Research articles for Molecular Biology BIOL 5304 project 2021 Selection is due October 25
(Schedule)
This list will be updated periodically.
To see an abstract of the papers click the link in the title of the article. These papers are all available in full-text (pdf) format.
From off-campus, you may need to go through the library's "Online Resources" for journals.
You may send me 2 or 3 PubMed links for consideration, notify me.
The selected articles are shown in the Table below:
| Student | Paper Selected |
commented |
| 1. Katherine Scalise | Bhatt PR, Scaiola A, Loughran G, Leibundgut M, Kratzel A, Meurs R, Dreos R, O'Connor KM, McMillan A, Bode JW, Thiel V, Gatfield D, Atkins JF, Ban N. Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science. 2021 Jun 18;372(6548):1306-1313 |
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| 2. Lindsey Philips | Stringer AM, Baniulyte G, Lasek-Nesselquist E, Seed KD, Wade JT. Transcription termination and antitermination of bacterial CRISPR arrays. Elife. 2020 Oct 30;9:e58182. |
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| 3. Jordan Wartell | Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proc Natl Acad Sci U S A. 2021 Apr 6;118(14):e2026656118. |
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| 4. Delaney Gaston | Shukla A, Yan J, Pagano DJ, Dodson AE, Fei Y, Gorham J, Seidman JG, Wickens M, Kennedy S. poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature. 2020 Jun;582(7811):283-288. (see comment) |
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| 5. Justin Patty | Liu S, Hua Y, Wang J, Li L, Yuan J, Zhang B, Wang Z, Ji J, Kong D. RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination. Cell. 2021 Mar 4;184(5):1314-1329.e10. |
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| 6. Travis Harris | Xiang K, Bartel DP. The molecular basis of coupling between poly(A)-tail length and translational efficiency. Elife. 2021 Jul 2;10:e66493. |
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| 7. Kyra Rozanitis | Yin H, Wei C, Lee JT. Revisiting the consequences of deleting the X inactivation center. Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):e2102683118. |
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| 8. Abigail White | Henry C, Loiseau L, Vergnes A, Vertommen D, Mérida-Floriano A, Chitteni-Pattu S, Wood EA, Casadesús J, Cox MM, Barras F, Ezraty B. Redox controls RecA protein activity via reversible oxidation of its methionine residues. Elife. 2021 Feb 19;10:e63747. |
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| 9. Katie Neal | Vargas-Rodriguez O, Badran AH, Hoffman KS, Chen M, Crnković A, Ding Y, Krieger JR, Westhof E, Söll D, Melnikov S. Bacterial translation machinery for deliberate mistranslation of the genetic code. Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2110797118. |
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| 10. Hannah Velasco | Wakabayashi H, Warnasooriya C, Ermolenko DN. Extending the Spacing between the Shine-Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation. J Mol Biol. 2020 Jul 24;432(16):4612-4622 |
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| 11. Morgan Smith | Matsumoto Y, Brooks RC, Sverzhinsky A, Pascal JM, Tomkinson AE. Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation. J Mol Biol. 2020 Dec 4;432(24):166698 |
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| 12. Patrick Isaac | Verosloff MS, Corcoran WK, Dolberg TB, Bushhouse DZ, Leonard JN, Lucks JB. RNA Sequence and Structure Determinants of Pol III Transcriptional Termination in Human Cells. J Mol Biol. 2021 Jun 25;433(13):166978. |
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| 13. Josephine Chiu | Stinson BM, Moreno AT, Walter JC, Loparo JJ. A Mechanism to Minimize Errors during Non-homologous End Joining. Mol Cell. 2020 Mar 5;77(5):1080-1091.e8 |
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| 14. Zuhair Almahayni | Chan KY, Li X, Ortega J, Gu L, Li GM. DNA polymerase θ promotes CAG•CTG repeat expansions in Huntington's disease via insertion sequences of its catalytic domain. J Biol Chem. 2021 Aug 30;297(4):101144. doi: 10.1016/j.jbc.2021.101144. |
