GEO series
Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen
GSE303855
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
45 samples
Submitted 2025/08/27
Platform GPL30882Platform GPL18573Platform GPL24676Platform GPL34284
Summary
The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their importance, the mechanisms governing LAD positioning in human cells remain poorly understood. To this end, we performed a genome-wide imaging-based screen and identified 101 genes critical for perinuclear LAD localization, with a significant enrichment for RNA-binding proteins. Among these, hnRNPK emerged as a key regulator, required for the perinuclear positioning of approximately 70% of LADs genome-wide. Loss of hnRNPK led to their repositioning away from the nuclear periphery without altering global heterochromatin state, yet resulted in misexpression of genes within these domains. Notably, hnRNPK-sensitive LADs are uniquely enriched for H3K27me3, distinguishing them from hnRNPK-insensitive LADs that are predominantly marked by H3K9me3. These findings reveal mechanistically distinct classes of LADs and suggest that specialized pathways underlie their spatial organization. Our results uncover a pivotal role for hnRNPK in regulating chromatin architecture and highlight the broader diversity of LAD tethering mechanisms.
Published in
Walsh PJ, Kraeutler EB, Linares-Saldana R et al.
· bioRxiv : the preprint server for biology 2025
· PMID 40832213
· doi:10.1101/2025.08.13.670143
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE303855_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 45 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1297768 and SRA study SRP604067. Searching any of these in the dataset finder brings you back here.
Study design
37 conditions, each sampled once — no replicated groups
RNA, siControl, ×4
Read from the first 40 of 45 sample titles: 37 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9136977 CHIP001, LMNB1, siControl, Rep1
- GSM9136978 CHIP002, Input, siControl, Rep1
- GSM9136979 CHIP003, LMNB1, siControl, Rep2
- GSM9136980 CHIP004, Input, siControl, Rep2
- GSM9136981 CHIP005, LMNB1, siControl, Rep3
- GSM9136982 CHIP006, Input, siControl, Rep3
- GSM9136983 CHIP007, LMNB1, siHNRNPK, Rep1
- GSM9136984 CHIP008, Input, siHNRNPK, Rep1
- GSM9136985 CHIP009, LMNB1, siHNRNPK, Rep2
- GSM9136986 CHIP010, Input, siHNRNPK, Rep2
- GSM9136987 CHIP011, LMNB1, siHNRNPK, Rep3
- GSM9136988 CHIP012, Input, siHNRNPK, Rep3
- GSM9136989 CHIP013, H3K9me2, siControl, Rep1
- GSM9136990 CHIP014, H3K9me3, siControl, Rep1
- GSM9136991 CHIP015, Input, siControl, Rep1
- GSM9136992 CHIP016, H3K9me2, siControl, Rep2
- GSM9136993 CHIP017, H3K9me3, siControl, Rep2
- GSM9136994 CHIP018, Input, siControl, Rep2
- GSM9136995 CHIP019, H3K9me2, siControl, Rep3
- GSM9136996 CHIP020, H3K9me3, siControl, Rep3
- GSM9136997 CHIP021, Input, siControl, Rep3
- GSM9136998 CHIP022, H3K9me3, siHNRNPK, Rep1
- GSM9136999 CHIP023, Input, siHNRNPK, Rep1
- GSM9137000 CHIP024, H3K9me3, siHNRNPK, Rep2
- GSM9137001 CHIP025, Input, siHNRNPK, Rep2
- GSM9137002 CHIP026, H3K9me3, siHNRNPK, Rep3
- GSM9137003 CHIP027, Input, siHNRNPK, Rep3
- GSM9137004 CHIP028, H3K27me3, siControl, Rep1
- GSM9137005 CHIP029, Input, siControl, Rep1
- GSM9137006 CHIP030, H3K27me3, siControl, Rep2
- GSM9137007 CHIP031, Input, siControl, Rep2
- GSM9137008 CHIP032, H3K27me3, siHNRNPK, Rep1
- GSM9137009 CHIP033, Input, siHNRNPK, Rep1
- GSM9137010 CHIP034, H3K27me3, siHNRNPK, Rep2
- GSM9137011 CHIP035, Input, siHNRNPK, Rep2
- GSM9154950 RNA, siControl, rep1
- GSM9154951 RNA, siControl, rep2
- GSM9154952 RNA, siControl, rep3
- GSM9154953 RNA, siControl, rep4
- GSM9154954 RNA, siHNRNPK, rep1
+ 5 more — browse all 45 samples with per-sample file links →
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