Show notes

Transcription

The video is coming soon to the channel.

Chapters

• 0:00 A gene being read
• 0:45 The gene, its promoter and the polymerase
• 1:24 A seedling in the dark
• 2:07 Light lets a transcription factor build up
• 2:51 The coactivator and the DNA loop
• 3:24 The general transcription factors
• 3:42 The TATA box and the saddle
• 4:35 Building the pre-initiation complex
• 5:27 Opening the DNA
• 6:04 Writing the first letters
• 6:54 Breaking free: the polymerase's tail
• 7:39 The cap
• 8:16 Elongation
• 8:49 The cut, the tail of A's and the torpedo
• 10:02 Many polymerases, one gene
• 10:13 One set of genes, many kinds of cells
• 11:05 Next: translation

Sources

79 sources. Each was checked against its record (Crossref, PubMed, the Protein Data Bank, or the textbook edition) and against the claim it supports.

Textbooks and reviews

• Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell, 4th ed. New York: Garland Science. Free on NCBI Bookshelf: www.ncbi.nlm.nih.gov/books/NBK21054/ (sections used: From DNA to RNA, www.ncbi.nlm.nih.gov/books/NBK26887/; An Overview of Gene Control, www.ncbi.nlm.nih.gov/books/NBK26885/; From RNA to Protein, www.ncbi.nlm.nih.gov/books/NBK26829/)
• Clark MA, Choi J, Douglas M (2018). Biology 2e. OpenStax, Rice University. ISBN 9781947172524. openstax.org/details/books/biology-2e (accessed 2026-10-20)
• Jakubowski H, Flatt P (n.d.). Fundamentals of Biochemistry III. LibreTexts. bio.libretexts.org/Bookshelves/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt) (accessed 2026-10-20)
• Ahern K, Rajagopal I, Tan T (n.d.). Biochemistry Free For All. LibreTexts. bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan) (accessed 2026-10-20)
• Lackie JM (2013). The Dictionary of Cell and Molecular Biology, 5th ed. Academic Press. ISBN 9780123849311. doi.org/10.1016/c2009-0-64239-2
• Arsovski AA, Galstyan A, Guseman JM, Nemhauser JL (2012). Photomorphogenesis. The Arabidopsis Book 10:e0147. doi.org/10.1199/tab.0147

The hook: Rubisco and how busy its gene is

• Bar-On YM, Milo R (2019). The global mass and average rate of rubisco. Proc Natl Acad Sci U S A 116:4738-4743. doi.org/10.1073/pnas.1816654116
• Valegård K, Hasse D, Andersson I et al. (2018). Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate. Acta Crystallogr D Struct Biol 74:1-9. doi.org/10.1107/S2059798317017132
• Tenorio Berrío R, Verhelst E, Eekhout T et al. (2025). Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics. New Phytol 246:840-858. doi.org/10.1111/nph.20446

The gene and its light switch

• Dedonder A, Rethy R, Fredericq H et al. (1993). Arabidopsis rbcS genes are differentially regulated by light. Plant Physiol 101:801-8. doi.org/10.1104/pp.101.3.801
• Donald RG, Cashmore AR (1990). Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J 9:1717-26. doi.org/10.1002/j.1460-2075.1990.tb08295.x
• Dreos R, Ambrosini G, Groux R et al. (2017). The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. Nucleic Acids Res 45:D51-D55. doi.org/10.1093/nar/gkw1069
• Hardtke CS, Gohda K, Osterlund MT et al. (2000). HY5 stability and activity in arabidopsis is regulated by phosphorylation in its COP1 binding domain. EMBO J 19:4997-5006. doi.org/10.1093/emboj/19.18.4997
• Lau K, Podolec R, Chappuis R et al. (2019). Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs. EMBO J 38:e102140. doi.org/10.15252/embj.2019102140
• Vijay-Kumar S, Bugg CE, Cook WJ (1987). Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194:531-44. doi.org/10.1016/0022-2836(87)90679-6

