
    Dionisio says:


    Thank you for bringing this very interesting topic up for discussion.

    Even the citing paper you referenced @1 has been cited by 15 PubMed Central articles.

  5. 5
    Dionisio says:

    I look forward to seeing gpuccio motivated by DLH’s OP to comment in this thread, if he can find some spare time. We miss his insightful commentaries.

  6. 6
    Dionisio says:

    DLH @1

    Here’s more from the paper you referenced @1:

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