Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin
Summary: Bacterial condensin preferentially loads onto single-stranded DNA (ssDNA) in vitro and onto rDNA in vivo to support proper chromosome compaction. Thus, the actively transcribing rDNA would provide the ssDNA region for the loading of bacterial condensin. We attempted to detect the ssDNA regi...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-12-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S258900422201776X |
| _version_ | 1811179740726296576 |
|---|---|
| author | Koichi Yano Hideki Noguchi Hironori Niki |
| author_facet | Koichi Yano Hideki Noguchi Hironori Niki |
| author_sort | Koichi Yano |
| collection | DOAJ |
| description | Summary: Bacterial condensin preferentially loads onto single-stranded DNA (ssDNA) in vitro and onto rDNA in vivo to support proper chromosome compaction. Thus, the actively transcribing rDNA would provide the ssDNA region for the loading of bacterial condensin. We attempted to detect the ssDNA region in the rrnI gene in situ. Non-denaturing sodium bisulfite treatment catalyzed the conversion of cytosines to thymines (CT-conversion) at the melted DNA of a genome. Using next-generation sequencing, we generated an average of 11,000 reads covering each cytosine on the rDNA segment. In principle, the CT-conversion rate is an accurate guide to detect ssDNA segment. We detected multiple ssDNA segments throughout the rDNA. The deletion mutations of the rDNA hindered the ssDNA formation at the 100-500 bp segment downstream of the promoter. These data support the idea that the ssDNA segment plays a crucial role as the condensin-loading site and suggest the mechanism of condensin loading onto rDNA. |
| first_indexed | 2024-04-11T06:38:42Z |
| format | Article |
| id | doaj.art-e3b8b3613dd14968bab4d0f2e1b7686b |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-11T06:38:42Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-e3b8b3613dd14968bab4d0f2e1b7686b2022-12-22T04:39:36ZengElsevieriScience2589-00422022-12-012512105504Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensinKoichi Yano0Hideki Noguchi1Hironori Niki2Microbial Physiology Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, JapanCenter for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan; Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, JapanDepartment of Genetics, SOKENDAI (the Graduate University for Advanced Studies), 1111, Yata, Mishima, Shizuoka 411-8540, Japan; Corresponding authorSummary: Bacterial condensin preferentially loads onto single-stranded DNA (ssDNA) in vitro and onto rDNA in vivo to support proper chromosome compaction. Thus, the actively transcribing rDNA would provide the ssDNA region for the loading of bacterial condensin. We attempted to detect the ssDNA region in the rrnI gene in situ. Non-denaturing sodium bisulfite treatment catalyzed the conversion of cytosines to thymines (CT-conversion) at the melted DNA of a genome. Using next-generation sequencing, we generated an average of 11,000 reads covering each cytosine on the rDNA segment. In principle, the CT-conversion rate is an accurate guide to detect ssDNA segment. We detected multiple ssDNA segments throughout the rDNA. The deletion mutations of the rDNA hindered the ssDNA formation at the 100-500 bp segment downstream of the promoter. These data support the idea that the ssDNA segment plays a crucial role as the condensin-loading site and suggest the mechanism of condensin loading onto rDNA.http://www.sciencedirect.com/science/article/pii/S258900422201776XBiological sciencesmolecular biologymolecular biology experimental approachmicrobiology |
| spellingShingle | Koichi Yano Hideki Noguchi Hironori Niki Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin iScience Biological sciences molecular biology molecular biology experimental approach microbiology |
| title | Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin |
| title_full | Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin |
| title_fullStr | Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin |
| title_full_unstemmed | Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin |
| title_short | Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin |
| title_sort | profiling a single stranded dna region within an rdna segment that affects the loading of bacterial condensin |
| topic | Biological sciences molecular biology molecular biology experimental approach microbiology |
| url | http://www.sciencedirect.com/science/article/pii/S258900422201776X |
| work_keys_str_mv | AT koichiyano profilingasinglestrandeddnaregionwithinanrdnasegmentthataffectstheloadingofbacterialcondensin AT hidekinoguchi profilingasinglestrandeddnaregionwithinanrdnasegmentthataffectstheloadingofbacterialcondensin AT hironoriniki profilingasinglestrandeddnaregionwithinanrdnasegmentthataffectstheloadingofbacterialcondensin |