Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme
Besides the common right-handed B- or A- structures, the alternate Z-conformation, which is left-handed, can be formed in both DNA and RNA molecules. It is in a higher energy state and well-studied mostly in vitro. However, formation of Z-conformation in living organisms and its biological significa...
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Thesis |
| Language: | English |
| Published: |
2012
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/47999 |
| _version_ | 1826116544400195584 |
|---|---|
| author | Feng, Shu |
| author2 | Peter Droge |
| author_facet | Peter Droge Feng, Shu |
| author_sort | Feng, Shu |
| collection | NTU |
| description | Besides the common right-handed B- or A- structures, the alternate Z-conformation, which is left-handed, can be formed in both DNA and RNA molecules. It is in a higher energy state and well-studied mostly in vitro. However, formation of Z-conformation in living organisms and its biological significance remains largely elusive. Here, a protein probe that could specifically bind to Z-conformation was used to map the Z-DNA distribution in the human genome. The probe is derived from the Z-DNA binding domain of the human double-stranded RNA adenosine deaminase 1 (ADAR1), named ZαADAR1. During our experiments, evidence suggested that the primary target of ZαADAR1 in vivo is RNA rather than DNA. Further studies revealed that ZαADAR1 could bind to ribosomes and inhibit translation in both E. coli and mammalian systems in a Z-conformation dependent manner. Potential ZαADAR1 binding sites on ribosomes were identified. Several binding sites were conserved between E. coli and human ribosomes, revealing that formation of Z-like RNA conformations might be a conserved property of the dynamic ribosome structure during translation. The implications for understanding biological functions of the full length ADAR1 were discussed. In vitro Chromatin Affinity Precipitation (ChAP) experiments using ZαADAR1 were also performed to map the Z-DNA distribution in the human genome, using human embryonic stem (huES) cells as the cell source. The data revealed that the ZαADAR1 binding sites were found to be enriched in centromere regions and G-bands, suggesting that formation of Z-DNA might contribute to specific chromatin structures. The enrichment of Z-DNA in transcription start sites then suggested that formation of Z-DNA is associated with transcription processes. Enrichment of SNPs in ZαADAR1 binding sites, especially in the centromere region, further suggested that formation of Z-DNA might be mechanistically linked to genetic instability and thus contributes to the evolution of centromere regions. Surprisingly, the ZαADAR1 binding sites did not coincide with Z-DNA forming sequences predicted based on in silico analyzes. This indicates that formation of Z-DNA in living cells is not purely depended on DNA sequence contexts, but is strongly affected by on the local physical environment. |
| first_indexed | 2024-10-01T04:13:27Z |
| format | Thesis |
| id | ntu-10356/47999 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:13:27Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | ntu-10356/479992023-02-28T18:37:01Z Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme Feng, Shu Peter Droge School of Biological Sciences DRNTU::Science::Biological sciences Besides the common right-handed B- or A- structures, the alternate Z-conformation, which is left-handed, can be formed in both DNA and RNA molecules. It is in a higher energy state and well-studied mostly in vitro. However, formation of Z-conformation in living organisms and its biological significance remains largely elusive. Here, a protein probe that could specifically bind to Z-conformation was used to map the Z-DNA distribution in the human genome. The probe is derived from the Z-DNA binding domain of the human double-stranded RNA adenosine deaminase 1 (ADAR1), named ZαADAR1. During our experiments, evidence suggested that the primary target of ZαADAR1 in vivo is RNA rather than DNA. Further studies revealed that ZαADAR1 could bind to ribosomes and inhibit translation in both E. coli and mammalian systems in a Z-conformation dependent manner. Potential ZαADAR1 binding sites on ribosomes were identified. Several binding sites were conserved between E. coli and human ribosomes, revealing that formation of Z-like RNA conformations might be a conserved property of the dynamic ribosome structure during translation. The implications for understanding biological functions of the full length ADAR1 were discussed. In vitro Chromatin Affinity Precipitation (ChAP) experiments using ZαADAR1 were also performed to map the Z-DNA distribution in the human genome, using human embryonic stem (huES) cells as the cell source. The data revealed that the ZαADAR1 binding sites were found to be enriched in centromere regions and G-bands, suggesting that formation of Z-DNA might contribute to specific chromatin structures. The enrichment of Z-DNA in transcription start sites then suggested that formation of Z-DNA is associated with transcription processes. Enrichment of SNPs in ZαADAR1 binding sites, especially in the centromere region, further suggested that formation of Z-DNA might be mechanistically linked to genetic instability and thus contributes to the evolution of centromere regions. Surprisingly, the ZαADAR1 binding sites did not coincide with Z-DNA forming sequences predicted based on in silico analyzes. This indicates that formation of Z-DNA in living cells is not purely depended on DNA sequence contexts, but is strongly affected by on the local physical environment. DOCTOR OF PHILOSOPHY (SBS) 2012-02-02T07:10:33Z 2012-02-02T07:10:33Z 2010 2010 Thesis Feng, S. (2010). Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/47999 10.32657/10356/47999 en 171 p. application/pdf |
| spellingShingle | DRNTU::Science::Biological sciences Feng, Shu Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme |
| title | Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme |
| title_full | Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme |
| title_fullStr | Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme |
| title_full_unstemmed | Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme |
| title_short | Natural-occurring Z-conformations in nucleic acids: probed by the Zα domain of human RNA editing enzyme |
| title_sort | natural occurring z conformations in nucleic acids probed by the zα domain of human rna editing enzyme |
| topic | DRNTU::Science::Biological sciences |
| url | https://hdl.handle.net/10356/47999 |
| work_keys_str_mv | AT fengshu naturaloccurringzconformationsinnucleicacidsprobedbythezadomainofhumanrnaeditingenzyme |