R-loops function as a balance for somatic reprogramming. The catalytic inactivation of RNaseH1 (RNaseH1^D209N) blocks reprogramming via inducing R-loops accumulation of somatic genes, while Sox2 blocks the activity of Ddx5 at R-loops of pluripotent genes to promote reprogramming. [IMAGE: GIBH]

R-loops are unique cell structures composed of RNA-DNA hybrids and a displaced single-stranded DNA that are commonly found in and around transcribed genes. However, R-loops are also dynamic and widespread entities that play unclear regulatory and epigenetic roles in the genome. A recent study by Chinese scientists at the Guangzhou Institutes of Biomedicine and Health (GIBH) of the Chinese Academy of Sciences has shed light on the activity of R-loops in the reprogramming of somatic cells to induce pluripotent stem cells (iPSCs). Their work reveals that R-loops influence the reprogramming of somatic cells into iPSCs, and that disrupting this activity leads to defects in the reprogramming of somatic cells into iPSCs.

R-loops may act as epigenetic markers by altering transcription factor binding, chromatin modifications, and DNA methylation. Researchers mapped the landscape of R-loops during OSKM (Oct4, Sox2, Klf4, and c-Myc, four transcription factors in the reprogramming cocktail) mediated somatic cell reprogramming and showed a dynamic association between R-loop formation and dissolution and the process of somatic cell reprogramming.

“Our data indicate that R-loops cause sharp changes at both the early and late stages of reprogramming, but they have transient and subtle changes at the intermediate stage, which shows a similar pattern with chromatin opening, DNA methylation, and gene expression during reprogramming,” said Yao Hongjie, author of the study from GIBH.

Yao and his colleagues found that some R-loops formed in advance of gene expression, suggesting R-loops are poising genes ready for transcription. Their research revealed that the transcription factor Sox2 (but not any other Yamanaka factor in the reprogramming cocktail) was intimately involved in forming a complex with R-loops. “It is not only a transcription factor that induces transcription but also an essential regulator that maintains the balance of R-loops, and further promotes reprogramming together with R-loop-resolving factors,” said Yao.

The results of this study were published online in the latest issue of Science Advances on June 10, entitled “R-loops Coordinate with Sox2 in Regulating Reprogramming to Pluripotency”.

For more information, please contact:

Yao Hongjie, Ph.D Principle Investigator

E-mail: yao_hongjie@gibh.ac.cn

CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

Source: Guangzhou Institutes of Biomedicine and Health,

Chinese Academy of Sciences