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看了一篇PRC1和PRC2组分探究的CHIP-seq文章

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发表于 2017-1-10 16:56:41 | 显示全部楼层 |阅读模式
我分享一下我刚刚看的一个chip-seq文章,做了4个IP,分别是Cbx7, Ring1B, and Suz12,RYBP 通篇就是在如何解释它们的peaks交叉情况!
chip-seq数据分析方法见我的博客:http://www.bio-info-trainee.com/2257.html


PRC1的组分异常复杂,包括 Cbx (Cbx2, Cbx4, Cbx6, Cbx7, or Cbx8); Ring1A or Ring1B; PHC (PHC1, PHC2, or PHC3); PCGF (PCGF1, PCGF2, PCGF3, PCGF4, PCGF5, or PCGF6); and RYBP or YAF2.
其中,a Ring1A/B E3 ligase subunit that monoubiquitinates histone H2A at lysine 119 (H2AK119ub)
但不是说都必须要有,而是它们的组合,形成了各种各样的PRC1,但是都统一叫做PRC1。
比如在mouse的ESCs里面,就有两种PRC1,它们的 Cbx7 or RYBP 是不可能共存的!我们可以把它们分别叫做, Cbx7-PRC1, RYBP-PRC1

Cbx7 的功能是把 Ring1B 招募到染色质上面,是必须的。它结合的基因多参与 early-lineage commitment of ESCs.
RYBP 可以增强PRC1的酶活性,它结合大基因多参与,regulation of metabolism and cell-cycle progression
RYBP 结合的基因要比 CBX7 结合的基因表达量高。 因为CBX7结合的同时,会招募PRC2这个抑制marker。
而PRC2 deposits the histone H3 lysine 27 trimethyl repressive mark (H3K27me3) through the Ezh1/2 histone methyltransferase enzymes.  



如何描述它们这些peaks的交叉情况呢?
We observed an overlap of RYBP peaks (3,918 in total) with 14%, 42%, and 37% of Cbx7, Ring1B, and Suz12 peaks, respectively
Moreover, although more than 90% of Cbx7 peaks contained Ring1B and Suz12, 20% were also bound by RYBP
尽管RYBP and Cbx7 在大部分情况下都是互相排斥的,但是也在少部分基因组区域存在共定位的现象。

Ring1B / Suz12的peaks情况可以被 Cbx7 和 RYBP 的peaks情况说明:
RYBP and Cbx7 都有的地方,有着高Ring1B/Suz12
Cbx7 but not RYBP的地方,Ring1B/Suz12会稍微低一点
RYBP but not Cbx7的地方,Ring1B/Suz12会更低一点
RYBP and Cbx7 都没有的地方,Ring1B/Suz12就最少!

RYBP的peaks的中点在TSS处,而其它peaks都在TSS下游一点点。
用Sequential ChIP (re-ChIP)实验的确可以看到RYBP和CBX7的peaks有重合。


而且RYBP还有一些peaks是其它PRC1所没有的,说明它可以独立于PRC1发挥作用

H2AK119ub 与 Ring1B/Suz12正相关,但是与RYBP只有25.7%交叉,与CBX7有着72%交叉,所以可以把 PRC1 target genes分成3类:
a first set with Cbx7/Ring1B/H2AK119ub; ~~~~GO/KEGG分析,
a second that contains RYBP and lower levels of Ring1B/H2AK119ub
a third set cobound by RYBP/Cbx7/Ring1B and that also contains H2AK119ub.



然后这些所有的gene list都可以拿去做GO/KEGG分析,看看是不是有什么biological meaning !
genes co-occupied by Ring1B/Cbx7/RYBP and H2AK119ub are involved in system development.
genes containing RYBP/Ring1B/H2AK119ub, but not Cbx7, have a strong association with the M phase of the meiotic cycle and cellular metabolism
genes with Cbx7/Ring1B/H2AK119ub are involved in developmental processes and mesoderm specification,
those containing RYBP/Cbx7/Ring1B/H2AK119ub predominantly represent the ectodermal fate and, to a lesser extent, mesoderm and endoderm fates  

超过700的基因有 RYBP/Cbx7/Ring1B的peaks,所以作者敲除Cbx7 看看 RYBP的peaks是否会变化,但是没有做CHIP-seq,只是做了ChIP-qPCR

下面这个结论很重要:
Overall, our ChIP-seq analysis allowed us to identify five types of genes according to the occupancy of PRC1 and PRC2: those with
(1) Ring1B/Cbx7/RYBP and Suz12 (725 genes);
(2) Ring1B/Cbx7/Suz12, but not RYBP (1,527 genes);
(3) Ring1B/RYBP/Suz12, but not Cbx7 (861 genes);
(4) only Ring1B and Suz12 (1,694 genes); or
(5) RYBP but no Polycomb proteins (1,674)
原文见:
  RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells.

https://www.ncbi.nlm.nih.gov/pubmed/23273917







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