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Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons.

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Paper

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The authors' code

Perl · 126 lines · 4.9 KB · GPL-3.0

  1. #!usr/bin/perl
  2. #peak_finding_with_FDR
  3. use warnings;
  5. #print "\nFiles should be either tab delimited .gff files, or .bedgraph files, with values for each GATC fragment\n\n";
  6. print "\nFiles should be tab delimited with values for each GATC fragment\n\n";
  8. @infiles = glob("*.bedgraph");
  9. @infiles = glob("*.gff") unless scalar(@infiles);
  11. #$file_num = @infiles; if($file_num ==0){die "\nNo files detected! - make sure they are .gff or .bedgraph files\n"};
  12. $file_num = @infiles; if($file_num ==0){die "\nNo files detected! - make sure they are .gff files\n"};
  14. use Cwd;
  15. my $dir = getcwd;
  16. $dir = substr($dir, 2); # gives current directory for calling up other perl programs
  18. $rep_num = 0;
  20. print "Files for processing are:\n\n";
  22. foreach $a (@infiles){
  23. if($a =~ m/rep1/){$path1 = $a; chomp $path1; print "1st replicate is $a\n"; $rep_num = $rep_num + 1;}
  24. if($a =~ m/rep2/){$path2 = $a; chomp $path2; print "2nd replicate is $a\n"; $rep_num = $rep_num + 1;}
  25. if($a =~ m/rep3/){$path3 = $a; chomp $path3; print "3rd replicate is $a\n"; $rep_num = $rep_num + 1;}
  26. }
  28. if($file_num != $rep_num){die "\n\nNumber of files does not match number of replicate data files\n- make sure all the replicate data files contain \"rep1\" or \"rep2\" etc\n";}
  31. print "\nNumber of replicates is $rep_num\n";
  32. if($rep_num == 1){$paths = $path1;}
  33. if($rep_num == 2){$paths = "$path1\t$path2";}
  34. if($rep_num == 3){$paths = "$path1\t$path2\t$path3";}
  36. print "\nEnter name for analysis\n\n";
  37. $exp_name = <STDIN>;
  38. chomp $exp_name;
  40. print "\nEnter FDR threshold \(usually 0.01 \(1 percent\)\)\n\n";
  41. $FDR_thres = <STDIN>;
  42. chomp $FDR_thres;
  45. #print "\nEnter ratio threshold \(usually 1\)\n\n";
  46. $data_thres = 0.2; # threshold of all ratio values that make up a peak
  47. #chomp $data_thres;
  50. mkdir 'FDR_analysis_for_'."$exp_name", 0755 or die "\nCan't make analysis directory!\n";
  51. mkdir 'FDR_analysis_for_'."$exp_name".'\logfiles', 0755 or die "\nCan't make analysis logfiles directory!\n";
  52. mkdir 'FDR_analysis_for_'."$exp_name".'\logfiles\shuffled_data', 0755 or die "\nCan't make shuffled data analysis logfiles directory!\n";
  53. mkdir 'FDR_analysis_for_'."$exp_name".'\logfiles\freq_data', 0755 or die "\nCan't make freq data analysis logfiles directory!\n";
  54. mkdir 'FDR_analysis_for_'."$exp_name".'\FDR_results', 0755 or die "\nCan't make FDR results directory!\n";
  58. ##################### make average and moving average files #######################
  60. system("$dir/sub_programs/split_files_and_average.pl", "$exp_name", "$paths", "$rep_num"); #starts perl prog to make RPM normalised files and average file
  63. ##################### Now to start FDR analysis##################################################################
  65. $replicate = 1;
  67. while($replicate < ($rep_num + 1)){
  69. chrom_analysis("2L");
  70. chrom_analysis("2R");
  71. chrom_analysis("3L");
  72. chrom_analysis("3R");
  73. chrom_analysis("4");
  74. chrom_analysis("X");
  76. sub chrom_analysis{ ####don't forget to close bracket!
  78. my $chrom = shift;
  79. my $chrom2 = "chr"."$chrom"; print "\n$chrom2\n";
  83. ################ now to randomise data set and calculate peak frequency ###############
  85. system("$dir/sub_programs/random_permutation_analysis.pl", "$exp_name", "$chrom", "$replicate", "$data_thres", "$dir"); #starts perl prog to randomise data set and look for peaks
  88. ########################now to look at real data###################################################
  90. system("$dir/sub_programs/real_data_analysis.pl", "$exp_name", "$chrom", "$replicate", "$data_thres", "$dir"); #starts perl prog to examine real data set and look for peaks
  93. ##############################now to merge FDR values and data########################################
  95. system("$dir/sub_programs/merge_FDR_values_and_data.pl", "$exp_name", "$chrom", "$replicate", "$dir"); #starts perl prog to merge FDR values and data
  98. ##################### find all regions with FDR less than 0.0001 ####################################
  100. system("$dir/sub_programs/assign_FDR_less_than_0.0001.pl", "$exp_name", "$chrom", "$replicate", "$data_thres", "$dir"); #Find regions with FDR < 0.0001
  102. system("$dir/sub_programs/assign_each_GATC_lowest_fdr.pl", "$exp_name", "$chrom", "$replicate", "$dir");
  104. system("$dir/sub_programs/make_peakfile.pl", "$exp_name", "$chrom", "$replicate", "$FDR_thres", "$dir");
  106. }
  107. $replicate = $replicate + 1;
  108. }
  111. system("$dir/sub_programs/merge_peak_files.pl", "$exp_name", "$rep_num", "$dir");
  113. system("$dir/sub_programs/assign_final_peaks_FDR_and_height.pl", "$exp_name", "$rep_num", "$FDR_thres", "$dir");
  115. system("$dir/sub_programs/compile_final_peak_file.pl", "$exp_name", "$FDR_thres", "$dir");
  117. system("$dir/sub_programs/assign_peak_to_gene.pl", "$exp_name", "$FDR_thres", "$dir");
  121. ################################ make unique gene list #################################
  123. system("$dir/sub_programs/make_unique_gene_list.pl", "$exp_name", "$dir");

