Elphege Nora Lab at UCSF
@elphegenoralab.bsky.social
Our laboratory seeks to understand how chromosome structure relates to genome functions
That was >40 years ago!
So many of John's papers still read incredibly prescient to this day.
Fun fact, John is still around and scheduled to give his faculty talk to my department this Wednesday.
So many of John's papers still read incredibly prescient to this day.
Fun fact, John is still around and scheduled to give his faculty talk to my department this Wednesday.
September 21, 2025 at 10:59 PM
That was >40 years ago!
So many of John's papers still read incredibly prescient to this day.
Fun fact, John is still around and scheduled to give his faculty talk to my department this Wednesday.
So many of John's papers still read incredibly prescient to this day.
Fun fact, John is still around and scheduled to give his faculty talk to my department this Wednesday.
Not sure that's what you want but group of John Sedat was mapping polytene chromosome folding in the mid-80s.
www.nature.com/articles/308...
rupress.org/jcb/article/...
www.nature.com/articles/308...
rupress.org/jcb/article/...
September 21, 2025 at 10:59 PM
Not sure that's what you want but group of John Sedat was mapping polytene chromosome folding in the mid-80s.
www.nature.com/articles/308...
rupress.org/jcb/article/...
www.nature.com/articles/308...
rupress.org/jcb/article/...
29 / and this one illustrates the dramatic differences in loop dynamics after depleting
NIPBL (slow rate, normal lifetime)
WAPL (very high lifetime)
PDS5 (high lifetime, high rate)
NIPBL (slow rate, normal lifetime)
WAPL (very high lifetime)
PDS5 (high lifetime, high rate)
August 19, 2025 at 9:24 PM
29 / and this one illustrates the dramatic differences in loop dynamics after depleting
NIPBL (slow rate, normal lifetime)
WAPL (very high lifetime)
PDS5 (high lifetime, high rate)
NIPBL (slow rate, normal lifetime)
WAPL (very high lifetime)
PDS5 (high lifetime, high rate)
28/ and some movies!
This one illustrates the difference in loop dynamics between high lifetime v.s. high rate, at equal processivity.
LEFT - High lifetime: loops take time to grow but remain for very long
RIGHT - High rate: loops grow super fast but eventually dissociate to reform
This one illustrates the difference in loop dynamics between high lifetime v.s. high rate, at equal processivity.
LEFT - High lifetime: loops take time to grow but remain for very long
RIGHT - High rate: loops grow super fast but eventually dissociate to reform
August 19, 2025 at 9:21 PM
28/ and some movies!
This one illustrates the difference in loop dynamics between high lifetime v.s. high rate, at equal processivity.
LEFT - High lifetime: loops take time to grow but remain for very long
RIGHT - High rate: loops grow super fast but eventually dissociate to reform
This one illustrates the difference in loop dynamics between high lifetime v.s. high rate, at equal processivity.
LEFT - High lifetime: loops take time to grow but remain for very long
RIGHT - High rate: loops grow super fast but eventually dissociate to reform
25/ There is more in the manuscript 📖 - including
▶️ calibration of models to experiments
▶️ how to titrate & measure chromatin bound cohesin
▶️ how extrusion rate affect compartmentalization & transcription
▶️ speculations about cell types that change expression levels of cohesin co-factors 💭
▶️ calibration of models to experiments
▶️ how to titrate & measure chromatin bound cohesin
▶️ how extrusion rate affect compartmentalization & transcription
▶️ speculations about cell types that change expression levels of cohesin co-factors 💭
August 16, 2025 at 3:03 AM
25/ There is more in the manuscript 📖 - including
▶️ calibration of models to experiments
▶️ how to titrate & measure chromatin bound cohesin
▶️ how extrusion rate affect compartmentalization & transcription
▶️ speculations about cell types that change expression levels of cohesin co-factors 💭
▶️ calibration of models to experiments
▶️ how to titrate & measure chromatin bound cohesin
▶️ how extrusion rate affect compartmentalization & transcription
▶️ speculations about cell types that change expression levels of cohesin co-factors 💭
24/ On the other hand, quantitative titrations showed that extrusion rates scale with NIPBL dosage 📐
This is a whole new way to think about the molecular origin of NIPBL haploinsufficiency in Cornelia de Lange patients, who suffer from partial reduction of NIPBL levels.
This is a whole new way to think about the molecular origin of NIPBL haploinsufficiency in Cornelia de Lange patients, who suffer from partial reduction of NIPBL levels.
