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Alternative splicing landscape of the neural transcriptome in a cytoplasmic-predominant Pten expression murine model of autism-like Behavior.

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  1. [1] § Materials and methods › Analysis of alternative splicing patterns from RNA-sequencing data ↔ rMATs_v.4.0.2_P14.sh, the whole file · a weak match · score 0.63 · alternative splicing events, WT MUT, rMATS, delta, bam, PSI
  2. [2] § Materials and methods › Analysis of alternative splicing patterns from RNA-sequencing data ↔ rMATs_v4.0.2_P40.sh, the whole file · a weak match · score 0.63 · alternative splicing events, WT MUT, rMATS, delta, bam, PSI

Paper

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The authors' code

Shell · 49 lines · 2.7 KB · no license · 1 match

  1. #!/usr/bin/env bash
  2. ##################################################################
  3. # AIM : to make a slurm script for rMATS 4.0.2 to run on replicate, sorted and indexed M3M4 bam files
  4. # Input:sorted and filtered and STAR bam files, mm10 gencode gtf file (gencode.vM16.annotation.gtf)
  5. # Ouput:slurm script that will create a directory containing files of AS analysis performed by rMATS, specifically the MATS_OUTPUT subdirectory that contains the delta
  6. # psi values per splicing event per gene
  7. # Author: Marilyn Seyfi
  8. # email: [email hidden]
  9. # Date: 11 Dec 2019
  10. ################################################################
  11. #------------------------- modify here -------------------
  12. # Dirs
  13. export bam_dir="/home/seyfim/isilon/NGS_Working/Stetson_Thacker/AlternativeSplicing_M3M4/fasta_and_bam_files/STAR_filtered_and_indexed_bam"
  14. export gtf_loc="/home/seyfim/isilon/NGS_Working/Library_Files/Genome/Mouse/mm10/gencode/gencode.vM16.annotation.gtf"
  15. export output_loc="/home/seyfim/isilon/NGS_Working/Stetson_Thacker/AlternativeSplicing_M3M4/rMATS/data/v.4.0.2"
  17. export H1="${bam_dir}/P14M3M4HetM1brainAligned.filtered.bam"
  18. export H2="${bam_dir}/P14M3M4HetM2brainAligned.filtered.bam"
  19. export H3="${bam_dir}/P14M3M4HetM3brainAligned.filtered.bam"
  20. export M1="${bam_dir}/P14M3M4MutM1brainAligned.filtered.bam"
  21. export M2="${bam_dir}/P14M3M4MutM2brainAligned.filtered.bam"
  22. export M3="${bam_dir}/P14M3M4MutM3brainAligned.filtered.bam"
  23. export W1="${bam_dir}/P14M3M4WtM1brainAligned.filtered.bam"
  24. export W2="${bam_dir}/P14M3M4WtM2brainAligned.filtered.bam"
  25. export W3="${bam_dir}/P14M3M4WtM3brainAligned.filtered.bam"
  29. echo "${W1},${W2},${W3}" >> wt_P14.txt
  30. echo "${H1},${H2},${H3}" >> het_P14.txt
  31. echo "${M1},${M2},${M3}" >> mut_P14.txt
  33. export WT="wt_P14.txt"
  34. export MUT="mut_P14.txt"
  35. export HET="het_P14.txt"
  37. #----------------------------------------------------------
  39. module load python/2.7.12
  40. module load samtools/0.1.19
  41. module load STAR/2.5.4b
  42. module load rMATS/4.0.2
  44. # /cm/shared/apps/rMATS/4.0.2/rmats.py --b1 p14_MUT.txt --b2 p14_HET.txt --gtf /home/seyfim/isilon/NGS_Working/Library_Files/Genome/Mouse/mm10/gencode/gencode.vM16.annotation.gtf --od /home/seyfim/isilon/NGS_Working/Stetson_Thacker/AlternativeSplicing_M3M4/rMATS/data/v.4.0.2/P14MutHet_output --nthread 20 --readLength 100 --libType fr-secondstrand
  47. /cm/shared/apps/rMATS/4.0.2/rmats.py --b1 ${WT} --b2 ${HET} --gtf ${gtf_loc} --od ${output_loc}/WtMut --nthread 28 --readLength 100 --libType fr-secondstrand
  48. /cm/shared/apps/rMATS/4.0.2/rmats.py --b1 ${WT} --b2 ${MUT} --gtf $gtf_loc --od $output_loc/WtHet --nthread 28 --readLength 100 --libType fr-secondstrand
  49. /cm/shared/apps/rMATS/4.0.2/rmats.py --b1 ${MUT} --b2 ${HET} --gtf $gtf_loc --od $output_loc/MutHet --nthread 28 --readLength 100 --libType fr-secondstrand