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| 15. Muaz Wahid | Liu Y, Rodriguez Y, Ross RL, Zhao R, Watts JA, Grunseich C, Bruzel A, Li D, Burdick JT, Prasad R, Crouch RJ, Limbach PA, Wilson SH, Cheung VG. RNA abasic sites in yeast and human cells. Proc Natl Acad Sci U S A. 2020 Aug 25;117(34):20689-20695 |
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| 16. Anaiya Deshong-Mcgruder | van den Boogaard ML, Oka R, Hakkert A, Schild L, Ebus ME, van Gerven MR, Zwijnenburg DA, Molenaar P, Hoyng LL, Dolman MEM, Essing AHW, Koopmans B, Helleday T, Drost J, van Boxtel R, Versteeg R, Koster J, Molenaar JJ. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma. Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2007898118. |
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| 17. Gabrielle Gard | Zhang H, Lyu Z, Fan Y, Evans CR, Barber KW, Banerjee K, Igoshin OA, Rinehart J, Ling J. Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22167-22172. |
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| 18. Madigan Eppink | Reyes GX, Kolodziejczak A, Devakumar LJPS, Kubota T, Kolodner RD, Putnam CD, Hombauer H. Ligation of newly replicated DNA controls the timing of DNA mismatch repair. Curr Biol. 2021 Mar 22;31(6):1268-1276.e6. |
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| 19. Anusha Iyengar | Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR 3rd, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell. 2020 Jan 23;180(2):263-277.e20. (see comment) |
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| 20. Rafay Wahid | Zhou W, Liang G, Molloy PL, Jones PA. DNA methylation enables transposable element-driven genome expansion. Proc Natl Acad Sci U S A. 2020 Aug 11;117(32):19359-19366. |
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| 21. Daniel Chavez | Portillo X, Huang YT, Breaker RR, Horning DP, Joyce GF. Witnessing the structural evolution of an RNA enzyme. Elife. 2021 Sep 9;10:e71557. |
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| 22. Brooke Koritala | Saha LK, Wakasugi M, Akter S, Prasad R, Wilson SH, Shimizu N, Sasanuma H, Huang SN, Agama K, Pommier Y, Matsunaga T, Hirota K, Iwai S, Nakazawa Y, Ogi T, Takeda S. Topoisomerase I-driven repair of UV-induced damage in NER-deficient cells. Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):14412-14420. |
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| 23. Andrew Wright | Gregory MT, Gao Y, Cui Q, Yang W. Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction. Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2103990118. |
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| 24. Kolos Nagy | Fernandez-Leiro R, Bhairosing-Kok D, Kunetsky V, Laffeber C, Winterwerp HH, Groothuizen F, Fish A, Lebbink JHG, Friedhoff P, Sixma TK, Lamers MH. The selection process of licensing a DNA mismatch for repair. Nat Struct Mol Biol. 2021 Apr;28(4):373-381. |
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| 25. Subash Swarna | Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E. Pre-termination Transcription Complex: Structure and Function. Mol Cell. 2021 Jan 21;81(2):281-292.e8. |
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| 26. Kyle Pekar | Briskin D, Wang PY, Bartel DP. The biochemical basis for the cooperative action of microRNAs. Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17764-17774. |
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| 27. Amber Siddiqui | Narain A, Bhandare P, Adhikari B, Backes S, Eilers M, Dölken L, Schlosser A, Erhard F, Baluapuri A, Wolf E. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol Cell. 2021 Aug 5;81(15):3110-3127.e14. |
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| 28. Harrison Cape | Pavlova NN, King B, Josselsohn RH, Violante S, Macera VL, Vardhana SA, Cross JR, Thompson CB. Translation in amino-acid-poor environments is limited by tRNAGln charging. Elife. 2020 Dec 8;9:e62307. |