August 16, 2025 at 3:03 AM
24/ On the other hand, quantitative titrations showed that extrusion rates scale with NIPBL dosage 📐
This is a whole new way to think about the molecular origin of NIPBL haploinsufficiency in Cornelia de Lange patients, who suffer from partial reduction of NIPBL levels.
This is a whole new way to think about the molecular origin of NIPBL haploinsufficiency in Cornelia de Lange patients, who suffer from partial reduction of NIPBL levels.
23/ The impact of extrusion rate on genome folding patterns and is VERY sensitive to NIPBL dosage: over-expressing NIPBL in normal cells is sufficient to increase extrusion rates so much chromosome compact into vermicelli
August 16, 2025 at 3:03 AM
23/ The impact of extrusion rate on genome folding patterns and is VERY sensitive to NIPBL dosage: over-expressing NIPBL in normal cells is sufficient to increase extrusion rates so much chromosome compact into vermicelli
22/ Fear not, this is simply because the rate changes offset each other, but lifetime remains high, just like in the WAPL mutant 🤙
In other words, the net rate of extrusion is set by the respective balance of NIPBL:PDS5 in the cell ⚖️
In other words, the net rate of extrusion is set by the respective balance of NIPBL:PDS5 in the cell ⚖️
August 16, 2025 at 3:03 AM
22/ Fear not, this is simply because the rate changes offset each other, but lifetime remains high, just like in the WAPL mutant 🤙
In other words, the net rate of extrusion is set by the respective balance of NIPBL:PDS5 in the cell ⚖️
In other words, the net rate of extrusion is set by the respective balance of NIPBL:PDS5 in the cell ⚖️
21/ The genetics check out with the biophysics:
Co-depleting NIPBL (which reduces extrusion rate) together with PDS5 (which increases extrusion rate AND increase lifetime) made Hi-C look like WAPL inactivation 🤯
Co-depleting NIPBL (which reduces extrusion rate) together with PDS5 (which increases extrusion rate AND increase lifetime) made Hi-C look like WAPL inactivation 🤯
August 16, 2025 at 3:03 AM
21/ The genetics check out with the biophysics:
Co-depleting NIPBL (which reduces extrusion rate) together with PDS5 (which increases extrusion rate AND increase lifetime) made Hi-C look like WAPL inactivation 🤯
Co-depleting NIPBL (which reduces extrusion rate) together with PDS5 (which increases extrusion rate AND increase lifetime) made Hi-C look like WAPL inactivation 🤯
19/ Timecourse microscopy experiments at the onset of G1 confirmed that PDS5 depletion causes vermicelli to form faster than after WAPL inactivation, supporting that PDS5 accelerate extrusion rate 🚄🚄🚄
August 16, 2025 at 3:03 AM
19/ Timecourse microscopy experiments at the onset of G1 confirmed that PDS5 depletion causes vermicelli to form faster than after WAPL inactivation, supporting that PDS5 accelerate extrusion rate 🚄🚄🚄
18/ Measuring extrusion rates in live cells is not directly possible.
But polymer simulations predicted that faster extrusion after PDS5 loss should create denser cohesin clusters (“vermicelli”) than those known to form after WAPL inactivation.
✔️That’s exactly what microscopy showed!
But polymer simulations predicted that faster extrusion after PDS5 loss should create denser cohesin clusters (“vermicelli”) than those known to form after WAPL inactivation.
✔️That’s exactly what microscopy showed!
August 16, 2025 at 3:03 AM
18/ Measuring extrusion rates in live cells is not directly possible.
But polymer simulations predicted that faster extrusion after PDS5 loss should create denser cohesin clusters (“vermicelli”) than those known to form after WAPL inactivation.
✔️That’s exactly what microscopy showed!
But polymer simulations predicted that faster extrusion after PDS5 loss should create denser cohesin clusters (“vermicelli”) than those known to form after WAPL inactivation.
✔️That’s exactly what microscopy showed!
17/ ✔️Satisfyingly, by iFRAP @lucagiorgetti.bsky.social indeed saw smaller increase in lifetime after PDS5 vs. WAPL depletion.
August 16, 2025 at 3:03 AM
17/ ✔️Satisfyingly, by iFRAP @lucagiorgetti.bsky.social indeed saw smaller increase in lifetime after PDS5 vs. WAPL depletion.