DamID_analysis_pipeline.pl at commit e322644, under GPL-3.0 · at the source

Overview

Authors: Freya Storer1, Colin D. McClure1, Alicia Estacio Gomez1, Lucy J. Minkley2, Tsz Lam Wong1, Nina Markevych1, Tony D. Southall1
ORCID iDs: Colin D. McClure, Tony D. Southall
  1. Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London, United Kingdom
  2. School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
Institutions: Imperial College London (United Kingdom); University of Nottingham (United Kingdom); Queen's Medical Centre (United Kingdom)
Journal: PLoS biology, volume 24, issue 7, article e3003863
Dates: received 27 July 2025; accepted 5 June 2026; published online 17 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pbio.3003863 · PMID 42467693 · PMCID PMC13432123 · OpenAlex W7169511132
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: drosophila (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Evoked potentials, Connectivity, fMRI & imaging
MeSH: Drosophila melanogaster*, Drosophila Proteins*, Neurons*, RNA Polymerase III*, RNA, Transfer*, RNA-Binding Proteins*, Animals, Brain, Female, Male (* major topic)
Journal subjects: Biology and Life Sciences, Genetics, Gene Expression, Biochemistry, Nucleic acids, RNA, Non-coding RNA, Transfer RNA, Cell Biology, Cellular Types, Animal Cells, Neurons, Neuroscience, Cellular Neuroscience, Chromosome Biology, Chromatin, Epigenetics, RNA interference, Genetic interference, Research and Analysis Methods, Animal Studies, Experimental Organism Systems, Model Organisms, Drosophila Melanogaster, Animal Models, Zoology, Entomology, Insects, Drosophila, Organisms, Eukaryota, Animals, Invertebrates, Arthropoda, Mathematical and Statistical Techniques, Statistical Methods, Multivariate Analysis, Principal Component Analysis, Physical Sciences, Mathematics, Statistics, DNA transcription
Topic: RNA Research and Splicing (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Wellcome Trust (104567/Z/14/Z); RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) (BB/X00256X/1)
Citations: not cited yet (Europe PMC); 54 references in the paper

