Regulation of chromatin transitions in the 3D architecture of the nucleus

The thesis explores the dynamic features and functions of chromatin crosstalk in the 3D nucleus space, with a focus on the regulation of chromatin transitions. In Paper I we employed the circular chromosome conformation capture assay (4C) and Chromatin in situ Proximity (ChrISP) technique to uncover an inter-chromosomal chromatin fiber interactome comprising both transcriptionally active circadian genes and repressed lamina-associated domains (LADs). Moreover, we documented that this interactome was under the control of the circadian clock. Synchronization of circadian transcriptional oscillations by external time cues thus involved the rhythmic mobility of clock-controlled genes between the transcriptionally permissive nuclear interior and the repressive environment of the lamina. The transient interactions between LADs and circadian genes were regulated by rhythmic complex-formation between the 3D genome organizers PARP1 and CTCF, which not only served as molecular ties of the chromatin fiber network, but also regulated chromatin mobility to and from the lamina and, as a consequence, circadian gene expression.

In Paper II, we described a novel principle regulating MYC expression in colon cancer cells. Using an innovated method, Nodewalk, and ChrISP, we thus found that the oncogenic colorectal super-enhancer (OSE) regulated MYC expression at the post-transcriptional level by facilitating "gene-gating". OSE/MYC complexes were dynamically tethered to the nuclear pores specifically in cancer cells by interactions between ELYS/AHCTF1 that connects chromatin to the NUP107 nuclear pore subcomplex and the ß-catenin-TCF4 complex. Tethering to the nuclear pores facilitated the nuclear export of MYC transcripts into the cytoplasm where the stability of MYC mRNAs is several-fold higher than in the nucleus, resulting in a several-fold increase of cellular MYC mRNA levels in human colon cancer cells. WNT signalling thus regulates pathological MYC mRNA export post-transcriptionally through ß-catenin-TCF4-ELYS complex formation.

In summary, this thesis describes new principles of gene regulation in the 3D nuclear architecture, including circadian transcriptional regulation and OSE-facilitated gene gating. They open up new avenues for our understanding of the function and dynamics of the 3D nuclear architecture and genome organization, and provide new directions for cancer treatment.

List of scientific papers

I. PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription. Zhao H*, Sifakis EG*, Sumida N*, Millán-Ariño L*, Scholz BA, Svensson JP, Chen X, Ronnegren AL, Mallet de Lima CD, Varnoosfaderani FS, Shi C, Loseva O, Yammine S, Israelsson M, Rathje LS, Németi B, Fredlund E, Helleday T, Imreh MP, Göndör A. Mol Cell. 2015. 59(6): p. 984-97. *These authors contributed equally.
https://doi.org/10.1016/j.molcel.2015.07.019

II. WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. Barbara A. Scholz#, Noriyuki Sumida#, Carolina Diettrich Mallet de Lima, Ilyas Chachoua, Mirco Martino, Ilias Tzelepis, Andrej Nikoshkov, Honglei Zhao, Rashid Mehmood, Emmanouil G. Sifakis, Deeksha Bhartiya, Anita Göndör* and Rolf Ohlsson*. #,*These authors contributed equally. [Accepted]
https://doi.org/10.1038/s41588-019-0535-3