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In sum turnover of telomere DNA is linked to rapid evolution of telomerase. Not sure whats driving the coevolution but we are investigating this. Whats cool is lewisii telomerase can convert a chr end to look like its own but it hasn't spread across species. Maybe fitness cost? Hopefully more soon!

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Results we see F1 hybrid chromosome ends have become M. lewisii like telomeres. Suggesting M. lewsii telomerase has converted M. verbenacues chromosome ends into M. lewisii telomeres. Possible dominance effects?

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Finally we asked was what happens to the telomere if you cross M. lewisii with sequence hterogeneous telomere to sister species that has only one type telomere repeat. Two possible outcomes and results will tell us the function of the telomerase. So we created F1 hybrid and nanopore sequenced it.

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We also conducted interspecies transcriptomics to show that this increased activity is not due to a change in the gene expression landscape of telomere regulating genes.

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What happens when you have two copies of TR? Well you have more template so more telomerase activity? We answered using TRAP assay but gave a twist by combing NGS with TRAP. We found M. lewisii telomerase has higher activity compared to its sister species without duplicated TR.

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We then conducted domain swap and site specific substitution to find the causal amino acid and located near a KRxR motif of TERT that was recently found to be important for TR binding.

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We tested the molecular interaction between TERT and TR using yeast three hybrid. Results show TERT from M. lewisii (which has duplicate TR) is able to bind both duplicate TRs. But in sister species M. verbenaceus (which only has one TR) its TERT is not able to bind the duplicated TR paralog.

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We first focused on the evolution of TERT the main catalytic component of the telomerase and directly interacts with the telomerase RNA (TR). We find TERT is rapidly evolving in lineages where the TR duplication had happened. Suggesting interesting TERT-TR coevolution might be happening.

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The duplicates are fairly divergent in sequence (12% diff for a ~200bp RNA molecule). And somehow telomerase interacts with both during telomere maintenance. How does it do it? And did it evolve something different as it use both? These are questions we ask in this study.

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Most organism telomere DNA consist of single repeat unit (in mammals TTAGGG) repeat thousands of times. But Mimulus lewisii has a special telomere thats a mix of TTTCGGG and TTCGGG repeat. We discovered this occurs cuz of duplication of telomerase RNA gene that acts as the scaffold of the telomerase

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Rapid evolution and functional divergence of the monkeyflower Mimulus lewisii telomerase

Excited to share a study led by my postdoc Naseem Samo. If you evolve an "unusual" telomere DNA does your telomerase also coevolve to maintain interaction with that strange telomere? Answer we find is YES! www.biorxiv.org/content/10.6...

biorxiv.org

Telomeres are nucleoprotein structures that protect chromosome ends and are maintained by the Telomerase Reverse Transcriptase (TERT) protein that uses a noncoding Telomerase RNA (TR) as a template. I...

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Jae Young Choi @jychoi.bsky.social · 27/05/2026

Is plant genome research program disappearing? Multiple people have told me through grapevine or rumor PGRP will be sunset very soon.

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Jae Young Choi @jychoi.bsky.social · 09/05/2026

Doing a meta study right now looking for long read data from over 3000 published studies and about 500 of them dont have the actual long read data available. Im manually doing this so theres some error but this is kind of high ish number to me.

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Jae Young Choi @jychoi.bsky.social · 30/04/2026

I'm looking to hire a postdoc. Please share if you can!

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Jae Young Choi @jychoi.bsky.social · 17/11/2025

Huh I remember seeing a similar thread at twitter eons ago. Is nature healing?

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Jae Young Choi @jychoi.bsky.social · 22/09/2025

Details of our study can be found in my previous threads from our biorxiv preprint. bsky.app/profile/jych...

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Jae Young Choi @jychoi.bsky.social · 22/09/2025

Excited to share a new method developed from my group thats published at Genome Biology. This was an amazing effort by my grad student Linh @linhngk.bsky.social. We developed Topsicle, a method that analyzes long read data for telomere analysis and length measuring. doi.org/10.1186/s130...

doi.org

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data - Genome Biology

Telomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many...

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Jae Young Choi @jychoi.bsky.social · 30/07/2025

Toxin antidote system found in speciation research is good examples of this.

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Reposted by Jae Young Choi

Li Zhao @lizhao.bsky.social · 15/07/2025

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

rdcu.be

Gene regulatory networks and essential transcription factors for de novo-originated genes

Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

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GitHub - jaeyoungchoilab/Topsicle: Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read.

Topsicle can work on either Nanopore or Pacbio data. And you don't need to have a reference genome. Just get your FASTQ and analyze with Topsicle! Our package can be found on github. If you're interested in the telomere length of your organism please try! github.com/jaeyoungchoi...

github.com

Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read. - jaeyoungchoilab/Topsicle

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We also used our method on 8 human cancer cell lines and compared it to Telogator which is a method developed mostly for mammalian telomeres. And results shows that our method is well correlated with Telogator.

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When we compare Topsicle estimates with gold standard direct estimates from Southern blots its fairly well correlated suggesting our method works pretty well. We tried our method in A. thaliana, maize, and monkeyflower and they all worked well.

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Topsicle performs fairly well under simulated reads of varying sizes and error rates. Interestingly under simulated coverages we saw that the genome coverage didnt have too much of an effect on telomere length estimates

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This is done by implementing a change point method. These are commonly used in electrical engineering to model signal intensity data and it also works well for our purpose. We implemented our approach into a program called Topsicle.

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Because long reads can be noisy looking exact matching telomere repeat sequence (e.g. AAACCCT) can miss repeat matches. Instead we search for k-mers of different sizes to fill in the gaps. From here telomere length is measured by finding the point where theres a sudden drop in telo density

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Instead we thought what about a genomics approach? Technically if a long read was sequenced from the telomere we should be able to use that read to estimate the telomere length. And thats what we did! We came up with a way to search for telomeric long reads

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My lab is interested in understanding what drives the genetic variation in telomeres of plants. We are interested in telomere length variation and to study this we need to measure length of the telomere but this protocol is often difficult to implement in a typical lab. Think of Southern blots

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Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

I'm very excited to share a new method my grad student @linhngk.bsky.social and I have developed. Here's Topsicle a new computational method for analyzing long read sequencing data and estimate telomere length. Please see our preprint or this thread for detail! www.biorxiv.org/content/10.1...

biorxiv.org

Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many b...

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Please give it a try if you're interested in measuring the telomere length of the organism you long read sequenced. Hopefully the peer reviewed manuscript of our method will come out shortly!

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And it performs fairly well against various error rates and genome coverage. We tested it against gold standard telomere length measurements made from several A. thaliana ecotypes and found it was highly correlated with Topsicle predictions as well.

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Topsicle searches for long reads from the telomere and then uses those as candidate telomere reads. Then we quantify telomere repeats with k-mer analysis and identify the telomere-subtelomere boundary using change point analysis.

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Traditional way of measuring telomere length is thru Southern blot but its a lost art not many know how to do. Instead we thought what about long read sequencing since long read from telomere could be used to identify the telomere and measure its length. So we developed Topsicle. *image not related*

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Telomere length is a really interesting phenotype where despite having crucial roles in maintaining genome stability its length can vary alot between individuals and even between species. Why is that? Is a major question many like to answer.

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