Bee genome changes dramatically through life

_{Denyse O'Leary

September 13, 2018

Epigenetics, Genetics}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

Pollinating Bee Remember old-fashioned, unalterable DNA? It was interesting stuff. So now this:

“A study of chemical tags on histone proteins hints at how the same genome can yield very different animals:”

The bee genome has a superpower. Not only can the exact same DNA sequence yield three types of insect—worker, drone, and queen—that look and behave very differently, but, in the case of workers, it dictates different sets of behaviors.

A key to the genome’s versatility seems to be epigenetic changes—chemical tags that, when added or removed from DNA, change the activity of a gene. Previous studies had shown distinct patterns of tags known as methyl groups on the genomes of bees performing different roles within their hives.Shawna Williams, “As Bees Specialize, So Does Their DNA Packaging” at The Scientist

One wonders what the tax-funded textbooks are still saying about DNA…

See also: Evolution is evolving? [It had better be.] The conference seems to be dedicated to the extended evolutionary synthesis, which it contrasts with the “modern synthesis”

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

Comments

To all: Now, please consider again the reasoning I quote (from my transcription regulation thread) at #45 here. I will try to put it even more cleraly, and to extend it to bees' eusociality, and to other similar examples in animal life. So, let's start again, conventionally, from the zygote in a muòticellular organism, such as humans. a) The zygote is a special information program, with the ability to develop into a whole organism. b) That information is not only in the genome (sequence of nucleotides), but also in the specific reading of genomic information available in the zygote, IOWs the sum total of its genetic and epigenetic information. c) The dynamic program expressed in the zygote starts a developmental process that will, in the end, generate the multicellular organism. d) That is done, primarily, by a highly ordered and functional process of cell differentiation, so that many different specific programs are generated in different cell types, by specific new genetic and epigenetic compbinations of functional information, so that the zygote may generate all the different cell types that are needed. e) But, of course, that is not enough. Cells must differentiate in spatial and temporal order, to generate tissues and organs and, in the end, the whole organism. f) To do that, the developing zygote generates, according to a well defined and hereditary program, already present in the total information content of the zygote itself, different and dynamic "environments", highly controlled by the program itself, defined by different components, such as the cellular content, the cell to cell interactions, and the structural components of the developing organism. Examples of such environments are the blastula, gastrula, the three germ layers, and so on. And the maternal components too. But also, for example, the bone marrow niches where blood cell production from hematopoietic stem cells takes place throughout life. g) All those components are of course "environment" to each individual cell, but they are an integral part of the developing program, and they are under the strict control of the program itself. h) But, of course, there is another kind of "environment", that is not under the control of the program. Let's call it "the random environment". IOWs, all those conditions that are contingent. Maybe contingent differences in the uterine environment, or just the way the embryo is implanted, or differences in outer stimuli (temperature, stress conditions, radiations, infections, and so on). We know that such influences, in certain cases, can even compromise the successful development of the organism. i) One thing is certain: these differences, because of their random (contingent) nature in relation to the developing organism, are not part of the program. They may generate individual differences in the organisms, good or bad, in the same way that environmental conditions will influence post-natal life. But they are not part of the program that defines the organism as a species. Indeed, the program itself must be able to cope with them, so that it can be successful in generating the organism in spite of contingent influences. j) In that sense, the ability of the program to generate a living and functional organism even in the presence of uncontrolled environmental contingencies is a triumph of its functional information. OK, now let's see how that applies to bees and to their eusociality. My point is that eusociality, in the measure that it is based on the hereditary program of bees (and it is, because it develops in a controlled way, and not out of contingent conditions) is a process similar to cell differentiation. So, as individual cells differentiate to perform different roles in the organism, in the same way individual organisms differentiate to perform different roles in the eusocial structure. And that happens under the control of the general program, and in spite of contingent factors. Because the organism differentiation, like the cell differentiation, is controlled by the hereditary program and its functional information: the same program that is present in the zygote, and its exclusive combination of genetic and epigenetic functional information. So, the functional information in eusocial animals has one added layer of functionality: the control of the specific phenotypic development of different organism types, and of their roles and behaviours in a well organized social structure that is hereditary and functional.gpuccio_{September 16, 2018
September
09
Sep
16
16
2018
03:17 AM
3
03
17
AM
PDT}

gpuccio: I’m glad to see you have started to lead this thread in the right direction. Thanks.OLV_{September 16, 2018
September
09
Sep
16
16
2018
03:09 AM
3
03
09
AM
PDT}

