Elementary 3D organization of active and silenced E. coli genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1135227 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR29808030_1.fastq.gz | Fastqsanger.gz | |||
| SRR29808030_2.fastq.gz | Fastqsanger.gz | |||
| SRR29808031_1.fastq.gz | Fastqsanger.gz | |||
| SRR29808031_2.fastq.gz | Fastqsanger.gz |
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Project description:Elementary 3D organization of active and silenced E. coli genome
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Project description:Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.
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Project description:Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.
2025-06-24 | GSE272159 | GEO
Project description:Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.
2025-06-24 | GSE272158 | GEO
Project description:Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.
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Project description:Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are preferentially formed in regions containing high density of active genes and clusters of architectural protein binding sites. Transcription of most genes is turned off during the heat shock response in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. New heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies at the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be quickly reconfigured to allow new interactions between distant sequences. Analysis of 3D chromatin organization using Hi-C in Drosophila Kc167 cells. Cells were grown at 25 C and heat shocked for 20 min at 36.5 C. Cells were also treated with flavopiridol or triptolide to inhibit transcription elongation or initiation, respectively. Cells were depeleted of Cap-H2 or Rad21 using RNAi. Finally, cells depleted of RAd21 were subjected to heat shock at 36.5 C for 20 min.
2015-02-24 | E-GEOD-63515 | biostudies-arrayexpress