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Conference Paper: Novel sequence motif regulates pluripotency

TitleNovel sequence motif regulates pluripotency
Authors
KeywordsGenome structure
Variation and function
KW048 - embryonic stem cell
KW064 - functional motifs
KW151 - regulation of transcription
KW092 - inheritance patterns
KW164 - systems biology
Issue Date2012
PublisherAmerican 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?
AbstractThe 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.
DescriptionPoster Session: Genome structure, variation and function
Persistent Identifierhttp://hdl.handle.net/10722/189725

 

DC FieldValueLanguage
dc.contributor.authorSong, Yen_US
dc.contributor.authorBao, Sen_US
dc.contributor.authorNiu, Gen_US
dc.contributor.authorZhao, Y-
dc.contributor.authorZhu, H-
dc.date.accessioned2013-09-17T14:55:56Z-
dc.date.available2013-09-17T14:55:56Z-
dc.date.issued2012en_US
dc.identifier.citationThe 2012 Annual Meeting of the American Society of Human Genetics (ASHG 2012), San Francisco, CA., 6-10 November 2012.en_US
dc.identifier.urihttp://hdl.handle.net/10722/189725-
dc.descriptionPoster Session: Genome structure, variation and function-
dc.description.abstractThe 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.languageengen_US
dc.publisherAmerican Society of Human Genetics (ASHG).-
dc.relation.ispartofAnnual Meeting of the American Society of Human Genetics, ASHG 2012en_US
dc.subjectGenome structure-
dc.subjectVariation and function-
dc.subjectKW048 - embryonic stem cell-
dc.subjectKW064 - functional motifs-
dc.subjectKW151 - regulation of transcription-
dc.subjectKW092 - inheritance patterns-
dc.subjectKW164 - systems biology-
dc.titleNovel sequence motif regulates pluripotencyen_US
dc.typeConference_Paperen_US
dc.identifier.emailSong, Y: songy@hku.hken_US
dc.identifier.emailZhu, H: zhuhch@hku.hk-
dc.identifier.authoritySong, Y=rp00488en_US
dc.description.naturelink_to_OA_fulltext-
dc.identifier.hkuros222294en_US
dc.publisher.placeUnited States-

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