More Evolution Evidence

[Amethyst]

Most human-chimp differences due to gene regulation

 

Most human-chimp differences due to gene regulation

 

The vast differences between humans and chimpanzees are due more to changes in gene regulation than differences in individual genes themselves, researchers from Yale, the University of Chicago, and the Hall Institute in Parkville, Victoria, Australia argue in the March 9 issue of the journal Nature.

 

The scientists provide powerful new evidence for a 30-year-old theory, proposed in a classic paper from Mary-Claire King and Allan Wilson of Berkeley. That 1975 paper documented the 99-percent similarity of genes from humans and chimps and suggested that altered gene regulation, rather than changes in coding, might explain how so few genetic changes could produce the wide anatomic and behavioral differences between the two.

 

Using novel gene-array technology to measure the extent of gene expression in thousands of genes simultaneously, this study shows that as humans diverged from their ape ancestors in the last five million years, genes for transcription factors -- which control the expression of other genes -- were four times as likely to have changed their own expression patterns as the genes they regulate.

 

Because they influence the activity of many "downstream" genetic targets, small changes in the expression of these regulatory genes can have an enormous impact.

 

"When we looked at gene expression, we found fairly small changes in 65 million years of the macaque, orangutan, and chimpanzee evolution," said study author Yoav Gilad, assistant professor of human genetics at the University of Chicago, "followed by rapid change, along the five million years of the human lineage, that was concentrated on these specific groups of genes. This rapid evolution in transcription factors occurred only in humans."

 

"For 30 years scientists suspected that gene regulation has played a central role in human evolution," said Kevin White, associate professor of genetics and ecology and evolution at Yale and senior author of the study. "In addition to lending support to the idea that changes in gene regulation are a key part of our evolutionary history, these new results help to define exactly which regulatory factors may be important, at least in certain tissues. This helps open the door to a functional dissection of the role of gene regulation during the evolution of modern humans."

 

To measure changes in gene expression from different species, White and Gilad developed the first multi-species gene array. This allowed them to compare the level of expression of more than 1,000 genes between humans, chimps, orangutans and rhesus macaques – representing about 70 million years of evolution. To make the samples comparable, the researchers studied tissue from the liver -- one of the most homogeneous sources -- from five adult males from each of the four species.

 

They focused their search on expression levels of two sets of genes, those that remained largely unchanged across all four species, suggesting that there was little room -- or need -- for improvement, and those that changed most dramatically, usually in the human lineage -- an indication of powerful incentives to adapt to a changing environment.

 

Of the 1,056 genes from all four species, 60 percent had fairly consistent expression levels across all four species. "The expression levels of these genes seem to have remained constant for about 70 million years," the authors wrote, "suggesting that their regulation is under evolutionary constraint."

 

Many of these genes are involved in basic cellular processes. The authors suggest that altering the regulation of these fundamental and ancient genes may be harmful. In fact, five of the 100 most stable genes have altered expression levels in liver cancer.

 

When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased expression in humans were among these. None of those with lower expression were transcription factors. This pattern, the authors note, is consistent with "directional selection."

 

Previous studies have found that many of these same genes have also evolved rapidly in humans, accumulating changes in their coding sequence as well as in expression rates. "Together," they add, "these findings raise the possibility that the function and regulation of transcription factors have been substantially modified in the human lineage."

 

This is a very efficient way to make big changes with very little effort, according to Gilad. By altering transcription factors, the entire regulatory network can change with very few mutations, increasing the impact and minimizing the risk.

 

"The big question," he said, "is why are humans so different? What sort of changes in the environment or lifestyle would drive such a rapid shift in the expression of genes -- in this case in the liver -- in humans and in no other primate?"

 

Part of the answer, he suspects, is rapid alterations in diet, probably related to the acquisition of fire and the emerging preference for cooked food. "No other animal relies on cooked food," he said. "Perhaps something in the cooking process altered the biochemical requirements for maximal access to nutrients as well as the need to process the natural toxins found in plant and animal foods."

[Amanda]

Most human-chimp differences due to gene regulation

 

Another great article Amethyst!