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| 29. Ben Pliske | Wiktor J, Gynnå AH, Leroy P, Larsson J, Coceano G, Testa I, Elf J. RecA finds homologous DNA by reduced dimensionality search. Nature. 2021 Sep;597(7876):426-429. doi: 10.1038/s41586-021-03877-6. |
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| 30. Bradley Dromgoole | Zinoviev A, Ayupov RK, Abaeva IS, Hellen CUT, Pestova TV. Extraction of mRNA from Stalled Ribosomes by the Ski Complex. Mol Cell. 2020 Mar 19;77(6):1340-1349.e6. |
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| 31. Rebecca Peterson | Felletti M, Romilly C, Wagner EGH, Jonas K. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability. Elife. 2021 Sep 15;10:e71611. |
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| 32. Brynne Hindle | Kovač A, Miskey C, Menzel M, Grueso E, Gogol-Döring A, Ivics Z. RNA-guided retargeting of Sleeping Beauty transposition in human cells. Elife. 2020 Mar 6;9:e53868. |
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| 33. Hassan El-Bardini | Thakur M, Mohan D, Singh AK, Agarwal A, Gopal B, Muniyappa K. Novel insights into ATP-Stimulated Cleavage of branched DNA and RNA Substrates through Structure-Guided Studies of the Holliday Junction Resolvase RuvX. J Mol Biol. 2021 Jun 25;433(13):167014. |
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| 34. Nicole Petchey | Paul MW, Sidhu A, Liang Y, van Rossum-Fikkert SE, Odijk H, Zelensky AN, Kanaar R, Wyman C. Role of BRCA2 DNA-binding and C-terminal domain in its mobility and conformation in DNA repair. Elife. 2021 Jul 13;10:e67926. |
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| 35. Will Saad | Baeza-Centurion P, Miñana B, Valcárcel J, Lehner B. Mutations primarily alter the inclusion of alternatively spliced exons. Elife. 2020 Oct 28;9:e59959. |
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| 36. Daniel Latour | Bai R, Wan R, Yan C, Jia Q, Lei J, Shi Y. Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Science. 2021 Jan 8;371(6525):eabe8863. |
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| 37. Cela Patras | Giramma CN, DeFoer MB, Wang JD. The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase. J Mol Biol. 2021 Aug 10;433(19):167189. |
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| 38. Jasmine Sun | Shikha S, Schneider A. |
No more articles will be added. (updated Mon, January 17, 2022 2:04 PM )
Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY.
Structured elements drive extensive circular RNA translation.
Mol Cell. 2021 Oct 21;81(20):4300-4318.e13.
Jayaram DR, Frost S, Argov C, Liju VB, Anto NP, Muraleedharan A, Ben-Ari A, Sinay R, Smoly I, Novoplansky O, Isakov N, Toiber D, Keasar C, Elkabets M, Yeger-Lotem E, Livneh E.
Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs.
Proc Natl Acad Sci U S A. 2021 Oct 5;118(40):e2018899118.
Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M.
The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes.
Mol Cell. 2021 Oct 7;81(19):3992-4007.e10.
Gebert D, Neubert LK, Lloyd C, Gui J, Lehmann R, Teixeira FK.
Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation.
Mol Cell. 2021 Oct 7;81(19):3965-3978.e5
Vindu A, Shin BS, Choi K, Christenson ET, Ivanov IP, Cao C, Banerjee A, Dever TE.
Translational autoregulation of the S. cerevisiae high-affinity polyamine transporter Hol1.
Mol Cell. 2021 Oct 7;81(19):3904-3918.e6.
Ghodke PP, Guengerich FP.
DNA polymerases η and κ bypass N2-guanine-O6-alkylguanine DNA alkyltransferase cross-linked DNA-peptides.
J Biol Chem. 2021 Aug 28;297(4):101124. doi: 10.1016/j.jbc.2021.101124.
Žumer K, Maier KC, Farnung L, Jaeger MG, Rus P, Winter G, Cramer P.
Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo.
Mol Cell. 2021 Aug 5;81(15):3096-3109.e8.
Zhou Y, Xu X, Wei Y, Cheng Y, Guo Y, Khudyakov I, Liu F, He P, Song Z, Li Z, Gao Y, Ang EL, Zhao H, Zhang Y, Zhao S.
A widespread pathway for substitution of adenine by diaminopurine in phage genomes.
