Beyond Base-Pairs: Mapping the Functional Genome
Regulatory sequences of mouse genome sequenced for first time
Popularly dubbed “the book of life,” the human genome is extraordinarily difficult to read. But without full knowledge of its grammar and syntax, the genome’s 2.9 billion base-pairs of adenine and thymine, cytosine and guanine provide limited insights into humanity’s underlying genetics.
In a paper published in the July 1, 2012 issue of the journal Nature, researchers at the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine open the book further, mapping for the first time a significant portion of the functional sequences of the mouse genome, the most widely used mammalian model organism in biomedical research.
“We’ve known the precise alphabet of the human genome for more than a decade, but not necessarily how those letters make meaningful words, paragraphs or life,” said Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego. “We know, for example, that only one to two percent of the functional genome codes for proteins, but that there are highly conserved regions in the genome outside of protein-coding that affect genes and disease development. It’s clear these regions do something or they would have changed or disappeared.”
Chief among those regions are cis-regulatory elements, key stretches of DNA that appear to regulate the transcription of genes. Misregulation of genes can result in diseases like cancer. Using high-throughput sequencing technologies, Ren and colleagues mapped nearly 300,000 mouse cis-regulatory elements in 19 different types of tissue and cell. The unprecedented work provided a functional annotation of nearly 11 percent of the mouse genome, and more than 70 percent of the conserved, non-coding sequences shared with other mammalian species, including humans.
As expected, the researchers identified different sequences that promote or start gene activity, enhance its activity and define where it occurs in the body during development. More surprising, said Ren, was that the structural organization of the cis-regulatory elements are grouped into discrete clusters corresponding to spatial domains. “It’s a case of form following function,” he said. “It makes sense.”
While the research is fundamentally revealing, Ren noted it is also just a beginning, a partial picture of the functional genome. Additional studies will be needed in other types of cells and at different stages of development.
“We’ve mapped and understand 11 percent of the genome,” said Ren. “There’s still a long way to march.”
As a gadget to plug into a USB port, the “MinION” recently unveiled by Oxford Nanopore lacks the touch-me buy-me pizazz of Jonathan Ive’s designs. And since it’s a prototype that no one outside the company and a few partner organisations has yet been able to see in action, it is hard to say how well it actually works. But as an embodiment of technological cool it strikes me as pretty much beyond compare. Inside the MinION is a little chip with 512 holes in it. Put some DNA into the MinION, and it will pull individual DNA molecules through those pores. DNA molecules carry genetic information in the form of four different chemical bases, like slightly different knots on a piece of string. As a DNA molecule goes through one of the MinION’s pores, the different knots on it are sensed electronically; the signals produced this way are processed inside the MinION and sent through the USB port to your computer, where the string of bases is reassembled as a genome sequence. How long are the pieces of string? The system can read individual strings tens of thousands of bases long—far longer than most sequencing technologies. A MinION should be able to read about a billion bases before its pores run out. That’s a third the length of a human genome. All in a device the size of a matchbox. (via THE GENOME GADGET | More Intelligent Life)
The irritational fears about human cloning that abound from all parts of the political spectrum should not surprise anyone who knows a little bit about the history of technology. Hardly anything significant has been invented that no segment of the population has denounced as evil: factories, trains, automobiles, telephones, televisions, computers. Not even medicine has been spared this vituperation, despite its obvious benefits to humanity. Before the merits of surgery became obvious, it was unimaginable that slicing the flesh of a human being could do more harm than good.
That people think clones are “designer babies” is especially specious, given that a clone is an exact genetic copy regenerated into a new life.
Trigger warning: hate speech terms.
I went to a late Fourth of July party last night with my parents. It was composed of mostly their friends people of retirement age or older. As I have been living with my parents for the past few months I’ve grown accustomed to the differences with older folks and younger folks. Of course there are other classics, a lack of keen eyesight inability to sense what’s around them, and other dulled senses like hearing.
As a man I was taller than just about every other man around me now that I’m a woman I’m still taller than everyone and I stick out like a sore thumb. I was in the 95th percentile for men, but now I’m in the 99th percentile for women. At first I felt very awkward about this, but over time I’ve just gotten used to being who I am. Some other women have even complimented me on my height.
Anyway, as everyone was just getting to desert and hanging out around the kitchen there was an old codger next to me one barstool over that asked one of the other people there “Who’s the Amazon?”. He clearly could not see me sitting 6 feet away from him.
“Oh, that’s uh, W****’s daughter.”
It was surprisingly jarring to me. The funny thing is, I often refer to myself as an Amazon. I’m 6’2” tall, and a friend who’s 6’4” tall who’s a big drag Queen. We call each other on Amazons all the time, but when someone outside of our group does it, it all of a sudden feels pejorative. I was a bit surprised because I never really thought of Amazon as pejorative term before.
I’m reminded of the comments a woman I went to school with once made during a class discussion. She was kind of soft butch lesbian, and she noted that and she called his cells a dyke of her friends were dykes, she heard some analyses the term recently who was not part of the community and it grated on her.
Language exists primarily to communicate. But it can also be used as a weapon. It is all too easy for one to use the term does not directly apply to them in describing somebody else can cause unintended damage by using it. They may know it is damaging language and use it anyway, it is up to the speaker to be well attentive to the words that they choose.
I was always taught to never say anything unless it was true, necessary and kind. I know many do not follow this type of perfect speech, but I feel that we as a society would all benefit greatly if we were truly careful before we spoke.
Unless we truly consider the feelings of others when we act, we will never truly have peace on this earth. Namasté.
When I see an amazing looking girl only to find out she weighs the same amount but is about about 5 inches taller than me. Wahhhhhhh tall girls have all the luck. Looking sexy and reaching all the things.
Ugh, I hate normal people with their relationships, wheres my curvy, tall, smart, amazing counterpart gonna show up? Sincerly, Forever waiting>:
She’s around, you will see.