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Researcher: Genome not an unstructured strand but “a highly structured and meaningful design”

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Subset of immune cells, named DN2a T cells, mature into DN2b T cells, controlled by forgotten DNA strands.

From Mario Aguilera at U San Diego News:

Intricate human physiological features such as the immune system require exquisite formation and timing to develop properly. Genetic elements must be activated at just the right moment, across vast distances of genomic space.

“Promoter” areas, locations where genes begin to be expressed, must be paired precisely with “enhancer” clusters, where cells mature to a targeted function. Faraway promoters must be brought in proximity with their enhancer counterparts, but how do they come together? When these elements are not in sync, diseases such as leukemia and lymphoma can result. How does this work?

Biologists at the University of California San Diego believe they have the answer.

Calling it the “big bang” of immune cell development, the researchers made their discovery within previously overlooked stretches of DNA located between genes. The results, published in the September 21 edition of the journal Cell, were led by Takeshi Isoda in Cornelis Murre’s laboratory in UC San Diego’s Division of Biological Sciences.

Through genomic studies and genetic experiments in mice, the scientists found that the ignored areas, known as “non-coding” DNA, activate a change in the 3D structure of DNA that brings promoters and enhancers together with stunning accuracy. Murre describes the mechanism as somewhat like a stiff wire—with enhancers and promoters on either end—that’s bended together into a loop and anchored in place. Enhancers and promoters, once distantly separated, are now repositioned in close proximity to initiate the development of immune system building blocks known as T cells.

“Nature is so clever. We think of the genome as an unstructured strand but in fact what we are seeing is a highly structured and meaningful design,” said Murre. “The process of architecture remodeling we’ve described allows the enhancer and promoter to find each other in 3D space at precisely the right time. The beauty is that it’s all very carefully orchestrated. We have seen one example but there are likely many others all occurring at the same time when cells are moving along the developmental pathway–that’s kind of amazing.” More.

Return to product information “Nature is so clever”? No, the programming that goes into nature is clever. See Evolutionary Informatics.

See also: Microprotein helps cells decide on best path to repair genes and avoid cancer

Researchers: Long-held view of cell division overturned (Transcription continues despite challenge during cell division.)

19 Replies to “Researcher: Genome not an unstructured strand but “a highly structured and meaningful design”

  1. 1
    Dionisio says:

    “the researchers made their discovery within previously overlooked stretches of DNA located between genes”?

    Duh! what else is new?
    Haven’t we heard this before?
    Same old, same old.

    As long as they stick to their narrow-minded reductionist bottom-up reverse engineering approach they’ll keep making these surprising/unexpected discoveries.

    Poor things.

  2. 2
    Dionisio says:

    ” but in fact what we are seeing is a highly structured and meaningful design”

    Did somebody say ‘design’?

    🙂

  3. 3
    Dionisio says:

    ” but in fact what we are seeing is a highly structured and meaningful design”

    Did somebody say ‘meaningful’?

    Does that have anything to do with complex functionally specified informational complexity?

  4. 4
    Dionisio says:

    ” but in fact what we are seeing is a highly structured and meaningful design”

    They ain’t seen nothin’ yet.

    The most fascinating discoveries are still ahead.

  5. 5
    Dionisio says:

    “…the scientists found that the ignored areas, known as “non-coding” DNA, activate a change in the 3D structure of DNA that brings promoters and enhancers together with stunning accuracy.”

    ignored areas, known as “non-coding” DNA???

    did somebody say ‘ignored’?

    Why did they ignore those areas before?

    Any valid reason for ignoring anything within the biological systems?

    Can someone provide a reasonable explanation?

  6. 6
    awstar says:

    “Nature is so clever”

    but not nearly as clever as the writers who use the term “forgotten strands” instead of “junk DNA”. For the sake of honesty, they should use the term “intentionally forgotten strands” so that those who intentionally hamper scientific progress can be called out for what they are.

  7. 7
    PaV says:

    Another day; another bad day for Darwinism.

  8. 8
    ET says:

    PaV- It’s amazing what some people will believe in the face of the evidence and all from the humble beginnings of replicating RNA’s. Utterly amazing…

  9. 9
    Dionisio says:

    “The beauty is that it’s all very carefully orchestrated.”

    Did somebody say ‘orchestrated’?

  10. 10
    Dionisio says:

    “that’s kind of amazing”

    Just “kind of”?

