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dc.contributor.advisorXie, Xiaoliang Sunney
dc.contributor.authorCai, Wenting
dc.date.accessioned2019-12-11T10:05:40Z
dash.embargo.terms2021-11-01
dc.date.created2019-11
dc.date.issued2019-08-15
dc.date.submitted2019
dc.identifier.citationCai, Wenting. 2019. Deciphering Transcriptome: Transcription Factors as Master Mind Behind Gene Expression. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:42013124*
dc.description.abstractTranscription Factors (TFs) are key players in orchestrating diversified transcriptomes across cell types. Known to function in co-operative pairs, TFs are dynamic and hard to be experimentally captured in motion. With an innovated scRNA-Seq technique, MALBAC-DT, the steady-state measurements were dissected deeper into the dynamic fluctuations. Provided with precise and accurate expression correlations, co-activated gene pairs were revealed to be expressed in the same cell at the same time, in contrast to the traditional terminology 'co-expression', which refers to the similar expression patterns across different cell populations. Further, in combination with motif analysis on open chromatin, we inferred the co-localized and co-activated combinatorial TF pairs (TF3C), which shed light onto the co-operative regulation of TFs on the target genes. Differential across cell types yet highly preserved within co-regulated gene clusters, TF3C led us to propose a transcription regulation scheme: gene looping of the target gene's promoter, enhancer, and TTS, assisted by the shared TF3Cs. Finally, we present a TF combinatorial regulation map that is unique to each cell-type, capturing the essence of the dynamic fluctuations otherwise convoluted in each cell population.
dc.description.sponsorshipChemistry and Chemical Biology
dc.format.mimetypeapplication/pdf
dc.language.isoen
dash.licenseLAA
dc.subjectTranscription Factors
dc.subjectTF3C
dc.subjectTF Co-localization
dc.subjectTF Co-activation
dc.subjectCombinatorial TF action
dc.titleDeciphering Transcriptome: Transcription Factors as Master Mind Behind Gene Expression
dc.typeThesis or Dissertation
dash.depositing.authorCai, Wenting
dash.embargo.until2021-11-01
dc.date.available2019-12-11T10:05:40Z
thesis.degree.date2019
thesis.degree.grantorGraduate School of Arts & Sciences
thesis.degree.grantorGraduate School of Arts & Sciences
thesis.degree.levelDoctoral
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy
thesis.degree.nameDoctor of Philosophy
dc.contributor.committeeMemberCohen, Adam
dc.contributor.committeeMemberPark, Hongkun
dc.type.materialtext
thesis.degree.departmentChemistry and Chemical Biology
thesis.degree.departmentChemistry and Chemical Biology
dash.identifier.vireo
dash.author.emailtingting4805@gmail.com


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