Abstract

The RNA-binding protein Sex-lethal (Sxl) is classically known as a master regulator of sex determination and mRNA splicing in Drosophila melanogaster. However, this role is not conserved across species, and functions beyond the canonical pathway remain poorly understood. In this study, we uncover a splicing-independent role for Sxl at the chromatin level in the Drosophila brain. Using Targeted DamID (TaDa) profiling in neurons, we identify widespread binding of Sxl to promoter regions, independent of sex or RNA binding activity. Notably, Sxl chromatin occupancy exhibits near-complete overlap with Polr3E (RPC37), an RNA Polymerase III subunit, with Sxl binding abolished upon Polr3E knockdown. Depletion of Sxl in mature male neurons induces widespread transcriptional changes, particularly in metabolic genes, and improves negative geotaxis during aging, phenotypes that closely mirror Polr3E knockdown. Conversely, overexpression of the brain-specific SxlRAC transcript leads to severe climbing deficits and upregulated gene expression associated with metabolism and translation. Manipulating Sxl levels in the brain significantly impacts select tRNA production and global protein synthesis rates. Together, these findings reveal a previously unrecognized role for Sxl in regulating Pol III activity via Polr3E, modulating tRNA synthesis and supporting neuronal metabolism. Given the emerging tie between Pol III regulation and neuronal aging, our study highlights Sxl as a novel factor in neuronal homeostasis.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

tonysouthall/Peak_calling_DamID

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: e32264456b5c472622c87c6f23c7a0855af375b7, 23 July 2019
Languages: Perl (1)
Size: 6 files, 1 script
Software Heritage: not archived
Found in: the text, “Targeted DamID”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
3 files
At the source: github.com/tonysouthall/Peak_calling_DamID

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1 script, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability

All raw sequence files and processed files have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GSE294838). This is a SuperSeries containing GSE239790 (Targeted DamID), GSE294835 (RNA-seq) and GSE294837 (small RNA-seq).

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 10 MeSH terms, 2 funders, 54 references.

Cite

This paper

Storer, F., McClure, C. D., Gomez, A. E., Minkley, L. J., Wong, T. L., Markevych, N., & Southall, T. D. (2026). Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons. PLoS biology, 24(7), e3003863. https://doi.org/10.1371/journal.pbio.3003863

BibTeX

@article{storer2026neuronal,
author = {Storer, Freya and McClure, Colin D. and Gomez, Alicia Estacio and Minkley, Lucy J. and Wong, Tsz Lam and Markevych, Nina and Southall, Tony D.},
title = {{Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons}},
journal = {PLoS biology},
year = {2026},
month = jul,
volume = {24},
number = {7},
pages = {e3003863},
publisher = {PLOS},
issn = {1544-9173},
doi = {10.1371/journal.pbio.3003863},
url = {https://doi.org/10.1371/journal.pbio.3003863},
pmid = {42467693},
pmcid = {PMC13432123}
}

RIS

TY - JOUR
AU - Storer, Freya
AU - McClure, Colin D.
AU - Gomez, Alicia Estacio
AU - Minkley, Lucy J.
AU - Wong, Tsz Lam
AU - Markevych, Nina
AU - Southall, Tony D.
TI - Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons
T2 - PLoS biology
J2 - PLoS Biol
PY - 2026
DA - 2026/07/17
VL - 24
IS - 7
SP - e3003863
SN - 1544-9173
PB - PLOS
DO - 10.1371/journal.pbio.3003863
UR - https://doi.org/10.1371/journal.pbio.3003863
LA - en
ER -

CSL-JSON

{
"id": "10.1371/journal.pbio.3003863",
"type": "article-journal",
"title": "Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons",
"container-title": "PLoS biology",
"author": [
{
"family": "Storer",
"given": "Freya"
},
{
"family": "McClure",
"given": "Colin D."
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{
"family": "Gomez",
"given": "Alicia Estacio"
},
{
"family": "Minkley",
"given": "Lucy J."
},
{
"family": "Wong",
"given": "Tsz Lam"
},
{
"family": "Markevych",
"given": "Nina"
},
{
"family": "Southall",
"given": "Tony D."
}
],
"container-title-short": "PLoS Biol",
"volume": "24",
"issue": "7",
"page": "e3003863",
"DOI": "10.1371/journal.pbio.3003863",
"PMID": "42467693",
"PMCID": "PMC13432123",
"ISSN": "1544-9173",
"publisher": "PLOS",
"URL": "https://doi.org/10.1371/journal.pbio.3003863",
"language": "en",
"issued": {
"date-parts": [
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2026,
7,
17
]
]
}
}

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