    In this case ‘amazing’ seems like an understatement. Doesn’t it?

  11. 11
    Dionisio says:

    why aren’t any politely dissenting interlocutors in this thread?

    🙂

  12. 12
    Dionisio says:

    obviously the question @11 seems rhetorical.
    doesn’t it?
    🙂

  13. 13
    Dionisio says:

    Original paper referenced here:

    Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

    http://www.cell.com/cell/fullt.....17)31050-4

  14. 14
    kurx78 says:

    “why aren’t any politely dissenting interlocutors in this thread?”
    Our politely dissenting interlocutors only choose battles they can win by rethoric.

  15. 15
    gpuccio says:

    Dionisio:

    “why aren’t any politely dissenting interlocutors in this thread?”

    OK, let’s see.

    They should explain how:

    1) The transcript from a non coding DNA region (lincRNA GM16084 or ThymoD), which

    2) is 620 bp long and derives from three different exons from a DNA segment (gene) 13044 bp long, and which

    3) has no protein coding function at all, still

    4) has a fundamental role in

    5) repositioning the enhancer for the very important Bcl11b protein coding gene from

    6) its starting peripheral position near the nuclear lamina to

    7) the nuclear interior, and

    8) induces structural changes in Chromatin Topology and

    9) juxtaposes the Bcl11b enhancer and promoter into a single-loop domain, by

    10) promoting demethylation at CTCF bound sites and

    11) activating cohesin-dependent looping, so that

    12) it can establish T cell identity and

    13) block lymphoid malignancy.

    Well, this just a brief summary. Those interested in the details (and there are a lot of them!) can check the paper itself.

    Talk of irreducible complexity!

    Talk of non coding-DNA functionality!

    OK, I can imagine the embarassment of our neo-darwinist friends.

    But, of course, those same people who cannot even begin to explain how a single protein coding gene can get its functional information, and who believe so strongly and obstinately in non coding DNA as junk, and who have been declaring for years that irreducible complexity is just a weird expression of Behe’s personal problems, will certainly be able to give us some brilliant story from their imagination to show how all that is possible, indeed perfectly expected, under a non design hypothesis. Just give them a few minutes…

    But no facts, please, give them no facts, I recommend. That could really confuse them! 🙂

  16. 16
    gpuccio says:

    Dionisio (and Seversky):

    Ah, and for all those who have read my post #8 here:

    https://uncommondescent.com/intelligent-design/is-origin-of-life-research-undergoing-a-renaissance/

    well, this is just one good example of how new facts constantly discovered in biology are daily supporting ID theory and falsifying neo-darwinism. 🙂

  17. 17
    Dionisio says:

    gpuccio,

    Thanks for your insightful (as usual) commentaries.

  18. 18
    Dionisio says:

    gpuccio @15:

    They should explain how:
    The transcript from a non coding DNA region (lincRNA GM16084 or ThymoD), which is 620 bp long and derives from three different exons from a DNA segment (gene) 13044 bp long, and which has no protein coding function at all, still has a fundamental role in repositioning the enhancer for the very important Bcl11b protein coding gene from its starting peripheral position near the nuclear lamina to the nuclear interior, and induces structural changes in Chromatin Topology and juxtaposes the Bcl11b enhancer and promoter into a single-loop domain, by promoting demethylation at CTCF bound sites and activating cohesin-dependent looping, so that it can establish T cell identity and block lymphoid malignancy.

    The best explanation the Neo-Darwinian folks could provide would be asking “huh? say what?”.

    But at the end they would respond that we just don’t understand evolution. Everything just somehow happened. We should study biology 101.

    Hey, they always win the debate.

    🙂

  19. 19
    Dionisio says:

    kurx78 @14:

    Our politely dissenting interlocutors only choose battles they can win by rhetoric.

    Ok, perhaps that explains their absence here.

    However, their prolific imagination would always produce a story that somehow explains every biological discovery.

    See gpuccio @15:

    But, of course, those same people who cannot even begin to explain how a single protein coding gene can get its functional information, and who believe so strongly and obstinately in non coding DNA as junk, and who have been declaring for years that irreducible complexity is just a weird expression of Behe’s personal problems, will certainly be able to give us some brilliant story from their imagination to show how all that is possible, indeed perfectly expected, under a non design hypothesis. Just give them a few minutes…

    🙂

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