Nuclear Organization

Interaktionen von RNAs und Proteinen

Sonja Prohaska

Computational EvoDevo groupUniversität Leipzig

SS2019

Interaktionen von RNAs und Proteinen

Nuclear Organization

DNA-DNA Interactions: Nuclear Organization

Interaktionen von RNAs und Proteinen

Nuclear Organization

Nuclear Bodies Associated and Their Function

Interaktionen von RNAs und Proteinen

Nuclear Organization

Organization of Nuclear Bodies by Long Noncoding RNAsarcRNAs: architectural long noncoding RNAs

I nascent arcRNAs serve as scaffold for RNA binding proteinsI results in strong local enrichment of specific factors

Interaktionen von RNAs und Proteinen

Nuclear Organization

Chromosome Terretories

Interaktionen von RNAs und Proteinen

Nuclear Organization

Attachment of Chromatin to Nuclear Envelope

I S/MARs: Scaffold/Membane attachment regions

Interaktionen von RNAs und Proteinen

Nuclear Organization

A Special Terretory: Ihe Inactive X Chromosome

Dosage compensition in placental mammalsWHAT is happening?

I random X-inactivation

I female: X, X → Xa (active), Xi (inactive)I male: X, Y → Xa

Interaktionen von RNAs und Proteinen

Nuclear Organization

X Chromosome Inactivation (XCI)HOW is it happening?

Interaktionen von RNAs und Proteinen

Nuclear Organization

XCI – Counting and Choosing

serveral model try to explainInteraktionen von RNAs und Proteinen

Nuclear Organization

XCI – Main Player(s) Xist (and Tsix)

I lncRNA Xist (X-inactive specific transcript)expressed from inactive X chromosomeis responsible for silencing the X in cis → Xi (inactive)

I lncRNA Tsix (antisense of Xist)expressed from active X chromosomeis responsible for silencing Xist in cis → Xa (active)

Interaktionen von RNAs und Proteinen

Nuclear Organization

The X Inactivation Center (Xic)

I Xist: X-inactivation specific transcript17kb, spliced and polyadenylated transcript

I Tsix: antisense RNA of Xist

I genes (RNA or protein coding) promoting Xist expression

I genes (RNA or protein coding) supressing Xist expression

Interaktionen von RNAs und Proteinen

Nuclear Organization

Proposed mechanisms

I Xist has binding sites for proteins (similar to arcRNAs)

I SPEN binds “repeatA” on Xistinteracts with SMRT-HDAC3 → deacetylationmay recruit PRC2 → H3K27me3 (repressive mark)may recruit PRC1 → H2AK119ub (repressive mark)excludes PolII from Xist-coated chromosome

I RBM15-WTAP interacts with Xistrecruits m6A mashiney that methylates XistYTHDC1 reads m6A enables transcriptional scilencing

I LBR (lamina binding receptor) links Xist-coated chromatin tolamin in the lamina

Interaktionen von RNAs und Proteinen

Nuclear Organization

Xist Spreading and Lamina Localization

Interaktionen von RNAs und Proteinen

Nuclear Organization

TADs at the Xic

Interaktionen von RNAs und Proteinen

Nuclear Organization

Measuring Chromatin Interactions

Chromosome Conformation Capture

I a method to measure chromatin-chromatin interactions

Hi-C Method

Interaktionen von RNAs und Proteinen

Nuclear Organization

Topologically Associated Domains (TADs)Structure of TADs

Interaktionen von RNAs und Proteinen

Nuclear Organization

Topologically Associated Domains (TADs)Functional/Regulatory Relevance

Interaktionen von RNAs und Proteinen

Nuclear Organization

ReferencesI van Bemmel et al.

The bipartite TAD organization of the X-inactivation center ensures opposingdevelopmental regulation of Tsix and XistNature Genetics 51, 1024–1034 (2019)

I Cerase et al.Phase separation drives X-chromosome inactivation: a hypothesisNature Structural and Molecular Biology 26, 331–334 (2019)

I Chen et al.Xist recruits the X chromosome to the nuclear lamina to enablechromosome-wide silencingScience 6311(354), 468–472 (2016)

I Wang et al.Comment on “Xist recruits the X chromosome to the nuclear lamina to enablechromosome-wide silencing”Science 6343(356), eaal4976 (2017)

I Pollex et al.Nuclear positioning and pairing of X-chromosome inactivation centers are notprimary determinants during initiation of random X-inactivationNature genetics 51.2 (2019): 285.

I da Rocha et al.Novel players in X inactivation: insights into Xist-mediated gene silencing andchromosome conformationNature Structural and Molecular Biology volume 24, pages 197–204 (2017)

Interaktionen von RNAs und Proteinen

Nuclear Organization