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Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology.

Code ↔ Paper

1 match between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 1 match
  1. [1] § Materials and Methods › ATAC sequencing and analysis ↔ bin/stats2multiqc.sh, lines 88–142 · score 0.67 · deepTools, peak calling, filtered, duplicates, Profiles, mapping

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Shell · 143 lines · 5 KB · CECILL-2.1 · 1 match

  1. #!/bin/bash
  3. function usage {
  4. echo -e "usage : stats2multiqc.sh -s SAMPLE_PLAN -d DESIGN -a ALIGNER [-p][-h]"
  5. echo -e "Use option -h|--help for more information"
  6. }
  8. function help {
  9. usage;
  10. echo
  11. echo "stat2multiqc.sh"
  12. echo "---------------"
  13. echo "OPTIONS"
  14. echo
  15. echo " -s SAMPLE_PLAN"
  16. echo " -d DESIGN"
  17. echo " -a ALIGNER"
  18. echo " [-p]: paired-end mode"
  19. echo " [-m]: Mitochondrial chromosome name"
  20. echo " [-h]: help"
  21. exit;
  22. }
  24. is_pe=0
  25. mito_name="chrM"
  26. while getopts "s:d:a:m:ph" OPT
  27. do
  28. case $OPT in
  29. s) splan=$OPTARG;;
  30. d) design=$OPTARG;;
  31. a) aligner=$OPTARG;;
  32. m) mito_name=$OPTARG;;
  33. p) is_pe=1;;
  34. h) help ;;
  35. \?)
  36. echo "Invalid option: -$OPTARG" >&2
  37. usage
  38. exit 1
  39. ;;
  40. :)
  41. echo "Option -$OPTARG requires an argument." >&2
  42. usage
  43. exit 1
  44. ;;
  45. esac
  46. done
  48. if [[ -z $splan ]]; then
  49. usage
  50. exit
  51. fi
  53. all_samples=$(awk -F, '{print $1}' $splan)
  55. echo -e "Sample_ID,Sample_name,Number_of_reads,Number_of_aligned_reads,Percent_of_aligned_reads,Number_of_mito,Percent_of_mito,Number_of_hq_mapped_reads,Percent_of_hq_mapped_reads,Number_of_lq_mapped_reads,Percent_of_lq_mapped_reads,Number_of_duplicates,Percent_of_duplicates,Number_of_usable_reads,Percent_of_usable_reads,TSS_enrichment,Fraction_of_reads_in_peaks" > mqc.stats
  57. for sample in $all_samples
  58. do
  59. #SAMPLE NAME
  60. sname=$(grep "$sample," $splan | awk -F, '{print $2}')
  62. #ALIGNMENT
  63. if [ $aligner == "bowtie2" ]; then
  64. nb_frag=$(grep "reads;" mapping/${sample}_bowtie2.log | sed 's/ .*//')
  65. if [[ $is_pe == 1 ]]; then
  66. nb_reads=$(( $nb_frag * 2 ))
  67. else
  68. nb_reads=$nb_frag
  69. fi
  70. elif [ $aligner == "bwa-mem" ]; then
  71. # bwa.log file is in reads number (not pairs)
  72. nb_reads=$(grep 'Total' mapping/${sample}_bwa.log | awk -F "\t" '{print $2}')
  73. if [[ $is_pe == 1 ]]; then
  74. nb_frag=$(( $nb_reads / 2 ))
  75. else
  76. nb_frag=$nb_reads
  77. fi
  78. tail -n +3 mapping/${sample}_bwa.log > mapping/${sample}_bwa.mqc
  79. elif [ $aligner == "star" ]; then
  80. nb_frag=$(grep "Number of input reads" mapping/${sample}Log.final.out | cut -d"|" -f 2 | sed -e 's/\t//g')
  81. if [[ $is_pe == 1 ]]; then
  82. nb_reads=$(( $nb_frag * 2 ))
  83. else
  84. nb_reads=$nb_frag
  85. fi
  86. fi
