Epigenetics

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I'm sorry that Epigenetics is over.  After listening to someone tell you cool stuff, practically every day, for weeks and weeks, it can be a letdown when class is over and your nice prof isn't talking to you any more.

It was a really interesting class, and I learned all sorts of things I never imagined.  It was a hard class (especially as my working knowledge of basic genetics is not what it could be), but I found it fascinating.

I loved learning about a cutting-edge subject. 

I think about the elementary physics class I started (which I'm signed up for again, starting next month).  Millions and millions and MILLIONS of people know WAY more about physics than I know (or than I would know had I completed the class!).  But epigenetics?  Certainly there are a LOT of people who know WAY more than I know about epigenetics.  But compared with the number who know more than I know about physics?  It's a much smaller number.  I think it's fun to be the only person in most places I go who knows anything about epigenetics....



I drew this cluster of genes because I wanted an image of what is going on here, and I couldn't find one that was ok to copy.  (Note that I found many images of this cluster online, as well as the ones she showed us in class.  My version is not a direct re-drawing of any image I've seen before....)

I have a few tweaks to make to it -- it is Igf2, not lgf2.  A different choice of font would be a good idea, at least for the names of the genes, in order to make clear it's capital-I,not lower-case-l.....

(Digression -- good old Courier!  End of Digression.)

This cluster of genes is an instance of a case where the maternal version of the cluster is typically quite different, epigenetically, from the paternal version.  The genes are the same, but the expression of those genes is different.

(Digression -- did you know that Australians may say "different to" rather than "different from"?  I didn't, before this class....  End of Digression.)

(Digression -- something that is methylated is usually silenced or not expressed.  End of Digression.)

The enhancers downstream (to the right, in this image) of the cluster want to reach Igf2 and enhance its expression, but when CTCF is bound to the imprint control region (as is typical for the maternal version of the cluster), the enhancers are blocked, so they enhance H19 instead.  Methylation of the imprint control region (typical of the paternal version of the cluster) prevents CTCF from binding, and Igf2 is expressed.   (Note that when the imprint control region is methylated, methylation often spreads to H19, and it, too, is methylated.)

If something goes wrong and a person ends up with two paternal versions of the Igf2/H19 cluster, twice as much Igf2 is made as should be made.  Beckwith-Wiedemann syndrome results, and a childhood kidney tumor (Wilm's tumor) is not uncommon. (Igf2 is a growth promoter, and "too much growth promoter" is one of the hallmarks of cancer.....)  

Dr. Marnie Blewitt, who taught Epigenetics, really did a good job.  I give her 75% of the credit for me knowing what I know about the subject, and the rest is me, working at understanding all of the material.  Any errors I make in discussing this are mine, of course.



I've never tried to make an image available on Wikimedia commons, but since there is no image of the Igf2/H19 cluster there (at least, when I searched, I couldn't find one), I may see what it takes to add an image.....  After tweaks, of course.

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understanding what we hear

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My epigenetics prof is in Australia.  For the most part, I haven't had any trouble understanding her.

This week, however, has presented challenges.

We've been learning how the epigenetic machinery is involved in cancer.  Whether things are hyPOmethylated or hyPERmethylated is a night-and-day sort of difference.

Here in Michigan, if a local person wanted to emphasize that difference, we might sit, hard, on that R.  "Hyperrrrrrrrrrrrrmethylated."

My Australian teacher touches lightly on her Rs, compared to people in my part of the world.  And her long O sound is different from ours, and is, to my ears, considerably closer to the sound she makes when she says "er" than my "o" is to my "er" (at least, it is, the way I hear it)............

Of course, context is (nearly) everything, as my neurobio prof said a week ago, when she discussed hearing.  Context is a huge clue as to whether something would be hyPOmethylated or hyPERmethylated............

And -- thank goodness we have video, rather than only audio.  I have been able tell, from context, and by watching my Aussie prof closely, whether she has said "hyPOmethylated" or "hyPERmethylated." 

All but once.  One time, I just couldn't tell..............

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"We are what our Mums Ate"

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Here's a newspaper article we read for Epigenetics this week -- "We are what our Mums Ate."

Really interesting, I thought................  Nutrition in the first 1000 days has a big impact on the health of an individual, throughout life.........

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when you're studying a brand-new field.....

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One of the things about studying a brand-new field is that there are few, if any, standards.  Take naming, for example.  Imprint control regions (ICRs), differentially methylated regions (DMRs), differentially methylated domains (DMDs), imprint control elements (ICEs), and designated imprinting centers (DICs) are ... all talking about the same thing.

This stuff is confusing enough without five different names for the same thing -- they need a naming-conventions committee!


On the other hand...................


Studying a brand-new field means that hardly anyone knows anything about it.  I know just a very little about epigenetics, and I know just a very little about what's going on in a human nervous system.

But I'm betting that there are tens of thousands, if not millions, of people on this planet who know way, Way, WAY more about neurobiology than I know.

I'm also betting that the number of people who know way, Way, WAY more about epigenetics than I know is way, way, way smaller than the number who know more than I do about neurobiology!

