Understanding the role of L1 antisense RNA on chromosome replication timing

Feb. 5, 2018

Story and photo by Nadir Balba

The Paper of the Month for January 2018 is "L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing" published in the Journal of Cell Biology. This project was led by a team from OHSU's Department of Biochemistry and Molecular Biology: Emily Platt, Ph.D., Leslie Smith, and Mathew Thayer, Ph.D., professor biochemistry and molecular biology, OHSU School of Medicine.

The process of DNA replication is complicated and involves multiple coordinated steps. Dr. Thayer's lab has a long-standing interest in understanding the mechanisms driving normal replication timing of chromosomes in human cells. This type of basic science research will have significant implications for improving our fundamental understanding of human genetics. The goal of the present study was to investigate how L1 retrotransposon anti-sense RNA, within two long non-coding RNA genes, helped maintain normal replication timing in human chromosomes.

Previous work from the Thayer lab showed that when certain regions in the human genome were disrupted, it significantly delayed the replication of the individual chromosomes. Their genetic analyses linked this activity to particular genomic regions, termed ASARs, which contained long non-coding RNAs expressed from a single chromosome and are replicated asynchronously. This was a bit surprising considering that non-coding RNA is never directly translated into proteins like other types of RNA. The team also discovered that these ASAR regions were enriched in Long Interspersed Nuclear Element 1 (L1) sequences which are eventually transcribed into RNA and physically "coat" the chromosomes. There were no previous studies that suggested a role for L1 RNA in any aspect of normal replication timing of human chromosomes. For the present study, the authors investigated ASAR6 and ASAR15 genes on human chromosomes 6 and 15, as they were identified as specific targets due to their effects on the timing of individual chromosomal replication.

The team found the timing of chromosome replication was directly related to individual L1 retrotransposons within the ASAR transcripts. The authors then used targeted CRISPR/Cas9 gene editing to delete a critical L1in human cell culture, which resulted in replication delay of human chromosome 6. The team next ectopically inserted this L1 sequence into a mouse chromosome, which in turn also caused replication delay. When the team knocked down, or decreased the expression of ASAR6 RNA, it restored normal replication timing to these mouse chromosomes. All this together demonstrates how L1 sequences within ASAR6 RNA are vital in controlling the timing of DNA replication.

"The team's very focused approach to the timing of chromosome replication is really intriguing," said Mary Heinricher, Ph.D., associate dean for basic research, OHSU School of Medicine, who explained she was fascinated by the study's precise characterization of the process.

These results have provided greater insight into the process of human DNA replicates. For one, it provides evidence that proper chromosome replication timing relies on the activity of transcripts generated from the non-coding regions, which comprise about 98 percent of the human genome. These regions were once ignored and sometimes referred to as "junk" DNA because it did not have any clear purpose. However, this work illustrates a growing body of evidence indicating the importance of non-coding DNA in controlling the replication of the human genome.

The authors also hope that the work will provide valuable insights into cancer biology. According to Dr. Platt, "chromosomes with disruptions in ASARs exhibit genomic instability, and this finding could indicate a mechanism of carcinogenesis." Future studies to better elucidate this instability may provide a more complete understanding of how cancer cells are formed and replicate in the human body.

The team will continue this line of research while searching for more target ASARs in different locations using genome-wide analyses. "Our preliminary results indicate that there is a genome-wide network of ASARs that function to ensure normal replication timing," said Dr. Platt. The team is also investigating how ASARs work together and what potential proteins interact with these RNAs.

Resources

• Read the paper

Citation

Platt, Emily J., Leslie Smith, and Mathew J. Thayer. "L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing." J Cell Biology (2017): jcb-201707082.

More Published Papers

• Previous School of Medicine Papers of the Month
• Recent OHSU published papers

Pictured, from left: Dr. Emily Platt, Leslie Smith and Dr. Matt Thayer