2022_NatComm_BImethods

This page contains the Computational Supplementary Methods (CSM) for the manuscript Pascual-Carreras et al, Nature Communications, 2023. We really apreciate if you cite this paper when using any of the referenced materials.

Abstract

For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process because the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the WNT/beta-catenin signal specifies anterior versus posterior identity. Initially, both ''wnt1'' and ''notum'' (Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a WNT/beta-catenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct WNT/betacatenin targets, which trigger the expression of posterior effectors. Finally, we identified FoxG as a ''wnt1'' up-stream regulator, probably via binding to its first intron enhancer.

Supplementary Material

Bioinformatics protocols for that manuscript are described, along with relevant figures and tables, in the main PDF file:

Computational Supplementary Methods (184.5MB PDF)

It contains links to all the scripts and files described there that are also distributed through this repository. The only exception due to its file size is the custom BSgenome Bioconductor package for the dd_Smes_g4 genome annotation dataset, which is available as a direct link from our web server to the gzipped tarball:

BSgenome.Smed.PlanMine.ddSmesg4_4.0.tar.gz (169M gzipped tarball)

You can easily install it after downloading on your local R distribution; just run the commands below on the shell command-line:

R CMD build BSgenome.Smed.PlanMine.ddSmesg4;
R CMD check BSgenome.Smed.PlanMine.ddSmesg4_4.0.tar.gz;
R CMD INSTALL BSgenome.Smed.PlanMine.ddSmesg4_4.0.tar.gz;

We wish you find those materials useful for your planarian research.

CopyLeft

Scripts developed at the lab are distributed under GNU-GPLv3 license. They are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

---

2022 - Computational Genomics Lab