  88. #Mapping stats (always in reads - so must be converted for PE)
  89. #These statistics are calculated after spike cleaning but before filtering
  90. nb_mapped=$(awk -F, '$1=="Mapped"{print $2}' mapping/${sample}_mappingstats.mqc)
  91. nb_mapped_hq=$(awk -F, '$1=="HighQual"{print $2}' mapping/${sample}_mappingstats.mqc)
  92. nb_mapped_lq=$(awk -F, '$1=="LowQual"{print $2}' mapping/${sample}_mappingstats.mqc)
  93. perc_mapped=$(echo "${nb_mapped} ${nb_reads}" | awk ' { printf "%.*f",2,$1*100/$2 } ')
  94. perc_mapped_hq=$(echo "${nb_mapped_hq} ${nb_reads}" | awk ' { printf "%.*f",2,$1*100/$2 } ')
  95. perc_mapped_lq=$(echo "${nb_mapped_lq} ${nb_reads}" | awk ' { printf "%.*f",2,$1*100/$2 } ')
  97. ##MITO
  98. if [[ -e mapping/stats/${sample}_raw.idxstats ]]; then
  99. nb_mito=$(awk -v mt=${mito_name} '$1==mt{print $3}' mapping/stats/${sample}_raw.idxstats)
  100. perc_mito=$(echo "${nb_mito} ${nb_mapped}" | awk ' { printf "%.*f",2,$1*100/$2 } ')
  101. else
  102. nb_mito='NA'
  103. perc_mito='NA'
  104. fi
  106. #PICARD
  107. if [[ -e mapping/${sample}.MarkDuplicates.metrics.txt ]]; then
  108. nb_dups_pair=$(grep -a2 "## METRICS" mapping/${sample}.MarkDuplicates.metrics.txt | tail -1 | awk -F"\t" '{print $7}')
  109. nb_dups_single=$(grep -a2 "## METRICS" mapping/${sample}.MarkDuplicates.metrics.txt | tail -1 | awk -F"\t" '{print $6}')
  110. nb_dups_optical=$(grep -a2 "## METRICS" mapping/${sample}.MarkDuplicates.metrics.txt | tail -1 | awk -F"\t" '{print $8}')
  111. nb_dups=$(( $nb_dups_pair * 2 + $nb_dups_single + $nb_dups_optical ))
  112. perc_dups=$(echo "${nb_dups} ${nb_mapped}" | awk ' { printf "%.*f",2,$1*100/$2 } ')
  113. else
  114. nb_dups='NA'
  115. perc_dups='NA'
  116. fi
  118. #Filtered bam
  119. if [[ -e mapping/stats/${sample}_filtered.stats ]]; then
  120. nb_filt=$(grep ^SN mapping/stats/${sample}_filtered.stats | cut -f 2- | grep "reads mapped:" | cut -f 2)
  121. perc_filt=$(echo "${nb_filt} ${nb_mapped}" | awk ' { printf "%.*f",2,$1*100/$2 } ')
  122. fi
  124. #TSS Enrichment
  125. if [[ -e deepTools/${sample}_NFR.plotProfile_corrected.tab ]]; then
  126. tsse=$(awk -F"\t" 'NR==3{mn=mx=$3;for(i=3;i<=NF;i++){if($i>mx){mx=$i}};printf("%.*f",2, mx-mn)}' deepTools/${sample}_NFR.plotProfile_corrected.tab)
  127. else
  128. tsse='NA'
  129. fi
  131. #PeakCalling
  132. if [ -e peakCalling/${sample}_macs2_peaks.FRiP_mqc.tsv ]; then
  133. frip=$(grep "$sample" peakCalling/${sample}_macs2_peaks.FRiP_mqc.tsv | awk '{print $2}')
  134. elif [ -e peakCalling/${sample}_macs2_peaks.FRiP_mqc.tsv ]; then
  135. frip=$(grep "$sample" peakCalling/${sample}_genrich_peaks.FRiP_mqc.tsv | awk '{print $2}')
  136. else
  137. frip='NA'
  138. fi
  140. #To file
  141. echo -e ${sample},${sname},${nb_frag},${nb_mapped},${perc_mapped},${nb_mito},${perc_mito},${nb_mapped_hq},${perc_mapped_hq},${nb_mapped_lq},${perc_mapped_lq},${nb_dups},${perc_dups},${nb_filt},${perc_filt},${tsse},${frip} >> mqc.stats
  142. done

