Monthly Letter

1. Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing.
Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, Yu EA, Schenk EL, Tan W, Zee A, Tan M, Gui P, Lea T, Wu W, Urisman A, Jones K, Sit R, Kolli PK, Seeley E, Gesthalter Y, Le DD, Yamauchi KA, Naeger DM, Bandyopadhyay S, Shah K, Cech L, Thomas NJ, Gupta A, Gonzalez M, Do H, Tan L, Bacaltos B, Gomez-Sjoberg R, Gubens M, Jahan T, Kratz JR, Jablons D, Neff N, Doebele RC, Weissman J, Blakely CM, Darmanis S, Bivona TG. Cell. 2020 Sep 3;182(5):1232-1251.e22. doi: 10.1016/j.cell.2020.07.017. Epub 2020 Aug 20.

2. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE; Deutsche COVID-19 OMICS Initiative (DeCOI). Cell. 2020 Sep 17;182(6):1419-1440.e23. doi: 10.1016/j.cell.2020.08.001. Epub 2020 Aug 5.

3. The Human and Mouse Enteric Nervous System at Single-Cell Resolution.
Drokhlyansky E, Smillie CS, Van Wittenberghe N, Ericsson M, Griffin GK, Eraslan G, Dionne D, Cuoco MS, Goder-Reiser MN, Sharova T, Kuksenko O, Aguirre AJ, Boland GM, Graham D, Rozenblatt-Rosen O, Xavier RJ, Regev A. Cell. 2020 Sep 17;182(6):1606-1622.e23. doi: 10.1016/j.cell.2020.08.003. Epub 2020 Sep 3.

4. A decade of advances in transposon-insertion sequencing.
Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T. Nat Rev Genet. 2020 Sep;21(9):526-540. doi: 10.1038/s41576-020-0244-x. Epub 2020 Jun 12.

5. Anti-human TREM2 induces microglia proliferation and reduces pathology in an Alzheimer's disease model.
Wang S, Mustafa M, Yuede CM, Salazar SV, Kong P, Long H, Ward M, Siddiqui O, Paul R, Gilfillan S, Ibrahim A, Rhinn H, Tassi I, Rosenthal A, Schwabe T, Colonna M. J Exp Med. 2020 Sep 7;217(9):e20200785. doi: 10.1084/jem.20200785.

6. Acute social isolation alters neurogenomic state in songbird forebrain.
George JM, Bell ZW, Condliffe D, Dohrer K, Abaurrea T, Spencer K, Leitão A, Gahr M, Hurd PJ, Clayton DF. Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23311-23316. doi: 10.1073/pnas.1820841116. Epub 2019 Jul 22.

7. Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation.
Lee H, Fenster RJ, Pineda SS, Gibbs WS, Mohammadi S, Davila-Velderrain J, Garcia FJ, Therrien M, Novis HS, Gao F, Wilkinson H, Vogt T, Kellis M, LaVoie MJ, Heiman M. Neuron. 2020 Sep 9;107(5):891-908.e8. doi: 10.1016/j.neuron.2020.06.021. Epub 2020 Jul 17.

8. Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing.
Abbasi S, Sinha S, Labit E, Rosin NL, Yoon G, Rahmani W, Jaffer A, Sharma N, Hagner A, Shah P, Arora R, Yoon J, Islam A, Uchida A, Chang CK, Stratton JA, Scott RW, Rossi FMV, Underhill TM, Biernaskie J. Cell Stem Cell. 2020 Sep 3;27(3):396-412.e6. doi: 10.1016/j.stem.2020.07.008. Epub 2020 Aug 4.

9. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.
Furlan M, Galeota E, Gaudio ND, Dassi E, Caselle M, de Pretis S, Pelizzola M. Genome Res. 2020 Sep 25. doi: 10.1101/gr.260984.120. Online ahead of print.

10. Targeting tumor-associated macrophages and granulocytic myeloid-derived suppressor cells augments PD-1 blockade in cholangiocarcinoma.
Loeuillard E, Yang J, Buckarma E, Wang J, Liu Y, Conboy C, Pavelko KD, Li Y, O'Brien D, Wang C, Graham RP, Smoot RL, Dong H, Ilyas S. J Clin Invest. 2020 Sep 14:137110. doi: 10.1172/JCI137110. Online ahead of print.

