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Conference Paper: Novel sequence motif regulates pluripotency
Title | Novel sequence motif regulates pluripotency |
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Authors | |
Keywords | Genome structure Variation and function KW048 - embryonic stem cell KW064 - functional motifs KW151 - regulation of transcription KW092 - inheritance patterns KW164 - systems biology |
Issue Date | 2012 |
Publisher | American Society of Human Genetics (ASHG). |
Citation | The 2012 Annual Meeting of the American Society of Human Genetics (ASHG 2012), San Francisco, CA., 6-10 November 2012. How to Cite? |
Abstract | The pluripotency of embryonic stem cells (ESCs), combined with theoretically unlimited self-renewal characteristic, has greatly promoted the development of ESCs applying in regenerative medicine and organ transplantation fields. Deciphering the mechanisms of pluripotency would offer a much deeper understanding of the specific reprogramming process of ESCs. In our study, we tried to understand the networked regulations on the genomic level. Thanks to recently developed next-generation sequencing technologies, genome-wide maps of chromatin state has been established. The patterns of mammalian chromatin can offer insights into the locations and functions of underlying regulatory elements and genes. Here, we tried to recognize the specific regulatory sequence characteristics from the open chromatin signals on ES cells' genome. After obtaining ‘informative’ ESC-specific open chromatin (OC) bins, which were open chromatin sequences with length around 500 bp and expressed significantly higher in ESCs than other tissues, we applied MEME’s ‘discriminative motif discovery’ model to extract ESC-specific OC motifs. Then we filtered motifs that were conserved with each other and significantly more enriched in ESC OC bins compared with non-ESC OC bins. Around 60 sequence motifs were disclosed and we found that there is bias of nucleotide occurrence in some of the identified ESC open chromatin regions. This knowledge spreads us a much clearer image about the short and specific sites, which would introduce TF-DNA interactions in vivo and maintain pluripotent stability, on the human genome. Furthermore, such knowledge may also help us design novel functional elements that could be in response to the inside environmental signals in the pluripotent cells. |
Description | Poster Session: Genome structure, variation and function |
Persistent Identifier | http://hdl.handle.net/10722/189725 |
DC Field | Value | Language |
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dc.contributor.author | Song, Y | en_US |
dc.contributor.author | Bao, S | en_US |
dc.contributor.author | Niu, G | en_US |
dc.contributor.author | Zhao, Y | - |
dc.contributor.author | Zhu, H | - |
dc.date.accessioned | 2013-09-17T14:55:56Z | - |
dc.date.available | 2013-09-17T14:55:56Z | - |
dc.date.issued | 2012 | en_US |
dc.identifier.citation | The 2012 Annual Meeting of the American Society of Human Genetics (ASHG 2012), San Francisco, CA., 6-10 November 2012. | en_US |
dc.identifier.uri | http://hdl.handle.net/10722/189725 | - |
dc.description | Poster Session: Genome structure, variation and function | - |
dc.description.abstract | The pluripotency of embryonic stem cells (ESCs), combined with theoretically unlimited self-renewal characteristic, has greatly promoted the development of ESCs applying in regenerative medicine and organ transplantation fields. Deciphering the mechanisms of pluripotency would offer a much deeper understanding of the specific reprogramming process of ESCs. In our study, we tried to understand the networked regulations on the genomic level. Thanks to recently developed next-generation sequencing technologies, genome-wide maps of chromatin state has been established. The patterns of mammalian chromatin can offer insights into the locations and functions of underlying regulatory elements and genes. Here, we tried to recognize the specific regulatory sequence characteristics from the open chromatin signals on ES cells' genome. After obtaining ‘informative’ ESC-specific open chromatin (OC) bins, which were open chromatin sequences with length around 500 bp and expressed significantly higher in ESCs than other tissues, we applied MEME’s ‘discriminative motif discovery’ model to extract ESC-specific OC motifs. Then we filtered motifs that were conserved with each other and significantly more enriched in ESC OC bins compared with non-ESC OC bins. Around 60 sequence motifs were disclosed and we found that there is bias of nucleotide occurrence in some of the identified ESC open chromatin regions. This knowledge spreads us a much clearer image about the short and specific sites, which would introduce TF-DNA interactions in vivo and maintain pluripotent stability, on the human genome. Furthermore, such knowledge may also help us design novel functional elements that could be in response to the inside environmental signals in the pluripotent cells. | - |
dc.language | eng | en_US |
dc.publisher | American Society of Human Genetics (ASHG). | - |
dc.relation.ispartof | Annual Meeting of the American Society of Human Genetics, ASHG 2012 | en_US |
dc.subject | Genome structure | - |
dc.subject | Variation and function | - |
dc.subject | KW048 - embryonic stem cell | - |
dc.subject | KW064 - functional motifs | - |
dc.subject | KW151 - regulation of transcription | - |
dc.subject | KW092 - inheritance patterns | - |
dc.subject | KW164 - systems biology | - |
dc.title | Novel sequence motif regulates pluripotency | en_US |
dc.type | Conference_Paper | en_US |
dc.identifier.email | Song, Y: songy@hku.hk | en_US |
dc.identifier.email | Zhu, H: zhuhch@hku.hk | - |
dc.identifier.authority | Song, Y=rp00488 | en_US |
dc.description.nature | link_to_OA_fulltext | - |
dc.identifier.hkuros | 222294 | en_US |
dc.publisher.place | United States | - |