stats2multiqc.sh at commit 1b162c1, under CECILL-2.1 · at the source

Overview

Authors: Sandra Sinnassamy1, Olivia Massiani Beaudoin1, Berangère Lombard2, Damarys Loew2, Tom Bonnifet1, Magali Fradet3, Héloïse Monnet3, Thomas Caille3, Nicolas Servant4, Rajiv L Joshi1, Julia Fuchs1
ORCID iDs: Olivia Massiani Beaudoin, Berangère Lombard, Damarys Loew, Héloïse Monnet, Thomas Caille, Rajiv L Joshi, Julia Fuchs
  1. CIRB, Collège de France, Université PSL, INSERM, CNRS, Paris, France
  2. Institut Curie, Université PSL, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
  3. Orion Technological Core, CIRB, Collège de France, Université PSL, INSERM, CNRS, Paris, France
  4. Institut Curie, INSERM U900, Mines Paris Tech, Université PSL, Paris, France
Institutions: Université Paris Sciences et Lettres (France)
Journal: Life science alliance, volume 9, issue 11, article e202503546
Dates: received 24 October 2025; accepted 10 August 2026; published online 21 August 2026; in print November 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.26508/lsa.202503546 · PMID 42629196 · PMCID PMC13498733 · OpenAlex W7203929265
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics
MeSH: Chromatin*, Long Interspersed Nucleotide Elements*, Neurons*, Animals, Cell Nucleus, Cells, Cultured, Gene Expression Regulation, Humans, Mice, Neurites, Protein Binding (* major topic)
Topic: Chromosomal and Genetic Variations (Plant Science, Agricultural and Biological Sciences), according to OpenAlex
Funding: Agence Nationale de la Recherche (French National Research Agency) (ANR-20-CE16-0022 NEURAGE, ANR-10-EQPX-03, ANR-10-INBS-09-08); Fondation du Collège de France; Fondation NRJ/Institut de France; Fondation Alzheimer; Fédération pour la Recherche sur le Cerveau (FRC); SiRIC-Curie program (INCa-DGOS-465, INCa-DGOS-Inserm_12554)
Citations: not cited yet (Europe PMC); 104 references in the paper

Abstract

Retrotransposons are emerging as novel regulators of embryonic and brain development. We recently demonstrated that the LINE-1–encoded protein ORF1p is abundantly expressed in adult mouse and human neurons, although its function remains unclear. Here, we characterize the ORF1p interactome in differentiated mouse and human neurons using mass spectrometry and identify novel partners implicated in gene regulation and neuron-specific processes. ORF1p localizes not only to neuronal nuclei, where it associates with chromatin under steady-state conditions, but also to neurites, supporting a role in neuronal physiology. To further explore its nuclear functions, we sorted human post-mortem neurons with high or low nuclear ORF1p levels and performed ORF1p knockdown in cultured human neurons, followed by chromatin accessibility assays. Both approaches revealed consistent patterns of differential chromatin accessibility dependent on ORF1p. Loss of ORF1p also led to the down-regulation of long, neuron-specific genes and altered neurite morphology. Together, these findings point to a physiological role of ORF1p in post-mitotic neurons, mediated through converging interactions with proteins and chromatin.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

orion-cirb/Axon_Skel_Analyzer

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: debbd7ca96c6e73d8a48c6c3ae0d404190f3490f, 22 May 2025
Size: 3 files, 0 scripts
Software Heritage: not archived
Found in: the text, “Image analysis”
Holds: README
Not found: license file, 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
1 file, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit debbd7c, when its fingerprint is the one OSCR verified. How this works.

  • README.md — Text, 61 lines, shown from its source
At the source: github.com/orion-cirb/Axon_Skel_Analyzer

bioinfo-pf-curie/atac-seq

License: CECILL-2.1
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 1b162c12d313677f8836c657adc3d8ec74c0e94d, 22 October 2021
Languages: Python (6), Shell (2), R (2)
Size: 119 files, 10 scripts
Software Heritage: not archived
Found in: the text, “ATAC sequencing and analysis”
Holds: README, license file, environment (environment.yml, conf/singularity.config, recipes/docker/bedtobigbed.Dockerfile, recipes/docker/bowtie2.Dockerfile, recipes/docker/bwa.Dockerfile, recipes/docker/deeptools.Dockerfile, recipes/docker/fastqc.Dockerfile, recipes/docker/genrich.Dockerfile, recipes/docker/homer.Dockerfile, recipes/docker/macs2.Dockerfile, recipes/docker/multiqc.Dockerfile, recipes/docker/onlyLinux.Dockerfile), documentation
Not found: CITATION.cff, tests, continuous integration
Tools: ggplot2 (2 files), reshape2 (2 files), NumPy (1 file), pandas (1 file), SAMtools (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
12 files
At the source: github.com/bioinfo-pf-curie/ATAC-seq/releases/tag/v1.0.2