11. scIGANs: single-cell RNA-seq imputation using generative adversarial networks.
Xu Y, Zhang Z, You L, Liu J, Fan Z, Zhou X. Nucleic Acids Res. 2020 Sep 4;48(15):e85. doi: 10.1093/nar/gkaa506.

12. The m(6)A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor.
Xiao Y, Thakkar KN, Zhao H, Broughton J, Li Y, Seoane JA, Diep AN, Metzner TJ, von Eyben R, Dill DL, Brooks JD, Curtis C, Leppert JT, Ye J, Peehl DM, Giaccia AJ, Sinha S, Rankin EB. Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21441-21449. doi: 10.1073/pnas.2000516117. Epub 2020 Aug 19.

13. A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis.
Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ Jr, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D; University of California, San Francisco MS-EPIC Team, Guo CY, Green AJ, Bove RM, DeRisi JL, Gelfand JM, Cree BAC, Zamvil SS, Baranzini SE, Hauser SL, Wilson MR. Proc Natl Acad Sci U S A. 2020 Sep 15;117(37):22932-22943. doi: 10.1073/pnas.2008523117. Epub 2020 Aug 28.

14. Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction.
Huang N, Fan X, Zaleta-Rivera K, Nguyen TC, Zhou J, Luo Y, Gao J, Fang RH, Yan Z, Chen ZB, Zhang L, Zhong S. Genome Biol. 2020 Sep 10;21(1):225. doi: 10.1186/s13059-020-02145-6.

15. Immobilization after injury alters extracellular matrix and stem cell fate.
Huber AK, Patel N, Pagani CA, Marini S, Padmanabhan KR, Matera DL, Said M, Hwang C, Hsu GC, Poli AA, Strong AL, Visser ND, Greenstein JA, Nelson R, Li S, Longaker MT, Tang Y, Weiss SJ, Baker BM, James AW, Levi B. J Clin Invest. 2020 Sep 21:136142. doi: 10.1172/JCI136142. Online ahead of print.

16. Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data.
Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Stein S, Xie Z, Park E, Wu YN, Xing Y. Am J Hum Genet. 2020 Sep 3;107(3):461-472. doi: 10.1016/j.ajhg.2020.07.005. Epub 2020 Aug 10.

17. Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications.
Kimura S, Dedon PC, Waldor MK. Nat Chem Biol. 2020 Sep;16(9):964-972. doi: 10.1038/s41589-020-0558-1. Epub 2020 Jun 8.

18. Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila.
Cho B, Yoon SH, Lee D, Koranteng F, Tattikota SG, Cha N, Shin M, Do H, Hu Y, Oh SY, Lee D, Vipin Menon A, Moon SJ, Perrimon N, Nam JW, Shim J. Nat Commun. 2020 Sep 8;11(1):4483. doi: 10.1038/s41467-020-18135-y.

19. Single-Cell RNA-seq Analysis Reveals a Crucial Role for Collagen Triple Helix Repeat Containing 1 (CTHRC1) Cardiac Fibroblasts after Myocardial Infarction.
Ruiz-Villalba A, Romero JP, Hernandez SC, Vilas-Zornoza A, Fortelny N, Castro-Labrador L, San Martin-Uriz P, Lorenzo-Vivas E, García-Olloqui P, Palacios M, Gavira JJ, Bastarrika G, Janssens S, Wu M, Iglesias E, Abizanda G, Martinez de Morentin X, Lasaga M, Planell N, Bock C, Alignani D, Medal G, Pelacho B, Prudovsky I, Jin YR, Ryzhov S, Yin H, Gomez-Cabrero D, Lindner V, Lara-Astiaso D, Prósper F. Circulation. 2020 Sep 25. doi: 10.1161/CIRCULATIONAHA.119.044557. Online ahead of print.

20. EZH2 regulates pancreatic cancer subtype identity and tumor progression via transcriptional repression of GATA6.
Patil S, Steuber B, Kopp W, Kari V, Urbach L, Wang X, Küffer S, Bohnenberger H, Spyropoulou D, Zhang Z, Versemann L, Bösherz MS, Brunner M, Gaedcke J, Ströbel P, Zhang JS, Neesse A, Ellenrieder V, Singh SK, Johnsen SA, Hessmann E. Cancer Res. 2020 Sep 9:canres.0672.2020. doi: 10.1158/0008-5472.CAN-20-0672. Online ahead of print.