 

 

Most human-chimp differences due to gene regulation

 

The vast differences between humans and chimpanzees are due more to changes in gene regulation than differences in individual genes themselves,

 

Using novel gene-array technology to measure the extent of gene expression in thousands of genes simultaneously, this study shows that as humans diverged from their ape ancestors in the last five million years, genes for transcription factors -- which control the expression of other genes -- were four times as likely to have changed their own expression patterns as the genes they regulate.

 

This rapid evolution in transcription factors occurred only in humans."

 

By altering transcription factors, the entire regulatory network can change with very few mutations, increasing the impact and minimizing the risk.

 

Amethyst, I thought we had informational genetic makeup inscribed in our DNA (blueprints), and mRNA read/transcribed this information... implementing these instructions into directing the system's body processes in development. So, is what this article is saying, is that the mRNA had alterations in how it transcribed this information, and not so much any change in DNA? If so, this itself seems like it would become a genetic trait?

 

I've read from another poster in a thread in the past, that one of the differences between us and other primates is that we maintained a youthful attitude much longer... hence, prolonging our quests for learning via our sustained curiosity. This gave us a big advantage in growing 'intelligence'. Would this be an example of a transcription factor controling the expression of the gene responsible for this trait?

 

"The big question," he said, "is why are humans so different? What sort of changes in the environment or lifestyle would drive such a rapid shift in the expression of genes -- in this case in the liver -- in humans and in no other primate?"

 

I know this article devoted a lot of significance in attributing this occurrence to the change in our eating habits from harnessing fire to cook our food, etc... yet, I'm curious if and how emotions might have impacted this process? Little attention seems to be given to this aspect in these studies, and doctors say even most illnesses are psychosomatic. Our evolution of standing upright all the time, to having an opposing thumb, adventuring into the savannah and beyond... certainly had to effect our capabilities of reasoning. This had to evoke a more diverse and stronger since of emotions, probably one being anger/frustration which is closely associated with impacting the liver.

[Amethyst]

Amethyst, I thought we had informational genetic makeup inscribed in our DNA (blueprints), and mRNA read/transcribed this information... implementing these instructions into directing the system's body processes in development. So, is what this article is saying, is that the mRNA had alterations in how it transcribed this information, and not so much any change in DNA? If so, this itself seems like it would become a genetic trait?

 

I've read from another poster in a thread in the past, that one of the differences between us and other primates is that we maintained a youthful attitude much longer... hence, prolonging our quests for learning via our sustained curiosity. This gave us a big advantage in growing 'intelligence'. Would this be an example of a transcription factor controling the expression of the gene responsible for this trait?

 

I'm hardly an expert, but I would think so (to both). There are people here with more scientific backgrounds than I have, though.

 

I know this article devoted a lot of significance in attributing this occurrence to the change in our eating habits from harnessing fire to cook our food, etc... yet, I'm curious if and how emotions might have impacted this process? Little attention seems to be given to this aspect in these studies, and doctors say even most illnesses are psychosomatic. Our evolution of standing upright all the time, to having an opposing thumb, adventuring into the savannah and beyond... certainly had to effect our capabilities of reasoning. This had to evoke a more diverse and stronger since of emotions, probably one being anger/frustration which is closely associated with impacting the liver.

 

Hmmm. I would disagree that most illnesses are psychosomatic. Certainly stress and other negative emotions can make some illnesses worse, but thinking you are sick doesn't necessarily make you sick unless you are an extreme hypchondriac (sp?) or something. You still have to catch the bug first.

 

Glad you liked the article.

[Amanda]

Hmmm. I would disagree that most illnesses are psychosomatic. Certainly stress and other negative emotions can make some illnesses worse, but thinking you are sick doesn't necessarily make you sick unless you are an extreme hypchondriac (sp?) or something. You still have to catch the bug first.

 

Amethyst, as I understand it... often times our emotional state can leave us predisposed to illnesses too. It is known that emotions do have a great influence on illnesses. Here is some of the known physical conditions known to be correlated with emotions found in this article here. The mind - body connection is a fascinating subject to me.

