Andrea Bernardini
@bernardini-andrea.bsky.social
Tenure track Researcher
Studying transcription factors & promoters
University of Milan 🇮🇹
previously in Tora's lab, IGBMC 🇫🇷
Studying transcription factors & promoters
University of Milan 🇮🇹
previously in Tora's lab, IGBMC 🇫🇷
Could these simple commonalities hint at a more complex architecture common to these IDRs? Are they targeting the same components? Could this "class" of activation domains explain the common function of these TFs as PIC-positioning factors? We discussed this and more in the article. 14/15
December 22, 2024 at 3:21 PM
Could these simple commonalities hint at a more complex architecture common to these IDRs? Are they targeting the same components? Could this "class" of activation domains explain the common function of these TFs as PIC-positioning factors? We discussed this and more in the article. 14/15
Our speculation is that a candidate rTF is likely ubiquitously expressed, not strictly inducible, and binds proximally to TSSs in a genome-wide scale. We noticed that many top candidate TFs adhering to those criteria shared similarities in the aa composition in regions outside their DBDs. 12/15
December 22, 2024 at 3:21 PM
Our speculation is that a candidate rTF is likely ubiquitously expressed, not strictly inducible, and binds proximally to TSSs in a genome-wide scale. We noticed that many top candidate TFs adhering to those criteria shared similarities in the aa composition in regions outside their DBDs. 12/15
A set of specific TF binding sites also impact on TSS selection (position). These motifs seem to have a function beyond merely regulating txn quantity. To summarize this concept, we proposed the term 'ruler motifs', since these motifs impart some sort of distance rules on where txn starts. 📏 8/15
December 22, 2024 at 3:21 PM
A set of specific TF binding sites also impact on TSS selection (position). These motifs seem to have a function beyond merely regulating txn quantity. To summarize this concept, we proposed the term 'ruler motifs', since these motifs impart some sort of distance rules on where txn starts. 📏 8/15
The list included many well-known Pol II transcription regulators. Co-translational interactions are far from an exception. 5/5
November 16, 2024 at 7:10 PM
The list included many well-known Pol II transcription regulators. Co-translational interactions are far from an exception. 5/5
We summarize different strategies to assemble these large multiprotein complexes (e.g. TFIID, SAGA and ATAC), using a variety of co- and post-translational assembly steps. 3/5
November 16, 2024 at 7:10 PM
We summarize different strategies to assemble these large multiprotein complexes (e.g. TFIID, SAGA and ATAC), using a variety of co- and post-translational assembly steps. 3/5
Your favorite protein complex might start to assemble during the synthesis of its subunits. This can have functional consequences (especially if the complex regulates many genes). L. Tora & I discuss these aspects in a review article.
doi.org/10.1016/j.jm...
1/5
doi.org/10.1016/j.jm...
1/5
November 16, 2024 at 7:10 PM
Your favorite protein complex might start to assemble during the synthesis of its subunits. This can have functional consequences (especially if the complex regulates many genes). L. Tora & I discuss these aspects in a review article.
doi.org/10.1016/j.jm...
1/5
doi.org/10.1016/j.jm...
1/5
What exactly determines the Transcription Start Sites (TSS) patterns at the beginning of every Pol II-transcribed gene? We (L. Tora lab & F. Mueller) delved into this fascinating question in an opinion article in Trends in Biochemical Sciences.
doi.org/10.1016/j.ti...
doi.org/10.1016/j.ti...
November 16, 2024 at 6:58 PM
What exactly determines the Transcription Start Sites (TSS) patterns at the beginning of every Pol II-transcribed gene? We (L. Tora lab & F. Mueller) delved into this fascinating question in an opinion article in Trends in Biochemical Sciences.
doi.org/10.1016/j.ti...
doi.org/10.1016/j.ti...
We could detect several pre-assembled TFIID “building blocks” present in the cytoplasm. These diverse assembly intermediates seem to converge on the nascent TAF1 polypeptide, which is equipped with several interaction domains to provide a flexible scaffold for the entire complex.