21. A comprehensive rat transcriptome built from large scale RNA-seq-based annotation.
Ji X, Li P, Fuscoe JC, Chen G, Xiao W, Shi L, Ning B, Liu Z, Hong H, Wu J, Liu J, Guo L, Kreil DP, Łabaj PP, Zhong L, Bao W, Huang Y, He J, Zhao Y, Tong W, Shi T. Nucleic Acids Res. 2020 Sep 4;48(15):8320-8331. doi: 10.1093/nar/gkaa638.

22. Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.
Hör J, Di Giorgio S, Gerovac M, Venturini E, Förstner KU, Vogel J. Nucleic Acids Res. 2020 Sep 18;48(16):9301-9319. doi: 10.1093/nar/gkaa676.

23. EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data.
Teschendorff AE, Zhu T, Breeze CE, Beck S. Genome Biol. 2020 Sep 4;21(1):221. doi: 10.1186/s13059-020-02126-9.

24. A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors.
Singh M, Bansal V, Feschotte C. Cell Rep. 2020 Sep 22;32(12):108175. doi: 10.1016/j.celrep.2020.108175. Epub 2020 Sep 3.

25. The Tug1 lncRNA locus is essential for male fertility.
Lewandowski JP, Dumbović G, Watson AR, Hwang T, Jacobs-Palmer E, Chang N, Much C, Turner KM, Kirby C, Rubinstein ND, Groff AF, Liapis SC, Gerhardinger C, Bester A, Pandolfi PP, Clohessy JG, Hoekstra HE, Sauvageau M, Rinn JL. Genome Biol. 2020 Sep 7;21(1):237. doi: 10.1186/s13059-020-02081-5.

26. Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma.
Grasso CS, Tsoi J, Onyshchenko M, Abril-Rodriguez G, Ross-Macdonald P, Wind-Rotolo M, Champhekar A, Medina E, Torrejon DY, Shin DS, Tran P, Kim YJ, Puig-Saus C, Campbell K, Vega-Crespo A, Quist M, Martignier C, Luke JJ, Wolchok JD, Johnson DB, Chmielowski B, Hodi FS, Bhatia S, Sharfman W, Urba WJ, Slingluff CL Jr, Diab A, Haanen JBAG, Algarra SM, Pardoll DM, Anagnostou V, Topalian SL, Velculescu VE, Speiser DE, Kalbasi A, Ribas A. Cancer Cell. 2020 Sep 8:S1535-6108(20)30416-5. doi: 10.1016/j.ccell.2020.08.005. Online ahead of print.

27. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.
Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagić I, Berger B. Nat Commun. 2020 Sep 16;11(1):4662. doi: 10.1038/s41467-020-18320-z.

28. A mouse tissue atlas of small noncoding RNA.
Isakova A, Fehlmann T, Keller A, Quake SR. Proc Natl Acad Sci U S A. 2020 Sep 25:202002277. doi: 10.1073/pnas.2002277117. Online ahead of print.

29. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis.
Lemeille S, Paschaki M, Baas D, Morlé L, Duteyrat JL, Ait-Lounis A, Barras E, Soulavie F, Jerber J, Thomas J, Zhang Y, Holtzman MJ, Kistler WS, Reith W, Durand B. Nucleic Acids Res. 2020 Sep 18;48(16):9019-9036. doi: 10.1093/nar/gkaa625.

30. pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools.
Germain PL, Sonrel A, Robinson MD. Genome Biol. 2020 Sep 1;21(1):227. doi: 10.1186/s13059-020-02136-7.

31. A mega-analysis of expression quantitative trait loci in retinal tissue.
Strunz T, Kiel C, Grassmann F, Ratnapriya R, Kwicklis M, Karlstetter M, Fauser S, Arend N, Swaroop A, Langmann T, Wolf A, Weber BHF. PLoS Genet. 2020 Sep 1;16(9):e1008934. doi: 10.1371/journal.pgen.1008934. eCollection 2020 Sep.