The coactivator and the loop

• Bäckström S, Elfving N, Nilsson R et al. (2007). Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Mol Cell 26:717-29. doi.org/10.1016/j.molcel.2007.05.007
• Soutourina J (2018). Transcription regulation by the Mediator complex. Nat Rev Mol Cell Biol 19:262-274. doi.org/10.1038/nrm.2017.115
• Allen BL, Taatjes DJ (2015). The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 16:155-66. doi.org/10.1038/nrm3951
• Abdella R, Talyzina A, Chen S et al. (2021). Structure of the human Mediator-bound transcription preinitiation complex. Science 372:52-56. doi.org/10.1126/science.abg3074
• Kagey MH, Newman JJ, Bilodeau S et al. (2010). Mediator and cohesin connect gene expression and chromatin architecture. Nature 467:430-5. doi.org/10.1038/nature09380

The core promoter: TATA box and TBP

• Molina C, Grotewold E (2005). Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6:25. doi.org/10.1186/1471-2164-6-25
• Yamamoto YY, Ichida H, Matsui M et al. (2007). Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 8:67. doi.org/10.1186/1471-2164-8-67
• Yamamoto YY, Ichida H, Abe T et al. (2007). Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic Acids Res 35:6219-26. doi.org/10.1093/nar/gkm685
• Lago C, Clerici E, Dreni L et al. (2005). The Arabidopsis TFIID factor AtTAF6 controls pollen tube growth. Dev Biol 285:91-100. doi.org/10.1016/j.ydbio.2005.06.006
• Faiger H, Ivanchenko M, Haran TE (2007). Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism. Nucleic Acids Res 35:4409-19. doi.org/10.1093/nar/gkm451
• Olson WK, Gorin AA, Lu XJ et al. (1998). DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A 95:11163-8. doi.org/10.1073/pnas.95.19.11163
• Wu J, Parkhurst KM, Powell RM et al. (2001). DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent. J Biol Chem 276:14614-22. doi.org/10.1074/jbc.M004402200
• Chen X, Qi Y, Wu Z et al. (2021). Structural insights into preinitiation complex assembly on core promoters. Science 372:eaba8490. doi.org/10.1126/science.aba8490

Opening, starting and escaping

• He Y, Yan C, Fang J et al. (2016). Near-atomic resolution visualization of human transcription promoter opening. Nature 533:359-65. doi.org/10.1038/nature17970
• Chen X, Liu W, Wang Q et al. (2023). Structural visualization of transcription initiation in action. Science 382:eadi5120. doi.org/10.1126/science.adi5120
• Holstege FC, Fiedler U, Timmers HT (1997). Three transitions in the RNA polymerase II transcription complex during initiation. EMBO J 16:7468-80. doi.org/10.1093/emboj/16.24.7468
• Pal M, Ponticelli AS, Luse DS (2005). The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II. Mol Cell 19:101-10. doi.org/10.1016/j.molcel.2005.05.024
• Sainsbury S, Niesser J, Cramer P (2013). Structure and function of the initially transcribing RNA polymerase II-TFIIB complex. Nature 493:437-40. doi.org/10.1038/nature11715
• Zhan Y, Grabbe F, Oberbeckmann E et al. (2024). Three-step mechanism of promoter escape by RNA polymerase II. Mol Cell 84:1699-1710.e6. doi.org/10.1016/j.molcel.2024.03.016
• Peller L (1977). Thermodynamic limits on the size and size distribution of nucleic acids synthesized in vitro: the role of pyrophosphate hydrolysis. Biochemistry 16:387-95. doi.org/10.1021/bi00622a008

