Jason Tan

Does every enhancer work with every promoter? With @jengreitz and @WJGreenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 biorxiv.org/content/10.648…

I used to think scientists argued about great truths. Now I’m a scientist. My team recently spent 40 minutes arguing about what to name our new algorithm.

Beautiful study - congrats! Excited to see direct experimental evidence for intrinsic promoter responsiveness. I like how the motif-level patterns connect with our promoter responsiveness/selectivity analysis from Puffin.

@BorisLenhard @anshulkundaje Could not agree more on the need to study promoter 'customizations' more! I prev (naively) thought that the core promoter is a "passive" entity. But that clearly obfuscates so much unexpected gene reg. Cool examples in ur study and biorxiv.org/content/10.648…

@anshulkundaje @yxjtan Absolutely. There is a superposition of discrete promoter architectures, physical overlap of multiple architectures (e.g. nature.com/articles/natur… ) and evolutionary promoter-specific customisations, which need to be pried apart, and this paper is a great step in that direction.

Fantastic, meticulous expts. & analysis to answer the mysterious question: how enhancers often affect specific promoters. The answer is probably much simpler than many may have expected. Great work by @yxjtan & team. Also check out the reporter assay artifacts they discovered!

@zhou_jian Fig4 of Dudnyk et al was very inspiring in the early stages of this analysis, and it was affirming when our data showed similar patterns! Would love to connect on future ideas for understanding prom. architecture with seq mutagenesis in silico and with MPRA

Great experience compiling years of collective screening experience to produce what we hope is a comprehensive protocol for others to accessibly scale up experiments! And some fun new data hidden in there :) thanks @JoshTycko for being better and faster at Twitter than me 🎉

This was all made possible by @JudhajeetR, @mayayayas, @bgrdoughty and my advisors who supported me down this rabbit hole. We look forward to your feedback! We’re excited to further explore possible mechanisms of responsiveness and incorporate it into more predictive modeling.🛑

Editing these motifs modulates promoter responsiveness to produce a non-intuitive effect: basal activity increases but maximum output decreases! Edits also redistribute TSSs, implicating recruitment or assembly of the PIC as possible mechanisms to mediate responsiveness.

Finally, how is responsiveness encoded? Most promoters lack classical “core promoter motifs” yet vary in responsiveness. With ProCapNet from @kellycochra and @anshulkundaje, we nominate several sequence motifs in the core promoter associated with differential responsiveness.

Genes with responsive promoters are regulated by more enhancers and sensitive to their perturbation. Genes with non-responsive promoters (many housekeeping genes) are insensitive to and skipped by enhancers.

Incorporating responsiveness into the Activity-by-Contact model improves prediction of native regulation and explains 2 long-observed phenomena: 1) Why are housekeeping genes often insensitive to distal enhancers? 2) How do enhancers skip active genes?

We find that promoters differ dramatically in their intrinsic capacity to be activated by *any* enhancer (>100-fold vs 1.1-fold) -- from highly- to effectively non-activatable! Promoter responsiveness scales the magnitude of activation while enhancer rank-order stays similar.

To cleanly re-assess E-P compatibility, we develop improved assays and apply them across >25,000 E-P pairs, including 7 endogenous loci supported by previous CRISPR tiling experiments.

Surprisingly, confounders in widely used upstream and STARR-seq designs distort measurements of enhancer activity and lead to contradictory conclusions about E-P compatibility!

Enhancer-promoter (E-P) wiring is complex and hard to predict. Decoding the underlying factors is essential for interpreting human genetic variants, modeling gene regulation, and designing gene therapies.

Prior studies used different reporter designs. After some tinkering, we began to suspect two variables were confounding results; so, we compared 6 designs head-to-head. Do the same E-P pairs give different results in different assays?

Does E-P compatibility play a role? We and others have used massively parallel reporter assays (MPRAs) to test thousands of combinations. Yet, findings have ranged widely — from enhancers activating all promoters equally to highly specific activation of select promoters.