 

Certain conditions have long been known to have strong psychogenic influence. This is the case for asthma, whose clinical description was so accurately noted in the time of early Greek physicians. In the 20th century and especially after 1940, a group of illnesses was identified as "psychosomatic" in response to widespread observations that the patient's emotional state had clear repercussions on the manifestations of the disease. In this group were placed conditions such as essential hypertension, asthma, ulcerative colitis, peptic ulcer, atopic dermatitis, and rheumatoid arthritis. Since then, many other conditions have been added to the list (from the APA, DSM-III): acne, allergic reactions, warts, urticaria, tension headaches skin diseases such as neurodermatitis, angina pectoris, coronary heart disease, diabetes mellitus, painful menstruation, obesity, migraine headaches, hyperthyroidism, and hypoglycemia among others.

 

With our increasing medical and psychological sophistication, however, we realize that more and more, if not all, diseases have some psychological components. Even the common flu, for example, is well known to be more virulent if the patient is depressed or stressed. The field of psychosomatic medicine is especially fascinating because it directly opens theoretical doors to issues concerning the relationship of the body to the mind.

[Amethyst]

See, to me that is like blaming the patient for being sick. I don't think that's right. It's not always someone's fault if they get sick.

[Flyby Stardancer]

Amethyst, I thought we had informational genetic makeup inscribed in our DNA (blueprints), and mRNA read/transcribed this information... implementing these instructions into directing the system's body processes in development. So, is what this article is saying, is that the mRNA had alterations in how it transcribed this information, and not so much any change in DNA? If so, this itself seems like it would become a genetic trait?

 

Part of it is regulatory codes in the DNA, as mentioned in the article.

 

Using novel gene-array technology to measure the extent of gene expression in thousands of genes simultaneously, this study shows that as humans diverged from their ape ancestors in the last five million years, genes for transcription factors -- which control the expression of other genes -- were four times as likely to have changed their own expression patterns as the genes they regulate.

 

Because they influence the activity of many "downstream" genetic targets, small changes in the expression of these regulatory genes can have an enormous impact.

 

The transcription factor genes lie in the DNA, and they control how other genes along the line are translated, how much (if at all), etc. etc. Often times, these transcription factors code for more than one genes.

 

An interesting thing we're doing in my genetics lab is inserting marked transcription factors into fly DNA to see what mutations we come up with. It's actually kinda fun! And the assistant professor that was just hired on for a tenure position actually uses these forced mutations as a part of work to help look at genes necesary for developement, and for looking at the causes of cancer.

[Amanda]

Because they influence the activity of many "downstream" genetic targets, small changes in the expression of these regulatory genes can have an enormous impact.

 

Flyby Stardancer, thank you for clarifying that for me. It all makes sense now. This part of the statement in the article threw me:

 

suggested that altered gene regulation, rather than changes in coding, might explain how so few genetic changes

 

Since you seem a lot more insightful into all this than I, why do you think that this situation seems to have happened more significantly in humans than the other primates? Could it be the extended ability to reason and this impact on our emotions?

[pandora]

That article did not site any studies that prove that ulcerative colitis is a nervous condition. Peptic ulcers are caused by bacteria... it is unknown why some can harbor the bacterium but not get an ulcer.

 

No offense, but I don't trust that article. It sounds like the same mentality that was used in the fifties and sixties. That article cites the DSM-III, which is considered out of date. (The DSM IV is now the "proper" version.)

 

I do not doubt that many disorders have a psychological compenent, but to say that some one gets asthma because of a fear of losing their mother is just STUPID. Somtimes, people develop asthma after exposure to certain chemicals, or long term low level exposure to chemicals. RA is an autoimmune condition.

 

I don't deny that it is possible that emotional states alter our physiological response to certain things, but methinks they attribute way too much to this process.

[Flyby Stardancer]

suggested that altered gene regulation, rather than changes in coding, might explain how so few genetic changes

 

Since you seem a lot more insightful into all this than I, why do you think that this situation seems to have happened more significantly in humans than the other primates? Could it be the extended ability to reason and this impact on our emotions?

Honestly? I have no idea. lol I don't know why something is favored over something else... I just had an idea of the processes they were talking about from class. The answer you're looking for is probably being studied.