jawa, I see you kind of led Amblyrhynchus and R J Sawyer to this point. Now it’s time for you to take a break and then come back ready to join the serious discussion gpuccio has just sparked starting at 44.PeterA_{September 16, 2018
September
09
Sep
16
16
2018
03:05 AM
3
03
05
AM
PDT}

gpuccio @47: I appreciate you have started to dig deep into the tremendously rich topic of this OP. Thanks!PeterA_{September 16, 2018
September
09
Sep
16
16
2018
02:59 AM
2
02
59
AM
PDT}

gpuccio: Excellent comments 44 and 45. Hopefully they help to take this discussion in the right direction (finally!). The main topic of this OP seems very related to your latest thread on transcription regulation and to the previous discussion thread on chromatin topology and functionality. Both discussions became rich sources of serious reference material for future discussions. Thanks!PeterA_{September 16, 2018
September
09
Sep
16
16
2018
02:55 AM
2
02
55
AM
PDT}

To all: Now, first of all let's read the abstract of the paper mentioned in the OP: Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development https://genome.cshlp.org/content/early/2018/08/20/gr.236497.118.abstract?sid=83ce03cc-d346-433d-b882-675433a8bbec
Abstract: The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen–worker morphological and reproductive divide is environmentally controlled during post-embryonic development by differential feeding. Previous studies implicated metabolic flux acting via epigenetic regulation, in particular DNA methylation and microRNAs, in establishing distinct patterns of gene expression underlying caste-specific developmental trajectories. We produce the first genome-wide maps of chromatin structure in the honey bee at a key larval stage in which developmental canalization into queen or worker is virtually irreversible. We find extensive genome-wide differences in H3K4me3, H3K27ac, and H3K36me3, many of which correlate with caste-specific transcription. Furthermore, we identify H3K27ac as a key chromatin modification, with caste-specific regions of intronic H3K27ac directing the worker caste. These regions may harbor the first examples of caste-specific enhancer elements in the honey bee. Our results demonstrate a key role for chromatin modifications in the establishment and maintenance of caste-specific transcriptional programs in the honey bee. We show that at 96 h of larval growth, the queen-specific chromatin pattern is already established, whereas the worker determination is not, thus providing experimental support for the perceived timing of this critical point in developmental heterochrony in two types of honey bee females. In a broader context, our study provides novel data on environmentally regulated organismal plasticity and the molecular foundation of the evolutionary origins of eusociality.
OK, so he paper is about epigenetic patterns that contribute to establish the two types of honey bee females that, together with the male drone, are the foundation fro the complex "eusociality" of bees, IOW a complex hereditary social structure that is established in bees. That said, I will reason about the meaning of all that. In next post.gpuccio_{September 16, 2018
September
09
Sep
16
16
2018
02:45 AM
2
02
45
AM
PDT}

Amblyrhynchus and R J Sawyer: gpuccio has written excellent comments addressed to both of you. Now is your turn tu show how serious is your participation in this website.PeterA_{September 16, 2018
September
09
Sep
16
16
2018
02:45 AM
2
02
45
AM
PDT}

R J Sawyer: Your comment #1, and some statements by Amblyrhynchus, are IMO a good point to start a serious discussion about the issue mentioned in the OP, rather than continuing a sterile debate about the title or individual "errors" or "intentions". So, let's start a discussion about what Amblyrhynchus calls “gene-environment interactions”. I would call it differently: "Functional information - environment interaction" because, as you may know having been a very kind and appreciated guest at my thread about transcription regulation: https://uncommondescent.com/intelligent-design/transcription-regulation-a-miracle-of-engineering/ I think that functional information is always in the form of a dynamic state involving both the genome abd everything else in the cell (let's say the epigenome), and that's the entity which interacts with environment or with anything else. That said, I think I have partially covered an important aspect of the interaction between the functional program and environment in the final part of my comment #200 in that thread, that I quote here for your convenience:
Each program written in the dynamic cell is a specific selection of information that can guide that specific cell in that specific state to some new specific state. And so on. Of course, much of that must be written in the DNA sequence: protein genes and promoters and enhancers and non coding genes are all written there. But they can only work in the appropriate dynamic context, and nowhere else. The complexity of that all is overwhelming. Add to that that many factors come from outside the cell, from the “environment”. But that environment is, of course, part of the program, part of the engineering. It includes signals from other cells, or even signals from environmental niches. But those signals are functional, not random. They have been engineered, too. The program, with its complexity, could never work if the signal from the environment were random. That’s why the embryo requires a very protected and controlled environment. Of course, random noise can always happen: it does happen, and often it can destroy or deform the program. As we well know. But, in general, the program works very well. Because the procedures are robust. And the general control is robust. There is a lot of very, very good engineering there. A lot of extremely good Intelligent Design.
I will try to develop better that point in my next post, with some more specific reference to bees, and of course both you and Amblyrhynchus are cordially invited to the discussion. :)gpuccio_{September 16, 2018
September
09
Sep
16
16
2018
12:35 AM
12
12
35
AM
PDT}