November 16, 2024 at 6:04 PM
We could detect several pre-assembled TFIID “building blocks” present in the cytoplasm. These diverse assembly intermediates seem to converge on the nascent TAF1 polypeptide, which is equipped with several interaction domains to provide a flexible scaffold for the entire complex.
We used a combination of molecular (systematic RIPs) and imaging approaches (IF+smiFISH) to detect the Co-TA events amongst TFIID subunits. Surprisingly, we found that TAF1 – the largest subunit – nucleates the recruitment of most of TFIID components during its translation.
November 16, 2024 at 6:04 PM
We used a combination of molecular (systematic RIPs) and imaging approaches (IF+smiFISH) to detect the Co-TA events amongst TFIID subunits. Surprisingly, we found that TAF1 – the largest subunit – nucleates the recruitment of most of TFIID components during its translation.
We found that many of the subunit-subunit interactions are established before the completion of protein synthesis. These co-translational assembly (Co-TA) events can occur when specific interaction domains are exposed by the nascent protein on the #ribosome during translation.
November 16, 2024 at 6:04 PM
We found that many of the subunit-subunit interactions are established before the completion of protein synthesis. These co-translational assembly (Co-TA) events can occur when specific interaction domains are exposed by the nascent protein on the #ribosome during translation.
How do big multiprotein complexes manage to be efficiently assembled and where the assembly process takes place? We investigated the assembly steps of one of the major components of the Pol II #transcription machinery in human cells: the basal transcription factor TFIID.
November 16, 2024 at 6:04 PM
How do big multiprotein complexes manage to be efficiently assembled and where the assembly process takes place? We investigated the assembly steps of one of the major components of the Pol II #transcription machinery in human cells: the basal transcription factor TFIID.
A big part of the project was devoted to define the origins of the splicing #isoforms that shape the TAD of NF-YA across vertebrates. 🔎 For example, we found that #sharks probably lost the main alternatively spliced exon of NF-YA (implications on bone formation?) 🦈 (6/8)
November 10, 2024 at 7:33 PM
Probably purifying selection puts a strong pressure on NF-YA, having no paralog #genes in vertebrates (with an important exception..🐠). Yet, such an extensive conservation for an intrinsically disordered TAD is remarkable. A hint to a peculiar mechanism of action? (5/8)
November 10, 2024 at 7:33 PM
Probably purifying selection puts a strong pressure on NF-YA, having no paralog #genes in vertebrates (with an important exception..🐠). Yet, such an extensive conservation for an intrinsically disordered TAD is remarkable. A hint to a peculiar mechanism of action? (5/8)
…for several extremely conserved motifs, shared with other deuterostomes. NF-YA TAD is old and contains molecular features that date back >600 million years ago. 🌌 The common thought that TADs are poorly conserved does not apply in this case. But why? (4/8)
November 10, 2024 at 7:33 PM
…for several extremely conserved motifs, shared with other deuterostomes. NF-YA TAD is old and contains molecular features that date back >600 million years ago. 🌌 The common thought that TADs are poorly conserved does not apply in this case. But why? (4/8)
How conserved is the Q-rich TAD? Short, yet surprising answer: a lot! We found >90% positions being identical among bony vertebrates (still less than the DNA-binding core). Conservation drops sharply moving outside vertebrate tree 📉, except… (3/8)
November 10, 2024 at 7:33 PM
How conserved is the Q-rich TAD? Short, yet surprising answer: a lot! We found >90% positions being identical among bony vertebrates (still less than the DNA-binding core). Conservation drops sharply moving outside vertebrate tree 📉, except… (3/8)
We analyzed 220 #vertebrate #species focusing on two related aspects: conservation of the TAD and origins of its alternatively-spliced regions (studied in development and cancer). (2/8)
November 10, 2024 at 7:33 PM
We analyzed 220 #vertebrate #species focusing on two related aspects: conservation of the TAD and origins of its alternatively-spliced regions (studied in development and cancer). (2/8)
If our model is true, placing the two proteins on opposite sides of the same DNA molecule would prevent direct interactions between the two TFs. Indeed, the addition of half-helical turn (+5bp) between the sites abolished DNA-binding cooperativity.
