Karthikeyan, R. | Search bioRxiv

bioRxiv2024

Distinct structural and functional heterochromatin partitioning of lamin B1 and B2 revealed using genome-wide Nicking Enzyme Epitope targeted DNA sequencing.

A genome-wide chromatin profiling technology, named as Nicking Enzyme Epitope targeted DNA sequencing (NEED-seq) in which antibody-targeted controlled nicking by Nt.CviPII-pGL is used to study specific protein-DNA complexes. NEED-seq is performed in situ in formaldehyde fixed cells, allowing for both visual and genomic resolution of epitope bound chromatin. When applied to nuclei, NEED-seq yielded genome-wide chromatin associated proteins and histone post-translational modifications (PTMs). NEED-seq of lamin B1/B2 demonstrated their association with heterochromatin. Lamin B1 and B2 associated domains (LAD) segregated to three different states, and states with stronger LAD correlated with heterochromatic marks. Hi-C analysis displayed A and B compartment with equal lamin B1/B2 distribution, although methylated DNA remained high in B compartment. LAD clustering with Hi-C resulted in subcompartments, with lamin B1-B2 partitioning to facultative and constitutive heterochromatin respectively and were associated with neuronal development. Thus, lamin B1 and B2 have structural and functional partitioning in mammalian nucleus. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/603107v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@44c36forg.highwire.dtl.DTLVardef@7ab1adorg.highwire.dtl.DTLVardef@126e99eorg.highwire.dtl.DTLVardef@1b38bd7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract: Model depicting association of lamin B1 and B2 in A (facultative heterochromatin) and B (constitutive heterochromatin) compartmentalization. C_FIG

genomics↗

bioRxiv2019

Transcriptome responses of intestinal epithelial cells induced by membrane vesicles of Listeria monocytogenes unveil novel insights into the host-pathogen cross talk

Membrane vesicles (MVs) serve as a vital source of virulence factors in many pathogenic organisms. The release of MVs by Listeria monocytogenes is only recently recognized, but its role in the pathogenesis is poorly understood. Here, we investigated the role of MVs of L. monocytogenes in virulence and host interactions. Proteomic analyses of whole cells and MVs of L. monocytogenes were performed using LC/MS/MS. A total of 1376 and 456 proteins were identified in the L. monocytogenes cells and MVs, respectively. Also, we have found that MVs contains active pore-forming listeriolysin (LLO), internalin B (inlB), phosphatidylinositol-specific phospholipase C (PI-PLC-A). We have previously reported that MVs of L. monocytogenes can infect and induce cytotoxicity in Caco-2 cells. In this study, we report the transcriptome response of Caco-2 cells upon infection with MVs as well as L. monocytogenes. In particular, we observed the up-regulation of autophagy-related genes in the early phase of infection with MVs. Transcription of inflammatory cytokines (CCL2, CXCL6, CXCL8, CXCL15, CXCL5, CXCL10) peaked at four h of infection. A large number of differentially expressed genes was associated with actin cytoskeleton rearrangement, autophagy, cell cycle arrest, and induction of oxidative stress. At a later time point, transcriptional programs generated upon infection with MVs point toward to evade innate immune signals, by modulating the expression of anti-inflammatory genes. KEGG pathway enrichment analysis revealed that MVs induce several signaling pathways such as PI3k-Akt signaling pathway, mitogen-activated protein kinase (MAPK) pathway, NOD-like receptor signaling pathway, cAMP signaling pathway, TNF, and NF-kB signaling pathway. Moreover, MVs induced the expression of cell cycle regulatory genes, which may result in the ability to prolong host cell survival, thus protecting the replicative niche for L. monocytogenes. Notably, we identified several non-coding RNAs (ncRNAs) are regulated during infection, suggesting that an early manipulation of the host gene expression may be essential for L. monocytogenes persistence and replication in host cells.

microbiology↗