biostudies-arrayexpressCarl MANNMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15189Cut & Tag was used to localize the 3 mouse HP1 proteins (Cbx1,Cbx3,Cbx5) to the genome of BMEL (bipotential mouse embryonic liver) cells. Het BMEL cells are Cbx1+/+, Cbx3+/+, Cbx5+/- HP1-TKO (triple knock-out cells) are Cbx1-/-, Cbx3-/-, Cbx5-/-. The HP1_TKO cells were used to verify the specificity of the Cut & Tag signals. HP1 localization was compared with the chromatin localization of select RNA exosome subunits and adapters to support a role for HP1 in targeting the RNA exosome to specific chromatin regions.biostudies-arrayexpressLibrary Construction - Libraries were PCR amplified for Illumina sequencing using primers described in https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3Growth Protocol - BMEL cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 10 µg/mL insulin, 30 ng/mL IGF-II, and 50 ng/mL EGF, at 37 °C under 5% CO2.Nucleic Acid Extraction - Permeabilized cells were treated for Cut & Tag experiments as per https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3.Sample Collection - BMEL cells were trypsinized and permeabilized with NE1 buffer as per https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3.Sequencing - Paired-end 42 bp sequencing was performed on an Illumina NextSeq 550.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were aligned on the mm10 reference genome with bowtie2 (parameters: --end-to-end --very-sensitive --no-mixed --no-discordant -k 1 -X 1000 --phred33 -I 25 -p 24 -x mm10). Bigwig files were generated from two merged HP1 CUT&Tag replicates, and they were normalized using CPM.Data Transformation - Bigwig files were generated from two merged HP1 CUT&Tag replicates, and they were normalized using CPM.UnknownTranscriptomicsGenomicsProteomicsNextSeq 550HP1, a hallmark of pericentromeric heterochromatin, is a chromatin-bound regulator of co-transcriptional processes including alternative splicing, but its role in RNA degradation remains unexplored. Here, we uncover a direct interaction between HP1 and the RNA exosome, a major RNA decay complex. In mouse embryonic liver cells, inactivation of all three HP1 isoforms led to accumulation of retrotransposon-derived RNAs and stabilization of enhancer RNAs. These changes coincided with increased activity at a subset of liver enhancers particularly sensitive to reduced exosome activity, many of which regulate genes encoding extracellular matrix components such as Col6a1 and Col6a2 . Stratifying hepatocellular carcinoma samples by HP1 expression further revealed that tumors with low HP1 were marked by reduced RNA degradation, and increased expression of a similar subset of genes encoding extracellular matrix components and possibly contributing to tumor stiffness. These results suggest that HP1’s impact on RNA turnover contributes to its function in cancer biology.CUT&TAGMus musculusTargeting of the nuclear RNA exosome to chromatin by HP1 affects the transcriptional program of liver cellsHiba Souaifan; Mickael Costallat; Laura Sitkiewicz; Kylian Godest; Florence Cammas; Carl Mann; Christian Muchardt; Christophe RachezCarl MANNfalseHP1, H3-K27me3, and H3-K9me3 Cut & Tag of Het (Cbx1+/+, Cbx3+/+, Cbx5+/-) and TKO (Cbx1-/-, Cbx3-/-, Cbx5-/-) bipotential mouse embryonic liver (BMEL) cellsCut & Tag was used to localize the 3 mouse HP1 proteins (Cbx1,Cbx3,Cbx5) to the genome of BMEL (bipotential mouse embryonic liver) cells. Het BMEL cells are Cbx1+/+, Cbx3+/+, Cbx5+/- HP1-TKO (triple knock-out cells) are Cbx1-/-, Cbx3-/-, Cbx5-/-. The HP1_TKO cells were used to verify the specificity of the Cut & Tag signals. HP1 localization was compared with the chromatin localization of select RNA exosome subunits and adapters to support a role for HP1 in targeting the RNA exosome to specific chromatin regions.2025-06-14T00:00:00Z2025-05-30T11:41:22.678Z2025-05-30T11:41:22.678ZE-MTAB-15189ERP17305410.1101/2025.02.14.638307EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184