{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sandra SINNASSAMY"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15856"],"description":["LINE-1 are the only active and autonomous transposable elements in the human genome and encode two proteins, the nucleic acid chaperone ORF1p and ORF2p, which has reverse transcriptase and endonuclease activities. ORF1p is present at steady-state in human and mouse neurons in the adult brain, but a physiological function of LINE-1 and/or ORF1p in mature neurons has not been investigated. We therefore perfomed siRNA-mediated knock-down of LINE-1 ORF1p followed by RNA-sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Lund human mesencephalic cells (LUHMES) cells were differentiated for 7 days, using  Advanced DMEM/F12 added with 1% N-2 supplement and GlutaMax, supplemented with 1 µg/ml doxycycline (Sigma), 2 ng/ml recombinant human GDNF (Peprotech, # 450-10) and 1mM cAMP (Sigma, # D0627).","Sample Treatment - Cells were transfected with siRNA at day 3 and retrieved at day 7 of differentiation (siRNA Control or siRNA ORF1)","Sample Collection - LUHMES cells were differentiated for 7 days. Cells were transfected with siRNA at day 3 and retrieved at day 7 of differentiation (siRNA Control or siRNA ORF1).","Sequencing - Libraries were sequenced as pair-end (PE) 150 bp using a  Novaseq x plus sequencer.","Nucleic Acid Extraction - RNA was harvested using Direct-zol™ RNA Microprep (Zymo, # R2062).","Library Construction - Libraries including rRNA removal were generated using the RNA Library Prep Kit for Illumina following manufacturer’s recommendations."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Mapping was performed by Hisat2 (v2.0.5) on human genome (hg38/GRCh38 assembly). Raw counts were then normalized by DESeq2."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"pubmed_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 downregulation 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."],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["Interactions of the LINE-1 encoded ORF1p with proteins and chromatin converge on a role in neuronal physiology"],"pubmed_authors":["Sandra Sinnassamy, Olivia Massiani Beaudoin, Berangère Lombard, Damarys Loew, Tom Bonnifet, Magali Fradet, Héloïse Monnet, Thomas Caille, Nicolas Servant, Rajiv L. Joshi, Julia Fuchs","Sandra SINNASSAMY"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq with and without siRNA ORF1 in post-mitotic human dopaminergic neurons (LUHMES cell line, differentiated)","description":"LINE-1 are the only active and autonomous transposable elements in the human genome and encode two proteins, the nucleic acid chaperone ORF1p and ORF2p, which has reverse transcriptase and endonuclease activities. ORF1p is present at steady-state in human and mouse neurons in the adult brain, but a physiological function of LINE-1 and/or ORF1p in mature neurons has not been investigated. We therefore perfomed siRNA-mediated knock-down of LINE-1 ORF1p followed by RNA-sequencing.","dates":{"release":"2026-04-01T00:00:00Z","modification":"2026-04-02T01:05:05.734Z","creation":"2025-10-24T14:56:37.349Z"},"accession":"E-MTAB-15856","cross_references":{"ENA":["ERP182906"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"],"doi":["10.1101/2025.09.05.674414"]}}