rMATs_v.4.0.2_P14.sh at commit b1c7a6f, no license · at the source

Overview

Authors: Stetson Thacker1,2, Marilyn Sefyi1, Charis Eng1,2,3,4,5
ORCID iDs: Stetson Thacker, Charis Eng
  1. Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA
  2. Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195 USA
  3. Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195 USA
  4. Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
  5. Germline High Risk Cancer Focus Group, Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
Institutions: Cleveland Clinic (United States); Cleveland Clinic Lerner College of Medicine (United States); Case Comprehensive Cancer Center; Case Western Reserve University (United States)
Journal: Translational psychiatry, volume 10, issue 1, article 380
Dates: received 7 April 2020; accepted 4 September 2020; published online 6 November 2020
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41398-020-01068-x · PMID 33159038 · PMCID PMC7648763 · OpenAlex W3096678460
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), mouse (organism), autism (population), cellular / molecular (subfield)
Methods: Statistics
Keywords: Autism spectrum disorders, Genomics
MeSH: Alternative Splicing*, Autism Spectrum Disorder*, Autistic Disorder*, Animals, Disease Models, Animal, Mice, PTEN Phosphohydrolase, Transcriptome (* major topic)
Topic: RNA Research and Splicing (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Ambrose Monell Foundation
Citations: cited by 19 papers (Europe PMC); 31 references in the paper

Abstract

Alternative splicing (AS) is a posttranscriptional mechanism regulating gene expression that complex organisms utilize to expand proteome diversity from a comparatively limited set of genes. Recent research has increasingly associated AS with increased functional complexity in the central nervous systems in higher order mammals. This work has heavily implicated aberrant AS in several neurocognitive and neurodevelopmental disorders, including autism. Due to the strong genetic association between germline PTEN mutations and autism spectrum disorder (ASD), we hypothesized that germline PTEN mutations would alter AS patterns, contributing to the pathophysiology of ASD. In a murine model of constitutional mislocalization of Pten, recapitulating an autism-like phenotype, we found significant changes in AS patterns across the neural transcriptome by analyzing RNA-sequencing data with the program rMATS. A few hundred significant alternative splicing events (ASEs) that differentiate each m3m4 genotype were identified. These ASEs occur in genes enriched in PTEN signaling, inositol metabolism, and several other pathways relevant to the pathophysiology of ASD. In addition, we identified expression changes in several splicing factors known to be enriched in the nervous system. For instance, the master regulator of microexons, Srrm4, has decreased expression, and consequently, we found decreased inclusion of microexons in the Ptenm3m4/m3m4 cortex (~10% decrease). We also demonstrated that the m3m4 mutation disrupts the interaction between Pten and U2af2, a member of the spliceosome. In sum, our observations point to germline Pten disruption changing the landscape of alternative splicing in the brain, and these changes may be relevant to the pathogenesis and/or maintenance of PTEN-ASD phenotypes.

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

Repository

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Thackes/PTEN-AlternativeSplicing

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: b1c7a6f7e45a7788de962d9e75bf45b8b2979caa, 20 July 2020
Languages: Shell (7), Python (3)
Size: 19 files, 10 scripts
Software Heritage: not archived
Found in: the text, “Analysis of alternative splicing patterns from R”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (3 files), pandas (3 files), STAR (3 files), SAMtools (2 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
11 files
At the source: github.com/Thackes/PTEN-AlternativeSplicing

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 2 keywords, 8 MeSH terms, 1 funder, 31 references.

Cite

This paper

Thacker, S., Sefyi, M., & Eng, C. (2020). Alternative splicing landscape of the neural transcriptome in a cytoplasmic-predominant Pten expression murine model of autism-like Behavior. Translational psychiatry, 10(1), 380. https://doi.org/10.1038/s41398-020-01068-x

BibTeX

@article{thacker2020alternative,
author = {Thacker, Stetson and Sefyi, Marilyn and Eng, Charis},
title = {{Alternative splicing landscape of the neural transcriptome in a cytoplasmic-predominant Pten expression murine model of autism-like Behavior}},
journal = {Translational psychiatry},
year = {2020},
month = nov,
volume = {10},
number = {1},
pages = {380},
publisher = {Nature Publishing Group},
issn = {2158-3188},
doi = {10.1038/s41398-020-01068-x},
url = {https://doi.org/10.1038/s41398-020-01068-x},
pmid = {33159038},
pmcid = {PMC7648763}
}

RIS

TY - JOUR
AU - Thacker, Stetson
AU - Sefyi, Marilyn
AU - Eng, Charis
TI - Alternative splicing landscape of the neural transcriptome in a cytoplasmic-predominant Pten expression murine model of autism-like Behavior
T2 - Translational psychiatry
J2 - Transl Psychiatry
PY - 2020
DA - 2020/11/06
VL - 10
IS - 1
SP - 380
SN - 2158-3188
PB - Nature Publishing Group
DO - 10.1038/s41398-020-01068-x
UR - https://doi.org/10.1038/s41398-020-01068-x
LA - en
ER -

CSL-JSON

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"container-title": "Translational psychiatry",
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"volume": "10",
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