Multi-omics studies of transcription regulatory mechanisms during human cell fate transition

Lysakovskaia, Kseniia

dc.contributor.advisor	Cramer, Patrick Prof. Dr.
dc.contributor.author	Lysakovskaia, Kseniia
dc.date.accessioned	2024-02-16T15:28:12Z
dc.date.issued	2024-02-16
dc.identifier.uri	http://resolver.sub.uni-goettingen.de/purl?ediss-11858/15121
dc.identifier.uri	http://dx.doi.org/10.53846/goediss-10357
dc.format.extent	139	de
dc.language.iso	eng	de
dc.subject.ddc	570	de
dc.title	Multi-omics studies of transcription regulatory mechanisms during human cell fate transition	de
dc.type	doctoralThesis	de
dc.contributor.referee	Cramer, Patrick Prof. Dr.
dc.date.examination	2023-02-20	de
dc.description.abstracteng	RNA polymerase II (Pol II) transcription is an essential process in living organisms that requires accurate regulation and coordination in order to produce protein-coding and many types of non-coding transcripts. One of the highly regulated transcriptional steps is promoter-proximal Pol II pausing that occurs shortly after initiation of transcription. Paused Pol II can either be released into productive elongation of transcription or terminated prematurely. Promoter-proximal Pol II pausing was demonstrated to tune gene expression in the cell fate transition processes ensuring controlled and rapid transcriptional response. However, the exact mechanisms underlying these processes remain to be further elucidated in a quantitative manner. Here, we investigate promoter-proximal Pol II regulation throughout the cell type switching by employing a reprogrammable human cell transdifferentiation as a model system. In order to assess the kinetics of Pol II transcription, we apply a multi-omics approach combining a measurement of new RNA synthesis by TT-seq and profiling of transcriptionally engaged Pol II by mNET-seq. We additionally introduce the estimation of promoter-proximal Pol II stability at terminal time points of transdifferentiation using a high-resolution ChIP-nexus technique with the time series of initiation inhibition treatment. We show the global changes in the transcription kinetic parameters including productive initiation frequency (pIF) and apparent pause duration (aPD) for the defined gene groups across the time course of transdifferentiation. Strikingly, the pausing-related factors occupancies analyzed by ChIP-seq exhibit the highest correlation with the pIF and partial correlation with the aPD parameters. Our stability measurements from the ChIP-nexus data indicate that Pol II is highly dynamic and relatively short-lived in the pausing region. Importantly, we suggest distinct mechanisms of promoter-proximal Pol II regulation for the upregulated (iMac) and downregulated (pre-B) gene groups based on our Pol II kinetics and stability estimations during the transdifferentiation. The productive transcription of pre-B genes appears to be downregulated through an increase of the prematurely terminating Pol II fraction rather than stable Pol II pausing. Also, the upregulation of the iMac genes is mediated by an increase of the actual transcription initiation rate along with modulating the productive RNA synthesis via prematurely terminating Pol II fraction in the promoter-proximal region. Taken together, our results illuminate the importance of the Pol II premature termination in transcriptional regulation of the cell stage-specific gene groups throughout the cell fate transition process. We note that our findings can be transferred to the biologically relevant systems for the future medical applications and drug development.	de
dc.contributor.coReferee	Dobbelstein, Matthias Prof. Dr.
dc.subject.eng	Gene regulation	de
dc.subject.eng	Transcription	de
dc.subject.eng	Transcription initiation	de
dc.subject.eng	Promoter-proximal Pol II pausing	de
dc.subject.eng	Premature termination	de
dc.subject.eng	Cell type transition	de
dc.subject.eng	Transdifferentiation	de
dc.subject.eng	Precursor B-cell leukemia	de
dc.subject.eng	Macrophage	de
dc.identifier.urn	urn:nbn:de:gbv:7-ediss-15121-4
dc.date.embargoed	2025-02-19
dc.affiliation.institute	Göttinger Graduiertenschule für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB)	de
dc.subject.gokfull	Biologie (PPN619462639)	de
dc.description.embargoed	2025-02-19	de
dc.identifier.ppn	1881080234
dc.identifier.orcid	0000-0002-7829-4243	de
dc.notes.confirmationsent	Confirmation sent 2024-02-16T19:45:01	de

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GGNB - Göttinger Graduiertenzentrum für Neurowissenschaften, Biophysik und molekulare Biowissenschaften [1169]
GGNB - Göttingen Graduate Center for Neurosciences, Biophysics and Molecular Biosciences

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