Science. 2021 Apr 30;372(6541):512-516.
Zahn KE, Jensen RB, Wood RD, Doublié S.
Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair.
Mol Cell. 2021 Apr 1;81(7):1534-1547.e4.
Yoo J, Lee D, Im H, Ji S, Oh S, Shin M, Park D, Lee G.
The mechanism of gap creation by a multifunctional nuclease during base excision repair.
Sci Adv. 2021 Jul 14;7(29):eabg0076.
Xu M, Axhemi A, Malgowska M, Chen Y, Leonard D, Srinivasan S, Jankowsky E, Taylor DJ.
Active and Passive Destabilization of G-Quadruplex DNA by the Telomere POT1-TPP1 Complex.
J Mol Biol. 2021 Apr 2;433(7):166846.
Workman RE, Pammi T, Nguyen BTK, Graeff LW, Smith E, Sebald SM, Stoltzfus MJ, Euler CW, Modell JW.
A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR-Cas expression.
Cell. 2021 Feb 4;184(3):675-688.e19.
Wilkinson ME, Fica SM, Galej WP, Nagai K.
Structural basis for conformational equilibrium of the catalytic spliceosome.
Mol Cell. 2021 Apr 1;81(7):1439-1452.e9.
Wang X, Dong Y, Zhao X, Li J, Lee J, Yan Z, Yang S, Wu W, Hou X, Liu G, Zhang Y, Song L, Cai G, Li Q, Ira G, Zhang X, Chen X.
Rtt105 promotes high-fidelity DNA replication and repair by regulating the single-stranded DNA-binding factor RPA.
Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):e2106393118.
Vrtis KB, Dewar JM, Chistol G, Wu RA, Graham TGW, Walter JC.
Single-strand DNA breaks cause replisome disassembly.
Mol Cell. 2021 Mar 18;81(6):1309-1318.e6.
Uzonyi A, Nir R, Shliefer O, Stern-Ginossar N, Antebi Y, Stelzer Y, Levanon EY, Schwartz S.
Deciphering the principles of the RNA editing code via large-scale systematic probing.
Mol Cell. 2021 Jun 3;81(11):2374-2387.e3.
Tomko EJ, Luyties O, Rimel JK, Tsai CL, Fuss JO, Fishburn J, Hahn S, Tsutakawa SE, Taatjes DJ, Galburt EA.
The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning.
J Mol Biol. 2021 Jul 9;433(14):166813.
Tilly BC, Chalkley GE, van der Knaap JA, Moshkin YM, Kan TW, Dekkers DH, Demmers JA, Verrijzer CP.
In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin.
Elife. 2021 Jul 27;10:e69424.
Thrun A, Garzia A, Kigoshi-Tansho Y, Patil PR, Umbaugh CS, Dallinger T, Liu J, Kreger S, Patrizi A, Cox GA, Tuschl T, Joazeiro CAP.
Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing.
Mol Cell. 2021 May 20;81(10):2112-2122.e7.
Takemata N, Bell SD.
Multi-scale architecture of archaeal chromosomes.
Mol Cell. 2021 Feb 4;81(3):473-487.e6.
Subramanian S, Gorday K, Marcus K, Orellana MR, Ren P, Luo XR, O'Donnell ME, Kuriyan J.
Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction.
Elife. 2021 Apr 13;10:e66181.
Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE.
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.
Proc Natl Acad Sci U S A. 2021 Jul 6;118(27):e2106388118.
Shiver AL, Osadnik H, Peters JM, Mooney RA, Wu PI, Henry KK, Braberg H, Krogan NJ, Hu JC, Landick R, Huang KC, Gross CA.
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.
Mol Cell. 2021 May 20;81(10):2201-2215.e9.
Schoof M, Boone M, Wang L, Lawrence R, Frost A, Walter P.
eIF2B conformation and assembly state regulate the integrated stress response.
Elife. 2021 Mar 10;10:e65703.
Anzelon TA, Chowdhury S, Hughes SM, Xiao Y, Lander GC, MacRae IJ.
Structural basis for piRNA targeting.