The tail and the cap

• Komarnitsky P, Cho EJ, Buratowski S (2000). Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev 14:2452-60. doi.org/10.1101/gad.824700
• Koiwa H, Hausmann S, Bang WY et al. (2004). Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases. Proc Natl Acad Sci U S A 101:14539-44. doi.org/10.1073/pnas.0403174101
• McCracken S, Fong N, Yankulov K et al. (1997). The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385:357-61. doi.org/10.1038/385357a0
• Garg G, Dienemann C, Farnung L et al. (2023). Structural insights into human co-transcriptional capping. Mol Cell 83:2464-2477.e5. doi.org/10.1016/j.molcel.2023.06.002
• Ramanathan A, Robb GB, Chan SH (2016). mRNA capping: biological functions and applications. Nucleic Acids Res 44:7511-26. doi.org/10.1093/nar/gkw551
• Topisirovic I, Svitkin YV, Sonenberg N et al. (2011). Cap and cap-binding proteins in the control of gene expression. Wiley Interdiscip Rev RNA 2:277-98. doi.org/10.1002/wrna.52
• Schwer B, Mao X, Shuman S (1998). Accelerated mRNA decay in conditional mutants of yeast mRNA capping enzyme. Nucleic Acids Res 26:2050-7. doi.org/10.1093/nar/26.9.2050
• Varshney D, Petit AP, Bueren-Calabuig JA et al. (2016). Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic Acids Res 44:10423-10436. doi.org/10.1093/nar/gkw637

Elongation

• Bernecky C, Herzog F, Baumeister W et al. (2016). Structure of transcribing mammalian RNA polymerase II. Nature 529:551-4. doi.org/10.1038/nature16482
• Gnatt AL, Cramer P, Fu J et al. (2001). Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292:1876-82. doi.org/10.1126/science.1059495
• Veloso A, Kirkconnell KS, Magnuson B et al. (2014). Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res 24:896-905. doi.org/10.1101/gr.171405.113
• Tantale K, Mueller F, Kozulic-Pirher A et al. (2016). A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting. Nat Commun 7:12248. doi.org/10.1038/ncomms12248

Cutting, the tail of As, and the torpedo

• Loke JC, Stahlberg EA, Strenski DG et al. (2005). Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol 138:1457-68. doi.org/10.1104/pp.105.060541
• Thomas PE, Wu X, Liu M et al. (2012). Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell 24:4376-88. doi.org/10.1105/tpc.112.096107
• Clerici M, Faini M, Muckenfuss LM et al. (2018). Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat Struct Mol Biol 25:135-138. doi.org/10.1038/s41594-017-0020-6
• Balbo PB, Bohm A (2007). Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis. Structure 15:1117-31. doi.org/10.1016/j.str.2007.07.010
• Decker CJ, Parker R (1993). A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev 7:1632-43. doi.org/10.1101/gad.7.8.1632
• Passmore LA, Coller J (2022). Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 23:93-106. doi.org/10.1038/s41580-021-00417-y
• West S, Gromak N, Proudfoot NJ (2004). Human 5' --> 3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432:522-5. doi.org/10.1038/nature03035
• Krzyszton M, Zakrzewska-Placzek M, Kwasnik A et al. (2018). Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes. Plant J 93:1017-1031. doi.org/10.1111/tpj.13826
• Zeng Y, Zhang HW, Wu XX et al. (2024). Structural basis of exoribonuclease-mediated mRNA transcription termination. Nature 628:887-893. doi.org/10.1038/s41586-024-07240-3

Genes, cells and transcription factors

• Lamesch P, Berardini TZ, Li D et al. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202-10. doi.org/10.1093/nar/gkr1090
• Pyke KA, Rutherford SM, Robertson EJ et al. (1994). arc6, A Fertile Arabidopsis Mutant with Only Two Mesophyll Cell Chloroplasts. Plant Physiol 106:1169-1177. doi.org/10.1104/pp.106.3.1169
• Bourbousse C, Mestiri I, Zabulon G et al. (2015). Light signaling controls nuclear architecture reorganization during seedling establishment. Proc Natl Acad Sci U S A 112:E2836-44. doi.org/10.1073/pnas.1503512112
• Riechmann JL, Heard J, Martin G et al. (2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105-10. doi.org/10.1126/science.290.5499.2105
• Lambert SA, Jolma A, Campitelli LF et al. (2018). The Human Transcription Factors. Cell 172:650-665. doi.org/10.1016/j.cell.2018.01.029
• Ma L, Li J, Qu L et al. (2001). Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13:2589-607. doi.org/10.1105/tpc.010229