I think it's cool to have the opportunity to be one of the not-so-many who know even a bit about epigenetics.

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epigenetics

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I actually have a pretty good idea what this means --

"Genomic imprinting is an epigenetic process resulting in the monoallelic parent-of-origin-specific expression of a subset of genes in the mammalian genome. The parental alleles are differentially marked by DNA methylation during gametogenesis when the genomes are in separate compartments. How methylation machinery recognizes and differentially modifies these imprinted regions in germ cells remains a key question in the field. While studies have focused on determining a sequence signature that alone could distinguish imprinted regions from the rest of the genome, recent reports do not support such a hypothesis. Rather, it is becoming clear that features such as transcription, histone modifications and higher order chromatin are employed either individually or in combination to set up parental imprints."

Five weeks ago I wouldn't have had a clue.


Pretty cool, that access to classes like Epigenetic Control of Gene Expression
is freely available to everyone with computer access!

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"mitotically heritable" arises all the time, and is hard to type!

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The definition of epigentics includes mitotic heritability.

I would just like to say that "mitotic" is not that easy to type, nor is "genetic."

My fingers are getting a workout in Epigenetics, which must mean that motor regions of my brain are getting one, too.  (In addition to the "higher functions" parts of my brain!)



This week we are learning in some depth about X inactivation.  X inactivation is what causes/allows a calico cat  to be a calico cat -- displaying, as she does, the coat-color factors she inherited from each of two different-colored parents, in random patches here and there on her body. 

Digression:  A calico cat's coat has patches of color pattern inherited from her mother, and patches of color pattern inherited from her father. Coat color in cats is on the X chromosome.  Any cat displaying two coat-color patterns -- a calico cat -- has two X chromosomes.  Which is why calico cats are essentially always female.  The rare male calico cat is XXY.
End of Digression.



This unit is really interesting, and I'm finding it much more accessible than last week's lecture (for whatever reason).  A pleasure and a surprise -- I was afraid this class might be going to be more and more opaque..........

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pluripotency vs. totipotency

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Learning a bit of Latin helped me with Dino class (all those dino species names!).

Now I'm finding it helpful in Epigenetics.

Some cells' descendants have the possibility to turn into ANY kind of cell that organism has.  A fertilized egg, for example.  One cell, whose descendants can turn into all the cell types required to make an adult of its species.  This is totipotency.

I was confused; I thought that was what pluripotency was.

Thank goodness for Wikipedia's entry on cell potency -- Toti comes from the Latin totus which means "entirely."  Pluri comes from the Latin plurimus, meaning "very many."

And potens is Latin for "having power."

Now we know.  Pluripotent cells' descendants can become a lot of different kinds of cells, but not ALL the kinds of cells in that kind of critter.  "Very powerful," but not "all-powerful" like totipotent cells.



I do much better at remembering/understanding when I know what the words mean!

And -- I can see how, if you were going to be a scientist, learning Latin could save you a lot of time when you come to needing to know the meanings of a lot of words with Latin roots!

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epigenetics

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Yikes!

It has taken me hours to listen to, and take notes on, the 12-minute lecture in which this slide was found!

At this point, I think I understand all the words (and acronyms) here (except I'm not sure whether KMT is synonymous with HMT or if the K is a typo...............  I know that sometimes K and H are interchangeable -- as with HATs and KATs -- but am not sure they are interchangeable here). 

I believe I have at least a hazy understanding of what the words and acronyms mean, and what the things those words and acronyms represent actually do, and why we care.


I'm glad I'm not expecting to launch myself into a career where I'll need to understand all of this well enough to do something with it!

It's possible that the point of this slide, for the purposes of this class, is that all of this is really complex. 

In which case -- point taken! 

(And, I bet it's actually a lot more complex than anyone suspects at this point, given the speed at which our knowledge about all of this is growing and changing....)

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epigenetics, calico cats, and a quote for the day

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Having added what I've learned in Epigenetics this week to what I knew before I started the class, I knew what this slide meant, except for "gastrulation".........

One of the things I love about watching taped lectures is that I can pause them and go look things up.  You can see what I gleaned from Wikipedia about gastrulation at the bottom of the image above (as always, click on an image if you wish to embiggen it).


And now, here's quote I promised, as extracted from the Wikipedia article on gastrulation:

Lewis Wolpert, pioneering developmental biologist in the field, has been credited for noting that "It is not birth, marriage, or death, but gastrulation, which is truly the most important time in your life."

Now you know.


Now, taking a tangent from our discussion of gastrulation.......

The results of X inactivation are visible on calico cats.  The genes for coat color, in cats, are on the X chromosome.  A cat may inherit one coat color from her mother, and a different coat color from her father.  When the female embryo is about 4 days old, one or the other of her X chromosomes is inactivated. As cells grow, divide, grow, divide, groups of cells with the same active X chromosome (from mother OR from father) get larger and larger.  By the time the cat is born, a female cat whose parents have two different coat colors has a coat with patches of different colors.

