Title: MicroRNAs: A Small Contribution from Worms

Her lab is interested in how expression and maturation of specific miRNA genes is controlled OR the mechanism by which these regulatory RNAs inhibit the expression of target mRNAs.
(my understanding is that her lab is primarily doing the former and trying to do the latter).

Today she talked about the former pathway. Specifically, she's focused on two Argonaute genes, alg-1 and alg-2.

Argonaute is miRNA splicer, cutting them into ~22-nt pieces. One common domain feature is that (almost) all argonaute genes have two domains, PAZ and PIWI.

alg-1 and alg-2 are very similar in sequence(sibling in a phylogeny tree). But their roles are sort of different. Mutating alg-1 causes a big effect. Mutating alg-2 almost has no effect. However, double mutants is lethal(synthetic lethal). By effect, i mean whether the pathway of hatching from lava to a worm, vulva development is affected.(my humble understanding, might not right)

These two genes are intriguingly related to sex. Female(XX) and male(XO, only one copy of X) have dosage compensation turned on and off respectively.

Fox-1-| Xol-1
Sex1 ------| Xol-1 ----| dosage compensation
XX lots lots few on
xO few few lots off

Mutating Fox-1 is no-effect.
Mutating Fox-1 and alg-2 is lethal.
Mutating sdc-2 is half(50%).
Mutating alg-2 and sdc-2 is lethal.

Mutating alg-1 causes a big effect.
Mutating alg-2 almost has no effect.
Mutating alg-1 and Sex-1 is ok(not sure, not lethal, but not normal development maybe)
Mutating alg-1 and alg-2 is lethal.
Mutating alg-2 and Sex-1 is lethal.

So clearly, alg-2 and sex-1 are related to Dosage compensation.

Then, Amy talked about pre-mir35 whose maturation is controlled by alg-2. Supposedly, alg-2 plays a role in Dosage compensation by means of mir35.

Interestingly, pre-mir35 is from a miRNA cluster which has >5 miRNAs sitting next to each other. Their maturation are all controlled by alg-2.

Final guessing picture is shown like this.

Sex-1(and others) mir-35 and alg-2
| |
- -
Xol-1 Proteins(unknown)
---------|--------------
-
sdc-2 bound mRNAs(i didn't understand)


Interesting point: there's something called P Bodies, which is suggested to be the site of degradation of mRNA.

ways of miRNA to control target mRNA(my own summary):
1. attach 3' of mRNA to affect its stability -> mRNA splicing
2. recruit mRNA to P Bodies
3. inhibit the attachment of polysome(rRNA complexes)

Title: Making sense of junk RNA

The host said this guy published >20 papers this year. Among them, 2 science and 2 nature.

What he's done is sort of breakthrough. Broaden the biology vision a lot.

In short, his research connected DNA tandem repeats, transposons, DNA methylation and small RNA all together.

Background

DNA methylation corresponds to H3k9 methylation but not H3K4 methylation. DDM1 mutant releases the methylation on heterochromatin and transposons, but not methylated genes(why?).

Argonaute genes:
AGO-1 and -2 is for 21nt siRNA and miRNA.
AGO-2, -3 and -7 are for 21nt trans-acting siRNA.
AGO-4, -6, -8 and -9 are for 24nt transposons, siRNA.


(his abstract is pretty good. I post here.)
Heterochromatin is composed of transposable elements(TE) and related repeates. Like transposable elements, heterochromatin silences genes located nearby, and plays a major role in epigenetic regulation of the genome. Small interfering RNA corresponding to heterochromatic sequences can be detected in plants, animals and fission yeast, indicating that these sequences are transcribed. We have used tiling microarrays to examine these transcripts and their regulation in plants and fission yeast. In plants, small interfering RNAs(siRNA) corresponding to different classes of TE depends on DNA methyltransferase MET1, the SWI /SNF ATPase, DDM1, or both, but not on the histone deacetylase SIL1. All three genes are required for silencing transposons in the absence of RNAi. In fission yeast and in Arabidopsis, centromeric repeats are continually transcribed on one strand, but the transcripts are rapidly turned over by RNA interference, through the combined action of RNA polymerase II, and the Argonaute(RITS) and RNA dependent RNA polymerase(RdRP) complexes, each of which is associated with heterochromatin. Histone H3K9me2 depends in part on RNAi, mediated by the Rik1-Clr4 complex. Rik1 has similarity to both DNA and RNA binding proteins, and may play a role in RNA processing. In pombe, mating type silencing in the absence of RNAi depends on histone deacetylation, resembling Tf2 LTR retrotransposons in this respect. In Arabidopsis, LTR retroelements inserted into pericentromeric repeats can also silence them, int he absence of RNAi. Thus both RNAi-dependent and RNAi-independent mechanisms are required to silence different TEs, involving different histone modifications in each case.

Following is from his talk.
1. RdRp silence Tandem Repeats in Neurospora, At, Ce.
2. Tandem repeats maintain siRNA like below.
|---|---|---|---|
=--->(by RdRp)
....(by slicer)
=-----|->
^ |
| |
-------
3. 15% transposons have siRNA
4. 75% TR have siRNA
5. heterochromatin RNA is a source of RNAi
6. DDM1 responsible for H3k9, with siRNA, mediates transposons
7. transposons are always co-transcribed with neighboring genes and centromeric repeats