Structures drawn (Protein Data Bank)

• PDB 5IU0: Rubisco from Arabidopsis thaliana. Valegård K et al. (2018) Acta Crystallogr D Struct Biol 74:1-9. doi.org/10.1107/S2059798317017132 doi.org/10.2210/pdb5iu0/pdb
• PDB 6QTO: Crystal structure of an Arabidopsis WD40 domain in complex with a transcription factor. Lau K et al. (2019) EMBO J 38:e102140. doi.org/10.15252/embj.2019102140 doi.org/10.2210/pdb6qto/pdb
• PDB 1UBQ: STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION. Vijay-Kumar S et al. (1987) J Mol Biol 194:531-44. doi.org/10.1016/0022-2836(87)90679-6 doi.org/10.2210/pdb1ubq/pdb
• PDB 7LBM: Structure of the human Mediator-bound transcription pre-initiation complex. Abdella R et al. (2021) Science 372:52-56. doi.org/10.1126/science.abg3074 doi.org/10.2210/pdb7lbm/pdb
• PDB 7EGB: TFIID-based holo PIC on SCP promoter. Chen X et al. (2021) Science 372:eaba8490. doi.org/10.1126/science.aba8490 doi.org/10.2210/pdb7egb/pdb
• PDB 8WAK: Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS.. Chen X et al. (2023) Science 382:eadi5120. doi.org/10.1126/science.adi5120 doi.org/10.2210/pdb8wak/pdb
• PDB 8WAS: Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS.. Chen X et al. (2023) Science 382:eadi5120. doi.org/10.1126/science.adi5120 doi.org/10.2210/pdb8was/pdb
• PDB 5FLM: Structure of transcribing mammalian RNA polymerase II. Bernecky C et al. (2016) Nature 529:551-4. doi.org/10.1038/nature16482 doi.org/10.2210/pdb5flm/pdb
• PDB 8P4A: Structural insights into human co-transcriptional capping - structure 1. Garg G et al. (2023) Mol Cell 83:2464-2477.e5. doi.org/10.1016/j.molcel.2023.06.002 doi.org/10.2210/pdb8p4a/pdb
• PDB 5E8J: Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM. Varshney D et al. (2016) Nucleic Acids Res 44:10423-10436. doi.org/10.1093/nar/gkw637 doi.org/10.2210/pdb5e8j/pdb
• PDB 6FUW: Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound to the PAS AAUAAA motif at 3.1 Angstrom resolution. Clerici M et al. (2018) Nat Struct Mol Biol 25:135-138. doi.org/10.1038/s41594-017-0020-6 doi.org/10.2210/pdb6fuw/pdb
• PDB 2Q66: Structure of Yeast Poly(A) Polymerase with ATP and oligo(A). Balbo PB et al. (2007) Structure 15:1117-31. doi.org/10.1016/j.str.2007.07.010 doi.org/10.2210/pdb2q66/pdb
• PDB 8JCH: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1 (Pol II Rat1-PTTC1). Zeng Y et al. (2024) Nature 628:887-893. doi.org/10.1038/s41586-024-07240-3 doi.org/10.2210/pdb8jch/pdb

Data and sequence records

• Tenorio Berrío et al. (2025) single-cell RNA data, young Arabidopsis leaves: NCBI GEO GSE273033. www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE273033 (our count of RBCS1A messages)
• EPDnew Arabidopsis promoter AT1G67090_1 (RBCS1A transcription start, TSS-seq). epd.expasy.org/cgi-bin/epd/get_doc?db=atEpdNew&format=genome&entry=AT1G67090_1
• GenBank X13611: Arabidopsis thaliana ats1A gene for ribulose 1,5-bisphosphate carboxylase small subunit. www.ncbi.nlm.nih.gov/nuccore/X13611
• UniProt O24646: Transcription factor HY5, Arabidopsis thaliana. www.uniprot.org/uniprotkb/O24646