November 10, 2024 at 7:27 PM
If our model is true, placing the two proteins on opposite sides of the same DNA molecule would prevent direct interactions between the two TFs. Indeed, the addition of half-helical turn (+5bp) between the sites abolished DNA-binding cooperativity.
After another full battery of off-rate EMSAs we found that the USR is sufficient and necessary for DNA-binding cooperativity with NF-Y. Also, different regions of the USR are employed to contact NF-Y depending on the spacing of the sites on DNA!
November 10, 2024 at 7:27 PM
After another full battery of off-rate EMSAs we found that the USR is sufficient and necessary for DNA-binding cooperativity with NF-Y. Also, different regions of the USR are employed to contact NF-Y depending on the spacing of the sites on DNA!
The USR is extremely conserved, it is an IDR and it works as a context-dependent TAD. To validate the structural observations we designed serially deleted constructs of USF1. With complete, partial and totally deleted USR.
November 10, 2024 at 7:27 PM
The USR is extremely conserved, it is an IDR and it works as a context-dependent TAD. To validate the structural observations we designed serially deleted constructs of USF1. With complete, partial and totally deleted USR.
EMSAs and structural data suggested that an extended region from USF1, upstream of its DNA-binding domain (DBD), could mediate contacts with NF-Y globular core. Protein disorder analyses predicted a long #IDR that includes the so-called USF-specific region (USR).
November 10, 2024 at 7:27 PM
EMSAs and structural data suggested that an extended region from USF1, upstream of its DNA-binding domain (DBD), could mediate contacts with NF-Y globular core. Protein disorder analyses predicted a long #IDR that includes the so-called USF-specific region (USR).
We isolated full-length complexes for Cryo-EM. No 3D reconstruction was possible (small size, highly flexible molecular species), but 2D averages were in accordance with SAXS models architecture. It is nice to SEE the strong DNA bending imposed by NF-Y.
November 10, 2024 at 7:27 PM
We isolated full-length complexes for Cryo-EM. No 3D reconstruction was possible (small size, highly flexible molecular species), but 2D averages were in accordance with SAXS models architecture. It is nice to SEE the strong DNA bending imposed by NF-Y.
Interestingly, the 10bp (HOXB4) vs 12bp (MLT1K LTR) spacing between binding sites imposes a 70° rotation along DNA axis. Yet the two TFs manage to cooperate by adapting their interaction surfaces.
November 10, 2024 at 7:27 PM
Interestingly, the 10bp (HOXB4) vs 12bp (MLT1K LTR) spacing between binding sites imposes a 70° rotation along DNA axis. Yet the two TFs manage to cooperate by adapting their interaction surfaces.
We isolated ternary complexes and our collaborators made some nice molecular models starting from #SAXS datasets. The scattering data are compatible with a direct protein-protein interaction between the two TFs on DNA. This seems to be mediated by an extended region of USF1 dimer.
November 10, 2024 at 7:27 PM
We isolated ternary complexes and our collaborators made some nice molecular models starting from #SAXS datasets. The scattering data are compatible with a direct protein-protein interaction between the two TFs on DNA. This seems to be mediated by an extended region of USF1 dimer.
We then removed USF1 1st transactivation domain (TAD1) and all the NF-Y domains outside the conserved core region. Result: DNA-binding cooperativity is fully maintained. Those regions are dispensable.
November 10, 2024 at 7:27 PM
We then removed USF1 1st transactivation domain (TAD1) and all the NF-Y domains outside the conserved core region. Result: DNA-binding cooperativity is fully maintained. Those regions are dispensable.