Amblyrhynchus at #40: I can agree with you that this thread is strange. But I believe that my comment #31 to you was intended to start a more serious discussion, beginning with a statement you yourself have made at #18. Can you answer my point, and maybe clarify better your point about messy hacks and historical contingency? So that I can maybe clarify my objections? That could be more interesting than debating how appropriate a title is. Whatever the title, the issue presented in New's OP is certainly important and interesting. Moreover, as at #40 you also mention the "gene-environment interactions" problem, that is certainly pertinent to this discussion, and has also been raised by R J Sawyer at comment #1, I invite you to join the discussion about that too, and to read my next comment to R J Sawyer about that point.gpuccio_{September 16, 2018
September
09
Sep
16
16
2018
12:20 AM
12
12
20
AM
PDT}

Amblyrhynchus, What exactly you don’t like about it? What exactly bothers you?jawa_{September 15, 2018
September
09
Sep
15
15
2018
09:29 PM
9
09
29
PM
PDT}

Yeah, that's good (though I don't thin "genome-effect" is a term that adds much to the world). I just don't why you have since gone into this crazy interrogation of which treads people comment on. What has compelled you to do this?Amblyrhynchus_{September 15, 2018
September
09
Sep
15
15
2018
08:12 PM
8
08
12
PM
PDT}

Amblyrhynchus @40: Please, read my comment @22, where I stated this: The title of the current OP, which was started Sept 13, is perhaps inaccurate because it could have said “genome effect” instead of just “genome”, I don’t have any problem with pointing at possible errors regardless of their source. You avoided the serious discussions with gpuccio but didn’t hesitate to discuss here about an error in the title ?jawa_{September 15, 2018
September
09
Sep
15
15
2018
07:45 PM
7
07
45
PM
PDT}

This thread just stranger and stranger... All Origines or News had to do was say, "quite right, the genome hasn't change here" and move on. Perhaps they could hve then thought about whether gene-environment interactions of the sort described here are a problem for evolutionary biology, but that may be too much to hope for. Instead, Origenes decided to google up some links and parade their ignorance of this topic. News and ET offer some lame excuse to claim (against the plain meaning of the word) that histones are part of the genome. And Jawa has launched into some spammy amateur detective routine to, I can only assume, distract from his fellow-travellers embarrassment. Why is so hard for any of you to simply admit this mistake and move on?Amblyrhynchus_{September 15, 2018
September
09
Sep
15
15
2018
06:47 PM
6
06
47
PM
PDT}

R J Sawyer @37: Are you saying that gpuccio chose “an OP title that is biased towards a view that cannot be proven or disproven” ? The evidences we know are sufficient proof for the veracity of the title gpuccio chose for his excellent OP and following comments. Actually, gpuccio himself presents some of those evidences with tremendous clarity. However, it’s an undeniable fact that you aren’t willing to accept the truth and nobody can force you to.jawa_{September 15, 2018
September
09
Sep
15
15
2018
04:37 PM
4
04
37
PM
PDT}

one that is demonstrably counter-factual.
Life requires a symbol system, just as it was predicted, prior to experimental confirmation. The only other example of this physical system is human language. So, wrapping up, we have a confirmed prediction and the universal experience of all research and observation. Which theory is “demonstrably counter-factual”, the theory that says the gene system is an inference to an intelligent act, or the one that says it’s an inference to an unguided physical process?Upright BiPed_{September 15, 2018
September
09
Sep
15
15
2018
02:42 PM
2
02
42
PM
PDT}

Jawa
Are you saying that you agree with that statement which explicitly implies that the transcription regulation process was intelligent designed? Is that right?
No. I don’t agree with it. But we are on UD, a site that advocates for design. I would expect OP titles to reflect this. But there is a difference between an OP title that is biased towards a view that cannot be proven or disproven and one that is demonstrably counter-factual.R J Sawyer_{September 15, 2018
September
09
Sep
15
15
2018
02:07 PM
2
02
07
PM
PDT}