15/ Experimentally, compartmentalization is much more suppressed after PDS5 vs. WAPL depletion 💡
August 16, 2025 at 3:03 AM
15/ Experimentally, compartmentalization is much more suppressed after PDS5 vs. WAPL depletion 💡
14/ 😬 Problem: Cohesin lifetime and extrusion rates contribute equally to processivity, making hard to disentangle their respective contributions
😮 However, we noticed in simulations that compartmentalization is better suppressed by high rates than by high lifetime
😮 However, we noticed in simulations that compartmentalization is better suppressed by high rates than by high lifetime
August 16, 2025 at 3:03 AM
14/ 😬 Problem: Cohesin lifetime and extrusion rates contribute equally to processivity, making hard to disentangle their respective contributions
😮 However, we noticed in simulations that compartmentalization is better suppressed by high rates than by high lifetime
😮 However, we noticed in simulations that compartmentalization is better suppressed by high rates than by high lifetime
13/ Hi-C after PDS5 depletion resembles but is not identical to WAPL depletion: chromosomes become even more compacted.
❓Can our polymer models tell us if it because PDS5 depletion increases cohesin lifetime or extrusion rate?
❓Can our polymer models tell us if it because PDS5 depletion increases cohesin lifetime or extrusion rate?
August 16, 2025 at 3:03 AM
13/ Hi-C after PDS5 depletion resembles but is not identical to WAPL depletion: chromosomes become even more compacted.
❓Can our polymer models tell us if it because PDS5 depletion increases cohesin lifetime or extrusion rate?
❓Can our polymer models tell us if it because PDS5 depletion increases cohesin lifetime or extrusion rate?
12/ We’ve learned more by considering the importance of NIPBL in the rate of extrusion. ⏬
PDS5 is an enigmatic co-factor. It is known to help unload cohesin but it also competes with NIPBL, preventing it from binding cohesin. Is PDS5 important for cohesin lifetime and/or for extrusion rates? 🎭
PDS5 is an enigmatic co-factor. It is known to help unload cohesin but it also competes with NIPBL, preventing it from binding cohesin. Is PDS5 important for cohesin lifetime and/or for extrusion rates? 🎭
August 16, 2025 at 3:03 AM
12/ We’ve learned more by considering the importance of NIPBL in the rate of extrusion. ⏬
PDS5 is an enigmatic co-factor. It is known to help unload cohesin but it also competes with NIPBL, preventing it from binding cohesin. Is PDS5 important for cohesin lifetime and/or for extrusion rates? 🎭
PDS5 is an enigmatic co-factor. It is known to help unload cohesin but it also competes with NIPBL, preventing it from binding cohesin. Is PDS5 important for cohesin lifetime and/or for extrusion rates? 🎭
11/ This explains how WAPL+NIPBL double mutants have near normal genome folding patterns (cohesin processivity is preserved), despite cohesin dynamics remaining abnormal
August 16, 2025 at 3:03 AM
11/ This explains how WAPL+NIPBL double mutants have near normal genome folding patterns (cohesin processivity is preserved), despite cohesin dynamics remaining abnormal
10/ Considering a role for NIPBL abundance in the RATE of loop extrusion offers the solution🔮
The size of cohesin loops is determined by cohesin processivity:
📏 Processivity = Lifetime * Rate
💡High lifetime (WAPL inactivation) is compensated by lowering the extrusion rate (NIPBL co-depletion)😲
The size of cohesin loops is determined by cohesin processivity:
📏 Processivity = Lifetime * Rate
💡High lifetime (WAPL inactivation) is compensated by lowering the extrusion rate (NIPBL co-depletion)😲
August 16, 2025 at 3:03 AM
10/ Considering a role for NIPBL abundance in the RATE of loop extrusion offers the solution🔮
The size of cohesin loops is determined by cohesin processivity:
📏 Processivity = Lifetime * Rate
💡High lifetime (WAPL inactivation) is compensated by lowering the extrusion rate (NIPBL co-depletion)😲
The size of cohesin loops is determined by cohesin processivity:
📏 Processivity = Lifetime * Rate
💡High lifetime (WAPL inactivation) is compensated by lowering the extrusion rate (NIPBL co-depletion)😲
9/ Is it because NIPBL depletion lowers cohesin loading?
❌No: In the background of WAPL depletion, lowering cohesin abundance directly does NOT restore Hi-C back to normal
❌No: In the background of WAPL depletion, lowering cohesin abundance directly does NOT restore Hi-C back to normal
August 16, 2025 at 3:03 AM
9/ Is it because NIPBL depletion lowers cohesin loading?
❌No: In the background of WAPL depletion, lowering cohesin abundance directly does NOT restore Hi-C back to normal
❌No: In the background of WAPL depletion, lowering cohesin abundance directly does NOT restore Hi-C back to normal
8/ We first explored a known but puzzling genetic interaction: inactivating WAPL (the cohesin unloader) increases cohesin lifetime tremendously and compacts chromosomes.
