Universität zu Köln

Pachano, Tomas ORCID: 0000-0003-2823-7715 (2022). Orphan CpG islands dictate the compatibility between poised enhancers and their target genes. PhD thesis, Universität zu Köln.

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Abstract

The establishment of cell type specific gene expression programs during vertebrate development is largely dependent on distal cis-regulatory sequences known as enhancers. An important question in enhancer biology is to understand how activating regulatory cues from enhancers are communicated specifically to their correct target gene and not others. It is widely assume that insulator elements can regulate enhancer specificity by restricting their search space to regions located within their same topological associated domain (TAD). However, recent evidences have identified examples in which genes do not respond to enhancers placed into their same TAD. Therefore, we hypothesize that genetic and/or biochemical compatibilities must further regulate how promoters respond to enhancers. Here, we uncover a novel role for CpG islands (CGIs) in dictating the compatibility between genes and distal enhancers. By using a CRISPR/Cas9 knockin strategy, we inserted poised enhancers (PEs) within topological associated domains (TADs) containing genes with different promoter types. Analysis of the resulting cell lines revealed that developmental genes with CGI-rich promoters are particularly responsive to PEs, and that such responsiveness depends on the presence of an orphan CGI in proximity to the PE sequence. We report here that CGIs can amplify the regulatory activity of PEs by conferring them a permissive topological configuration that increases the responsiveness of target genes with CGI-associated promoters. Our results provide major insights into fundamental and unresolved questions of cisregulatory control during cell differentiation including: (i) the genetic factors controlling the topological features of enhancers; (ii) the regulatory rules dictating the compatibility and responsiveness between genes and enhancers. Moreover, our data will help to understand the pathomechanisms of human congenital diseases involving structural variants.

Item Type:	Thesis (PhD thesis)
Translated abstract:	Abstract Language eingebracht werden. Daher stellen wir die Hypothese auf, dass genetische und/oder biochemische Kompatibilit ten das Ansprechen des Promotors auf Enhancer weiter regulieren müssen. Hier entdecken wir eine neue Rolle von CpGInseln (CGIs) bei der Bestimmung der Kompatibilit t zwischen Genen und distalen Enhancern. Mit einer CRISPR/Cas9-Knock-in-Strategie fügten wir balancierte Enhancer (PEs) in topologisch assoziierte Dom nen (TADs) ein, die Gene mit unterschiedlichen Promotortypen enthalten. Die Analyse der resultierenden Zelllinien zeigte, dass Entwicklungsgene mit CGIreichen Promotoren besonders auf PEs ansprechen und dass eine solche Reaktionsf higkeit von der Anwesenheit eines verwaisten CGI in der N he der PE-Sequenz abh ngt. Wir berichten hier, dass CGIs die regulatorische Aktivit t von PEs verst rken k nnen, indem sie ihnen eine permissive topologische Konfiguration verleihen, die die Reaktionsf higkeit von Zielgenen mit CGI-assoziierten Promotoren erh ht. Unsere Ergebnisse liefern wichtige Einblicke in grundlegende und ungel ste Fragen der cis-regulatorischen Kontrolle w hrend der Zelldifferenzierung, einschlie lich: (i) die Bedeutung von Enhancer-Promotor-Pre-Looping, um einheitliche und pr zise Genexpressionsprofile w hrend Entwicklungsüberg ngen zu etablieren; (ii) die genetischen Faktoren, die die topologischen Merkmale von Enhancern kontrollieren; (iii) die regulatorischen Regeln, die die Kompatibilit t und Reaktionsf higkeit zwischen Genen und Enhancern diktieren. Darüber hinaus werden unsere Daten dazu beitragen, die 12 ZUSAMMENFASSUNG Pathomechanismen angeborener Erkrankungen des Menschen mit strukturellen Varianten zu verstehen. German
Creators:	Creators Email ORCID ORCID Put Code Pachano, Tomas pachano.tomas@gmail.com orcid.org/0000-0003-2823-7715 UNSPECIFIED
Contributors:	Contribution Name Email Author Pachano, Tomas pachano.tomas@gmail.com
URN:	urn:nbn:de:hbz:38-554117
Date:	24 February 2022
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Zentrum für Molekulare Medizin
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Enhancer English Gene regulation English Development English
Date of oral exam:	17 January 2022
Referee:	Name Academic Title Uhlirova, Mirka Prof. Dr. Tessarz, Peter Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/55411