Nature. 2021 Sep 1. doi: 10.1038/s41586-021-03856-x.
He L, Zhao C, Zhang Q, Zinta G, Wang D, Lozano-Durán R, Zhu JK.
Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability.
Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2107320118.
Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F.
FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.
Mol Cell. 2021 Sep 2;81(17):3542-3559.e11.
Schep R, Brinkman EK, Leemans C, Vergara X, van der Weide RH, Morris B, van Schaik T, Manzo SG, Peric-Hupkes D, van den Berg J, Beijersbergen RL, Medema RH, van Steensel B.
Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.
Mol Cell. 2021 May 20;81(10):2216-2230.e10.
Santos-Rosa H, Millán-Zambrano G, Han N, Leonardi T, Klimontova M, Nasiscionyte S, Pandolfini L, Tzelepis K, Bartke T, Kouzarides T.
Methylation of histone H3 at lysine 37 by Set1 and Set2 prevents spurious DNA replication.
Mol Cell. 2021 Jul 1;81(13):2793-2807.e8.
Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD.
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator.
Elife. 2021 Apr 27;10:e68068.
Saldi T, Riemondy K, Erickson B, Bentley DL.
Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing.
Mol Cell. 2021 Apr 15;81(8):1789-1801.e5.
Rudnizky S, Khamis H, Ginosar Y, Goren E, Melamed P, Kaplan A.
Extended and dynamic linker histone-DNA Interactions control chromatosome compaction.
Mol Cell. 2021 Aug 19;81(16):3410-3421.e4.
Roy U, Kwon Y, Marie L, Symington L, Sung P, Lisby M, Greene EC.
The Rad51 paralog complex Rad55-Rad57 acts as a molecular chaperone during homologous recombination.
Mol Cell. 2021 Mar 4;81(5):1043-1057.e8.
Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF.
A high-resolution protein architecture of the budding yeast genome.
Nature. 2021 Apr;592(7853):309-314.
Richards J, Belasco JG.
Widespread Protection of RNA Cleavage Sites by a Riboswitch Aptamer that Folds as a Compact Obstacle to Scanning by RNase E.
Mol Cell. 2021 Jan 7;81(1):127-138.e4.
Ricci-Tam C, Ben-Zion I, Wang J, Palme J, Li A, Savir Y, Springer M.
Decoupling transcription factor expression and activity enables dimmer switch gene regulation.
Science. 2021 Apr 16;372(6539):292-295.
Reid DA, Reed PJ, Schlachetzki JCM, Nitulescu II, Chou G, Tsui EC, Jones JR, Chandran S, Lu AT, McClain CA, Ooi JH, Wang TW, Lana AJ, Linker SB, Ricciardulli AS, Lau S, Schafer ST, Horvath S, Dixon JR, Hah N, Glass CK, Gage FH.
Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons.
Science. 2021 Apr 2;372(6537):91-94.
Regadas I, Dahlberg O, Vaid R, Ho O, Belikov S, Dixit G, Deindl S, Wen J, Mannervik M.
A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation.
Mol Cell. 2021 Apr 15;81(8):1766-1780.e10.
Raper AT, Maxwell BA, Suo Z.
Dynamic Processing of a Common Oxidative DNA Lesion by the First Two Enzymes of the Base Excision Repair Pathway.
J Mol Biol. 2021 Mar 5;433(5):166811.
Puri N, Fernandez AJ, O'Shea Murray VL, McMillan S, Keck JL, Berger JM.
The molecular coupling between substrate recognition and ATP turnover in a AAA+ hexameric helicase loader.
Elife. 2021 May 26;10:e64232.
Pundir S, Ge X, Sanyal S.
GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors.
J Biol Chem. 2021 Jan-Jun;296:100681.
Prieler S, Chen D, Huang L, Mayrhofer E, Zsótér S, Vesely M, Mbogning J, Klein F.
Spo11 generates gaps through concerted cuts at sites of topological stress.
Nature. 2021 Jun;594(7864):577-582.
Portman JR, Brouwer GM, Bollins J, Savery NJ, Strick TR.