Does every enhancer work with every promoter? With @jengreitz and @WJGreenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 biorxiv.org/content/10.648…

1/ 🧵Happy to share our preprint from @WJGreenleaf’s Lab: beCasKAS, our method to directly detect #CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. biorxiv.org/content/10.110…

@yesokyeahsure @ruima for me it was 北京卫视 养生堂 (not by force but by just it being the only tv in the house) and likewise extremely grateful

@ruima my parents forced me to watch 新闻联播 every night before dinner. it was very expensive back in the day by satellite only. i am grateful they did.

How to raise bilingual & bicultural kids (Chinese + English), my journey thus far: I’m raising kids that I hope will grow up feeling like they belong in more than one place. And not just in the “my mom makes me go to Chinese school on weekends” kind of way lol but I mean actually being able to live, think, and connect in two languages and two cultures. I just got back from WAIC (the World Artificial Intelligence Conference in Shanghai), and honestly, being there made everything I’ve been doing feel even more urgent and obvious. Like, yes, this is the right path. There’s really no reason to raise your kid not knowing Chinese if you have any connection to it. If you’re wondering how to even begin with all this (especially if Chinese isn’t your “default” language anymore, my husband and I speak mostly English to each other, but we’re both bilingual), here’s what’s worked for us so far: 1. First of all, you have to start early. Like, baby-is-born early. Not because babies are going to know the difference, but because you need to get used to hearing yourself say things in Chinese out loud, every single day, in every kind of mood, to your kid. And let me tell you, if you’re not used to it, if you and your partner usually speak English (like we do), it can feel super awkward at first. But it works. Now I feel absolutely weird if I don’t speak Chinese to my kiddos. 2. You can’t let Chinese become the “home-only” language. If you only speak Chinese at the dinner table but switch to English at the playground, your kid’s going to internalize that Chinese is something private, maybe a little embarrassing, or just not something that belongs in “real life.” So I make a point of speaking Chinese to my toddler everywhere. The upside (by the way) is that other Chinese parents will hear us and say, “Wow, your kid speaks Chinese so well!” and my kid is starting to understand that it’s a compliment. Some external validation is definitely OK. It tells her this language isn’t just something weird mommy makes her do ... it’s impressive and special!! 3. But it’s not just about “keeping the language.” It’s about using it to do things. I want my kid to see that Chinese isn’t just a set of commands from mom, but a way of exploring the world and expressing thoughts. You’ve got to regularly use Chinese to learn about the world, to communicate with people, and to acquire new knowledge. Otherwise, it just becomes this decorative skill with no real function. 4. You also have to make it fun. Like, joyful and personal. When they’re younger, find entertainment they like in Chinese. For me growing up, it was wuxia martial arts novels. For my husband, it was comic books. But the point is, we both found something in Chinese that felt like ours (not something we were doing just because our parents wanted us to). My 3-year-old is still a bit young for this, but I think around age five is when that kind of independent connection starts to click. Eventually, of course, entertainment won’t be enough. They’ll need to learn how to learn in Chinese in an academic or professional context, and that’s when parents really need to step up and either create the right opportunities or go find the right programs.** 5. And you need to inoculate your kid against bullying and weird comments. Inevitably there will be people (Chinese, American, others) who make fun of your kid for knowing another language, or for not knowing enough of it, or not knowing the “right” stuff. (Most people in China are actually super kind about this, but I’ve definitely met some mean new immigrants here in the U.S. who make fun of me for not knowing their hometown or some random celebrity. Like, “oh lookie here, someone who clearly didn’t grow up in China.” FU lol.) It sucks, but it happens. I just don’t want that to be the reason my kid stops trying. At the end of the day, I’m not trying to raise a perfect native speaker. Let’s be honest, language skills alone are going to get commoditized fast. AI can already translate, transcribe, and do a lot of what we used to think made someone “bilingual.” What I’m trying to do is raise someone who’s comfortable living between cultures. Someone who can connect, explain, understand nuance, and read a room, whether that room is in Shanghai or San Francisco. What’s going to matter is whether your kid can build real trust and real relationships. PS: I’ll keep sharing anything I find helpful, and I’d love to hear your ideas too. I’ll probably start a group chat at some point when I have a bit more time! **If you're building or know of such programs, do let's chat, a few friends and I are looking into creating some for our own kids ~~