R J Sawyer @32: Ok, are you saying that you don’t have a problem with the scandalously “heretic” statement that gpuccio chose for the title of his excellent OP? Are you saying that you agree with that statement which explicitly implies that the transcription regulation process was intelligent designed? Is that right?jawa_{September 15, 2018
September
09
Sep
15
15
2018
12:50 PM
12
12
50
PM
PDT}

Ambly
Histones are not part of the genome.
ET
Where do you think they are coded? What do you think they do?
As with all proteins, they are coded in the genome. They are not part of the genome.R J Sawyer_{September 15, 2018
September
09
Sep
15
15
2018
09:33 AM
9
09
33
AM
PDT}

I hadn't supposed that the sequence changed. If a genome is, in some sense, a language, it could change dramatically via small substitutions, without the sequence changing, couldn't it? Suppose we changed "John shoved a cap right in my face!" to "John shoved a cop, right in my face!" The substitution was small. Now, assuming John survives the encounter (natural selection? ;) ), the outcome for John will likely be different...News_{September 15, 2018
September
09
Sep
15
15
2018
08:04 AM
8
08
04
AM
PDT}

R J Sawyer:
The title of the OP is misleading. The DNA sequences do not change.
As you have been told no one said they do Ambly:
Histones are not part of the genome
Where do you think they are coded? What do you think they do?ET_{September 15, 2018
September
09
Sep
15
15
2018
07:33 AM
7
07
33
AM
PDT}

Just to sate Jawa’s curiosity at 27, I didn’t have a problem with GP’s title because it may be accurate. The title of this OP is just factually wrong and misleading.R J Sawyer_{September 15, 2018
September
09
Sep
15
15
2018
06:23 AM
6
06
23
AM
PDT}

Amblyrynchus at #18:
I hadn’t seen the thread. I actually have a paper focusing on chromatin state in review just now. Let’s just say my experience of that project has reaffirmed my view that eukaryotic genomes are messy hacks fill of historical contingency…
Well, messy hacks that seem to work really fine, I would say. I am certainly not denying the "historical contingency". I am not sure what you mean, but in general I can agree with the idea. But if such complex systems work so well, and generate well differentiated cell types and tissues and organisms of amazing functional complexity in spite of all the possible "historical contingency", that is even more surprising.gpuccio_{September 15, 2018
September
09
Sep
15
15
2018
02:04 AM
2
02
04
AM
PDT}

Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variationsOLV_{September 14, 2018
September
09
Sep
14
14
2018
07:57 PM
7
07
57
PM
PDT}

jawa, I agree with Peter. Who cares about what those guys said or didn't say? Let's move on.OLV_{September 14, 2018
September
09
Sep
14
14
2018
07:51 PM
7
07
51
PM
PDT}

jawa, can you leave that guy alone and focus in on the material to discuss? We have a fascinating topic to dig in but you are spending time in a court-style cross-examination that seems irrelevant.PeterA_{September 14, 2018
September
09
Sep
14
14
2018
07:48 PM
7
07
48
PM
PDT}

R J Sawyer @26: Maybe inconsistence is not the right term in this case. Please help me to understand: Apparently you found problems in the title of the current OP but didn't find any problem in the title of gpuccio's OP. Apparently you strongly disagree with the title of the current "bee genome" OP, but do you agree with the title of gpuccio's OP? If that is not inconsistence, then what is it?jawa_{September 14, 2018
September
09
Sep
14
14
2018
07:35 PM
7
07
35
PM
PDT}

Jawa
Can you explain that inconsistency?
What’s inconsistent? On GP’s thread I posted an admittedly off topic suggestions that GP and I went back and forth a couple times and I left so as not to drag the thread off on a tangent. I had no desire to comment on the content of the OP. On this thread my comments (except the last two) have been on topic.R J Sawyer_{September 14, 2018
September
09
Sep
14
14
2018
07:17 PM
7
07
17
PM
PDT}

Peter, thanks for providing the link to the paper. Here's the PDF.OLV_{September 14, 2018
September
09
Sep
14
14
2018
07:15 PM
7
07
15
PM
PDT}

UB @20: Good point. Thanks.OLV_{September 14, 2018
September
09
Sep
14
14
2018
07:14 PM
7
07
14
PM
PDT}

Apparently this is the paper associated with the article that inspired this OP: Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval developmentPeterA_{September 14, 2018
September
09
Sep
14
14
2018
07:12 PM
7
07
12
PM
PDT}

Prev 1 … 4 5 6 7 Next

You must be logged in to post a comment.

Leave a Reply