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Project:

Background:

  • AGO4 is the effector in Pol IV-dependent sRNAs mediated RdDM pathway;
  • Pol IV, RDR2, and DCL3 sequentially contribute to the production of Pol IV-dependent sRNAs, which, in recent model, can stabilize the AGO4 protein in cell;
  • pol iv and rdr2 mutants eliminate AGO4, while DCL3 only partially decreases the AGO4, therefore other sRNAs might be produced and stabilize AGO4;
  • DCL3 homologous DCL2 and DCL3 also produce different kinds of sRNAs.

Aim:

  • to explore the potential sRNAs loaded  to AGO4 in dcl3 mutant, as these sRNAs might contribute to the stabilization of AGO4 protein in cell.
  • Problem to solve: how do the profiles of sRNAs (as well as their origin locus) in dcl3 and dcl2/3/4 mutants change?

Methods:

  • by compare the sRNAs groups based on length or gene/sequence types between dcl3 and dcl2/3/4 mutants, we will find out the sRNAs deduced in dcl2/3/4, which might load to AGO4 and contribute the stabilization of AGO4 in dcl3 mutant.
  • Note: we unfortunately can't find out the data for sRNAs loaded to AGO4 in dcl3 and dcl2/3/4 mutants, which will directly indicate the change of sRNAs loaded to AGO4, giving that AGO4 is stabilized when sRNAs are loaded.

Concept map:

Reference:

1, Groth M. et al, SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation. PNAS. 2014. 111(49): 17666-71.

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2 Comments

  1. I tried to clean up your formatting.  Also, remember to use the outline we talked about last week in class.

  2. Check out FastX clipper and FastX quality trimmer for adapter removal in iPlant. They can be found in the DE under applications, the Hannon lab documentation can be found here: http://hannonlab.cshl.edu/fastx_toolkit/.