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 10 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • 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

Datasets cited

Data Availability

The ATAC-seq and RNA-seq data stemming from human differentiated neurons in culture (LUHMES) are available at EBI-EMBL ArrayExpress database under the following accession numbers: ATAC-seq: E- (https://www.ebi.ac.uk/biostudies/ArrayExpress/studies/E-MTAB-15871?query=E-MTAB-15871)MTAB-15871 (https://www.ebi.ac.uk/biostudies/ArrayExpress/studies/E-MTAB-15871?query=E-MTAB-15871) RNA-seq: E- (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15856)MTAB-15856 (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15856)

The mass spectrometry raw data are available on the PRIDE database with the accession number PXD066047 (https://www.ebi.ac.uk/pride/archive?keyword=PXD066047). The ATAC-seq data stemming from post-mortem human brain tissue are only available upon request from the authors because of privacy and ethical restrictions.

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, 11 authors, 11 MeSH terms, 6 funders, 104 references.

Cite

This paper

Sinnassamy, S., Massiani Beaudoin, O., Lombard, B., Loew, D., Bonnifet, T., Fradet, M., Monnet, H., Caille, T., Servant, N., Joshi, R. L., & Fuchs, J. (2026). Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology. Life science alliance, 9(11), e202503546. https://doi.org/10.26508/lsa.202503546

BibTeX

@article{sinnassamy2026interactions,
author = {Sinnassamy, Sandra and Massiani Beaudoin, Olivia and Lombard, Berangère and Loew, Damarys and Bonnifet, Tom and Fradet, Magali and Monnet, Héloïse and Caille, Thomas and Servant, Nicolas and Joshi, Rajiv L and Fuchs, Julia},
title = {{Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology}},
journal = {Life science alliance},
year = {2026},
month = aug,
volume = {9},
number = {11},
pages = {e202503546},
publisher = {Life Science Alliance LLC},
issn = {2575-1077},
doi = {10.26508/lsa.202503546},
url = {https://doi.org/10.26508/lsa.202503546},
pmid = {42629196},
pmcid = {PMC13498733}
}

RIS

TY - JOUR
AU - Sinnassamy, Sandra
AU - Massiani Beaudoin, Olivia
AU - Lombard, Berangère
AU - Loew, Damarys
AU - Bonnifet, Tom
AU - Fradet, Magali
AU - Monnet, Héloïse
AU - Caille, Thomas
AU - Servant, Nicolas
AU - Joshi, Rajiv L
AU - Fuchs, Julia
TI - Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology
T2 - Life science alliance
J2 - Life Sci Alliance
PY - 2026
DA - 2026/08/21
VL - 9
IS - 11
SP - e202503546
SN - 2575-1077
PB - Life Science Alliance LLC
DO - 10.26508/lsa.202503546
UR - https://doi.org/10.26508/lsa.202503546
LA - en
ER -

CSL-JSON

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"id": "10.26508/lsa.202503546",
"type": "article-journal",
"title": "Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology",
"container-title": "Life science alliance",
"author": [
{
"family": "Sinnassamy",
"given": "Sandra"
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{
"family": "Massiani Beaudoin",
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{
"family": "Lombard",
"given": "Berangère"
},
{
"family": "Loew",
"given": "Damarys"
},
{
"family": "Bonnifet",
"given": "Tom"
},
{
"family": "Fradet",
"given": "Magali"
},
{
"family": "Monnet",
"given": "Héloïse"
},
{
"family": "Caille",
"given": "Thomas"
},
{
"family": "Servant",
"given": "Nicolas"
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{
"family": "Joshi",
"given": "Rajiv L"
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{
"family": "Fuchs",
"given": "Julia"
}
],
"container-title-short": "Life Sci Alliance",
"volume": "9",
"issue": "11",
"page": "e202503546",
"DOI": "10.26508/lsa.202503546",
"PMID": "42629196",
"PMCID": "PMC13498733",
"ISSN": "2575-1077",
"publisher": "Life Science Alliance LLC",
"URL": "https://doi.org/10.26508/lsa.202503546",
"language": "en",
"issued": {
"date-parts": [
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21
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]
}
}

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