I knew calico cats were always female, but I never knew why until I watched this video a couple of weeks ago.   (It's kinda long, but it's pretty accessible, I think.   A person doesn't have to understand all of it to be entranced by it........)



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taking notes

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I've talked before about trying to figure out a way for me to be happy taking (and keeping and searching...) notes in my Coursera classes.

This attempt is made more complex as I take into account the files of info prepared for us by the teaching staff.  Each class seems to be different, in regard to the kind and format of the content they have made available, which means that a note-taking method that works in one class doesn't make sense for another.

Epigentics has a pdf of the slides for the class.  Adobe Reader now allows a person to annotate a pdf.

So that's what I'm doing in Epigenetics...........  I downloaded a copy of the pdf, and I'm annotating my copy of that pdf as I see fit.  Here's an example.

Click on the image if you wish to embiggen it.

My notes are in the smaller font, in the lower right corner.


The original image on the slide is Nucleosome organization, by Derekk2 (via Wikimedia Commons).


I've struggled to get my added text to turn into a moveable text box (so I can put it just where I want it).  I am still not sure how to get it to do that.  But once I figure that out, I'll be relatively comfortable with this method of note-taking.

I wish there was a way for me to embed pics in the pdf, but I haven't seen a way to do that.  Maybe I would have to get the upgraded version you have to pay for, in order to do that...........

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epigenetics

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I'd been thinking of epigenetics as the influence of environment on genetic expression, but that's not right.  At least -- not if I think of "environment" as what's going on outside an organism.....

We all begin from one cell, which divides and divides, and then all those cells grow and divide, and turn into all the different kinds of cells in our bodies, and keep on growing and dividing and growing, until we turn into ourselves.

Each of our cells contains our personal genome.  The SAME genome in each of our cells.

So how is it that bone cells are bone cells, and liver cells are liver cells, and blood cells are blood cells, if they all have the same genetic material?

Epigenetics, that's how.  It's epigenetic info that tells a bone cell to be a bone cell (not a liver cell or a blood cell).............

I learned about epigenetics in What A Plant Knows, in the context of the way plants can react to environmental stress and pass adaptations to that stress along to their offspring.  I was clueless about epigenetics being in play, all the time, in every cell (telling a cell to be a leaf cell rather than a root cell, say.......).  It makes perfect sense, but I never thought of it...........

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update on my Coursera classes

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I have been "just listening" to all the classes I've signed up for so far this year.

How Things Work 1 ended a couple of months ago.  I feel bad about this one.  I was so thrown for a loop at learning that A) pounds and kilos do not measure the same thing, along with B) no one ever told me!, that I had to just stop dead and work on taking it in.  By the time I'd revised my world view sufficiently to proceed, I was so far behind that I never caught up.  I surely hope he offers this class again soon.  I would like to give it another shot.  I believe I can still listen to the lectures.  I should find out, and do that, if I can......

The Music of the Beatles is over (will be offered again in July 2014).  I listened to all the lectures, and listened to a significant amount of music related to the class on youtube.

Marine Megafauna: An Introduction to Marine Science and Conservation is over.  I listened to all the lectures but the last week.  That was when we got to the heavy-duty "conservation" part of the class, and I really don't think I want to listen to "Whales and the Age of Sail"..............  I have a general idea of the atrocities we perpetrated on whales, and I really don't want to know the details...........

Archaeology's Dirty Little Secrets ended last week.  I took Secrets last summer, and loved it, so I took it again to enjoy the new bits and savor the old.  No notes/exercises/exams for me, this time around.

Roman Architecture ends this week (I have one lecture worth of videos to watch and take notes on).  I've listened to all the lectures, and have taken reasonable notes, for my own possible future reference (should I go somewhere where the works she described still exist), but have not written any papers nor taken any quizzes/exams.

Music's Big Bang: The Genesis of Rock 'n' Roll ends next week (and I'm caught up for this week).  Just listening.  No notes, no homework, no quizzes/exams.  Greater familiarity with some of the pre-rock music he is talking about has not helped me to enjoy it more.  Some of those styles just do not float my boat.  Unlike the other rock classes I've taken, he has played us a significant amount of music.  No whole pieces, but healthy chunks of many pieces.  I haven't felt compelled to search out more of it on youtube.


It's good that my plate is almost cleared -- in addition to Maps and the Geospatial Revolution and Epigenetic Control of Gene Expression, I'm signed up for Understanding the Brain: The Neurobiology of Everyday Life.  (all of these start next week)

Our neuro bio teacher is totally geeked about teaching the class.  She has a blog and a twitter feed.......  Gotta love her level of enthusiasm, and her conviction that the world would be a better place if everyone knew more about brains.


I'm not making decisions ahead of time about whether I will or won't do more than "just listen" in neuro bio or epigenetics.  I will do the labs for maps, because I learned so much from them last time, but I don't know if I'll take any quizzes/exams........


And -- I'm working at NOT looking at what other offerings might be available just now...........  Which is hard, because you can't count on these classes being offered in the future, and what if I missed the one offering of a totally dynamite class???

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