Cotranscriptional R-loop formation by Mfd involves topological partitioning of DNA.
Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2019630118.
Plaskon DM, Henderson KL, Felth LC, Molzahn CM, Evensen C, Dyke S, Shkel IA, Record MT Jr.
Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise.
Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):e2021941118.
Pezo V, Jaziri F, Bourguignon PY, Louis D, Jacobs-Sera D, Rozenski J, Pochet S, Herdewijn P, Hatfull GF, Kaminski PA, Marliere P.
Noncanonical DNA polymerization by aminoadenine-based siphoviruses.
Science. 2021 Apr 30;372(6541):520-524.
Petracovici A, Bonasio R.
Distinct PRC2 subunits regulate maintenance and establishment of Polycomb repression during differentiation.
Mol Cell. 2021 Jun 17;81(12):2625-2639.e5.
Petela NJ, Gonzalez Llamazares A, Dixon S, Hu B, Lee BG, Metson J, Seo H, Ferrer-Harding A, Voulgaris M, Gligoris T, Collier J, Oh BH, Löwe J, Nasmyth KA.
Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes.
Elife. 2021 Jul 14;10:e67268.
Pendlebury DF, Zhang J, Agrawal R, Shibuya H, Nandakumar J.
Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites.
Nat Struct Mol Biol. 2021 Aug;28(8):671-680.
Pauszek RF 3rd, Lamichhane R, Rajkarnikar Singh A, Millar DP.
Single-molecule view of coordination in a multi-functional DNA polymerase.
Elife. 2021 Mar 11;10:e62046.
Park S, Prévost K, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Massé E, Fei J.
Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells.
Elife. 2021 Feb 22;10:e64207.
Pandey M, Bansal S, Bar S, Yadav AK, Sokol NS, Tennessen JM, Kapahi P, Chawla G.
miR-125-chinmo pathway regulates dietary restriction-dependent enhancement of lifespan in Drosophila.
Elife. 2021 Jun 8;10:e62621.
Panday A, Willis NA, Elango R, Menghi F, Duffey EE, Liu ET, Scully R.
FANCM regulates repair pathway choice at stalled replication forks.
Mol Cell. 2021 Jun 3;81(11):2428-2444.e6.
Mylonas C, Lee C, Auld AL, Cisse II, Boyer LA.
A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation.
Nat Struct Mol Biol. 2021 May;28(5):435-442.
Mendel M, Delaney K, Pandey RR, Chen KM, Wenda JM, Vågbø CB, Steiner FA, Homolka D, Pillai RS.
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing.
Cell. 2021 Jun 10;184(12):3125-3142.e25.
Mandell ZF, Oshiro RT, Yakhnin AV, Vishwakarma R, Kashlev M, Kearns DB, Babitzke P.
NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA.
Elife. 2021 Apr 9;10:e61880.
Małecka EM, Woodson SA.
Stepwise sRNA targeting of structured bacterial mRNAs leads to abortive annealing.
Mol Cell. 2021 May 6;81(9):1988-1999.e4.
Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, Bzikadze AV, Kremitzki M, Graves-Lindsay TA, Jain C, Hoekzema K, Murali SC, Munson KM, Baker C, Sorensen M, Lewis AM, Surti U, Gerton JL, Larionov V, Ventura M, Miga KH, Phillippy AM, Eichler EE.
The structure, function and evolution of a complete human chromosome 8.
Nature. 2021 May;593(7857):101-107.
Loats AE, Carrera S, Fleming AF, Roberts ARE, Sherrard A, Toska E, Moorhouse AJ, Medler KF, Roberts SGE.
Cholesterol is required for transcriptional repression by BASP1.
Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2101671118.
Lai YC, Liu Z, Chen IA.
Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.
Proc Natl Acad Sci U S A. 2021 May 25;118(21):e2025054118.
Kühnlein A, Lanzmich SA, Braun D.
tRNA sequences can assemble into a replicator.
Elife. 2021 Mar 2;10:e63431.
Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, Ren B.
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
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Elife. 2020 Apr 27;9:e55336. (see commentary)
Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN
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