Co-depleting NIPBL alongside WAPL fixes Hi-C close to normal, but without restoring normal cohesin dynamics. How? 🤷
Co-depleting NIPBL alongside WAPL fixes Hi-C close to normal, but without restoring normal cohesin dynamics. How? 🤷
August 16, 2025 at 3:03 AM
8/ We first explored a known but puzzling genetic interaction: inactivating WAPL (the cohesin unloader) increases cohesin lifetime tremendously and compacts chromosomes.
Co-depleting NIPBL alongside WAPL fixes Hi-C close to normal, but without restoring normal cohesin dynamics. How? 🤷
Co-depleting NIPBL alongside WAPL fixes Hi-C close to normal, but without restoring normal cohesin dynamics. How? 🤷
6/ ✔️However, simulations reducing extrusion RATE did a fantastic job at modeling NIPBL depletion
August 16, 2025 at 3:03 AM
6/ ✔️However, simulations reducing extrusion RATE did a fantastic job at modeling NIPBL depletion
4/ We deployed a polymer modeling approach to investigate how Hi-C and microscopy readouts are affected by each loop extrusion parameters:
1️⃣ the number of loaded cohesins (separation between extruders)
2️⃣ their residence time on chromatin (lifetime)
3️⃣ how fast they extrude (rate)
1️⃣ the number of loaded cohesins (separation between extruders)
2️⃣ their residence time on chromatin (lifetime)
3️⃣ how fast they extrude (rate)
August 16, 2025 at 3:03 AM
4/ We deployed a polymer modeling approach to investigate how Hi-C and microscopy readouts are affected by each loop extrusion parameters:
1️⃣ the number of loaded cohesins (separation between extruders)
2️⃣ their residence time on chromatin (lifetime)
3️⃣ how fast they extrude (rate)
1️⃣ the number of loaded cohesins (separation between extruders)
2️⃣ their residence time on chromatin (lifetime)
3️⃣ how fast they extrude (rate)
3/ Directly cutting cohesin abundance by half, through partial degron induction, led to much milder folding defects than NIPBL depletion.
So NIPBL must be doing something else to loop extrusion beyond merely loading cohesin 🤔❓
So NIPBL must be doing something else to loop extrusion beyond merely loading cohesin 🤔❓
August 16, 2025 at 3:03 AM
3/ Directly cutting cohesin abundance by half, through partial degron induction, led to much milder folding defects than NIPBL depletion.
So NIPBL must be doing something else to loop extrusion beyond merely loading cohesin 🤔❓
So NIPBL must be doing something else to loop extrusion beyond merely loading cohesin 🤔❓
2/ NIPBL is widely considered as the cohesin loader.
We acutely lowered NIPBL expression in cells with a degron, down to ~5-10%. This caused major Hi-C defects, just as we would expect if cohesin had stopped loading.
Yet to our surprise cohesin binding is only reduced 2-fold by NIPBL depletion. 🤨
We acutely lowered NIPBL expression in cells with a degron, down to ~5-10%. This caused major Hi-C defects, just as we would expect if cohesin had stopped loading.
Yet to our surprise cohesin binding is only reduced 2-fold by NIPBL depletion. 🤨
August 16, 2025 at 3:03 AM
2/ NIPBL is widely considered as the cohesin loader.
We acutely lowered NIPBL expression in cells with a degron, down to ~5-10%. This caused major Hi-C defects, just as we would expect if cohesin had stopped loading.
Yet to our surprise cohesin binding is only reduced 2-fold by NIPBL depletion. 🤨
We acutely lowered NIPBL expression in cells with a degron, down to ~5-10%. This caused major Hi-C defects, just as we would expect if cohesin had stopped loading.
Yet to our surprise cohesin binding is only reduced 2-fold by NIPBL depletion. 🤨
26/ This was a hand in hand collaboration between experimentalists in our group led by @rinishah.bsky.social , and physicists in @gfudenberg.bsky.social ’s lab led by Max Tortora, with help from @nesslfy.bsky.social in @lucagiorgetti.bsky.social ’s lab.
A fun thank-you video for reading that far:
A fun thank-you video for reading that far:
August 16, 2025 at 2:40 AM
26/ This was a hand in hand collaboration between experimentalists in our group led by @rinishah.bsky.social , and physicists in @gfudenberg.bsky.social ’s lab led by Max Tortora, with help from @nesslfy.bsky.social in @lucagiorgetti.bsky.social ’s lab.
A fun thank-you video for reading that far:
A fun thank-you video for reading that far: