Week9-Lecture 20,21

Lecture 20 – Observing

Goal:
To understand techniques for obtaining information from the human genome.

Objectives: Students should be able to...

Describe how a SNP chip works and the information obtained from performing a SNP chip.
Define polygenic disease and list examples of polygenic diseases.
Explain how different types of human cells function differently despite the cells having the same DNA.
Describe methods of measuring genome-wide gene expression.
Explain how identifying differences in genome-wide gene expression can be a diagnostic tool.
Outline the experimental steps for determining the genomic loci specific that a protein binds (ChIP-seq)

ChIP-seq, or Chromatin Immunoprecipitation - sequencing.

1. Obtain cells with estrogen receptor bound to the genome.

2. Add a chemical that cross-links proteins to DNA.

3. Randomly cut the DNA.

4. Add an antibody that specifically recognizes the estrogen receptor protein.

5. Using one of many biochemical techniques, purify the antibody attached to the estrogen receptor protein with the attached DNA.

6. Isolate the bound DNA from the protein and sequence the DNA.

7. Map those sequences to your reference genome sequence to determine their locations.

Lecture 21 – Completing the triangle: Perturbing the genome to probe function

Goals:
To understand how to use the 7.00x triangle that shows how a gene relates to function or protein using biochemistry, genetics, recombinant DNA, and genomics.
To identify how molecular biology and current research tools link genetics and genes to biochemistry and proteins and help to determine the function of genes and proteins.
Objectives: Students should be able to…
Describe how to add an extra copy of a gene to add back a function of a protein.
Explain how to make a transgenic mouse to test the phenotype of a mutation.
Explain how to constitutively knock out a gene by homologous recombination.
Explain how to conditionally knock out a gene with the Cre-lox system.
Describe the mechanism of RNA interference (RNAi) and how RNAi affects gene expression.
Identify the natural function of the RNAi system in eukaryotic cells.
Describe how to use TALEN proteins to regulate gene expression and edit the genome.
Describe how to use CRISPR/Cas9 to edit the genome.
Identify the natural function of the CRISPR/Cas9 system in bacteria.
Choose which genome-altering experimental tool to use to solve a given question.

昨天做PSet之前又把这两周视频回顾了一遍，超激动。。题目设置思路也很好（不行，要剧透的感觉。。过了DDL再来写好了。。） 2014-08-24
这两周的内容与疾病认识的关联性比较大，有为最后的application打基础的意思，其实内容不算很复杂（如下表），但是整个思路我超爱的。。。。。

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虽然个人觉得Lecture18稍有拖沓，但是之后火速恢复了节奏。。。
1 mutation-allele-disease
通过强劲的HGP （因为原来的方法太pain才会有那么多人参加人类基因组计划？Lander君无意间泄露了懒人改变世界的秘密2333），可以测序患者家族Pedigree里的个体，我们就可以知道具体哪个位点的碱基不是跟大众一样的了。。。所谓HGP后的美好世界，各种mutation被发现啊。。。这么多突变，哪个才是致病（在某家族）的呢？
STEP1 根据突变的位置，碱基改变对编码蛋白的影响，保守性（能长存的东西还是有价值的，所谓要看名著啊）来初步认定是不是会consequential也就是会不会致病吧。。。

STEP2 之后就是对双链里每个allele的判断，所谓upper strand和lower strand，杂合子和纯合子，显性遗传和隐性遗传会不一样的。每个allele里可以有数个mutation，有的mutation会consequential，有的不会，从而判断allele的致病性。。。
STEP3 把每个allele对应到个人，以分析出致病的突变。。。PSet里给出的表格真的很贴心，很方便做题的。。。（这个DDL之后我可以开心的贴了）

但是，但是。。。“In the complex real world of human genetics, sometimes, mutations that appear likely to be consequential turn out not to cause disease while others which appear unlikely to be consequential are found to cause disease.”现实还是复杂的（哪里有二次元的世界简单安全。。。）
以上，有思路构建的感觉，从Lecture里提到的“HD，双向”到联系里的“Noonan’s syndrome和先天听力障碍 ”都可以走这条线。。。
2 追寻祖先的历程
所谓的走出非洲事件。。那个跟尼尔德（特）人有过affair的非洲祖祖祖祖祖祖母的后代是亚裔跟高加索人的共同祖先？ （我怎么看那个非洲同学的表情都好好笑偶，泥垢了）。。。
关于自然选择，个人觉得不是说那么混了就是基因好了-适应环境了-把其他人都PK掉了。。。是后代够多，活到了现在吧（照这个意思，咱大中华绝对可以是优势人群，都不用鼓励生育的唉） 。。。不过要是再来个物种灭绝啥的就不好说了。。。。
线粒体是侵入人体细胞共生的某古早生物，真心推荐香槟校的Emergence of Life。。。从最早的核酸“混居”到各种“共生”，常觉得两课有印证。。对了，推荐过这俩联合的http://mooc.guokr.com/post/608104/ 。。。整个思路会宽很多。。
3 大波Noble prize技术袭来

【General strategy for gene targeting in mice】

图片来源http://www.nobelprize.org/nobel_prizes/medicine/laureates/2007/press.html

各种基因导入，基因沉默技术。。。ES什么的，Lander娓娓道来，然后一句“这个得了某某年诺贝尔奖偶（你们想不到也是可以理解的吗）”，直接跪了。。

（基因knock in，诺奖）
之前某人跟我吹嘘的loxP,Gre什么的也褪去了光环，明白是怎么回事了，虽说建模什么的还是很不容易的。。。RNAi（诺奖）的发现故事还是很有趣的，这个技术还是比较普及的低门槛dirty trick。。。。TALEN和CRSPR之前看文献的时候见过，没有细看，原来也是这样nice的东东，从植物到“前病毒”，果然各种被钻空子，各种dll被破解。。。。
PS 这两周视频可以直接看唉。。。不过，WEEK 11又挂在YOUTUBE了，翻啊翻啊翻啊翻。。。