32. Robust partitioning of microRNA targets from downstream regulatory changes.
Patel RK, West JD, Jiang Y, Fogarty EA, Grimson A. Nucleic Acids Res. 2020 Sep 25;48(17):9724-9746. doi: 10.1093/nar/gkaa687.

33. Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi.
Li SJ, Zhang X, Lukeš J, Li BQ, Wang JF, Qu LH, Hide G, Lai DH, Lun ZR. Nucleic Acids Res. 2020 Sep 25;48(17):9747-9761. doi: 10.1093/nar/gkaa700.

34. RUNX1 and CBFβ-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development.
Zhen T, Cao Y, Ren G, Zhao L, Hyde RK, Lopez G, Feng D, Alemu L, Zhao K, Liu PP. Blood. 2020 Sep 14:blood.2020007747. doi: 10.1182/blood.2020007747. Online ahead of print.

35. NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome.
Yakhnin AV, FitzGerald PC, McIntosh C, Yakhnin H, Kireeva M, Turek-Herman J, Mandell ZF, Kashlev M, Babitzke P. Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21628-21636. doi: 10.1073/pnas.2006873117. Epub 2020 Aug 17.

36. Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population.
Milner JJ, Nguyen H, Omilusik K, Reina-Campos M, Tsai M, Toma C, Delpoux A, Boland BS, Hedrick SM, Chang JT, Goldrath AW. Proc Natl Acad Sci U S A. 2020 Sep 25:202008571. doi: 10.1073/pnas.2008571117. Online ahead of print.

37. The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor.
Turner-Evans DB, Jensen KT, Ali S, Paterson T, Sheridan A, Ray RP, Wolff T, Lauritzen JS, Rubin GM, Bock DD, Jayaraman V. Neuron. 2020 Sep 1:S0896-6273(20)30613-9. doi: 10.1016/j.neuron.2020.08.006. Online ahead of print.

38. Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.
Heavner WE, Ji S, Notwell JH, Dyer ES, Tseng AM, Birgmeier J, Yoo B, Bejerano G, McConnell SK. Proc Natl Acad Sci U S A. 2020 Sep 18:202008013. doi: 10.1073/pnas.2008013117. Online ahead of print.

39. XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing.
Winkelman JT, Pukhrambam C, Vvedenskaya IO, Zhang Y, Taylor DM, Shah P, Ebright RH, Nickels BE. Mol Cell. 2020 Sep 3;79(5):797-811.e8. doi: 10.1016/j.molcel.2020.07.006. Epub 2020 Aug 3.

40. Single-Cell RNA-seq Unveils Unique Transcriptomic Signatures of Organ-Specific Endothelial Cells.
Paik DT, Tian L, Williams IM, Rhee S, Zhang H, Liu C, Mishra R, Wu SM, Red-Horse K, Wu JC. Circulation. 2020 Sep 15. doi: 10.1161/CIRCULATIONAHA.119.041433. Online ahead of print.

41. Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.
Tavares CDJ, Aigner S, Sharabi K, Sathe S, Mutlu B, Yeo GW, Puigserver P. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22204-22213. doi: 10.1073/pnas.2000643117. Epub 2020 Aug 26.

42. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human.
Pan H, Xue C, Auerbach BJ, Fan J, Bashore AC, Cui J, Yang DY, Trignano SB, Liu W, Shi J, Ihuegbu CO, Bush EC, Worley J, Vlahos L, Laise P, Solomon RA, Connolly ES, Califano A, Sims PA, Zhang H, Li M, Reilly MP. Circulation. 2020 Sep 23. doi: 10.1161/CIRCULATIONAHA.120.048378. Online ahead of print.

43. Unravelling the genetic basis for the rapid diversification of male genitalia between Drosophila species.
Hagen JFD, Mendes CC, Booth SR, Jimenez JF, Tanaka KM, Franke FA, Baudouin-Gonzalez L, Ridgway AM, Arif S, Nunes MDS, McGregor AP. Mol Biol Evol. 2020 Sep 15:msaa232. doi: 10.1093/molbev/msaa232. Online ahead of print.

44. Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling.
Yao J, Wu DC, Nottingham RM, Lambowitz AM. Elife. 2020 Sep 2;9:e60743. doi: 10.7554/eLife.60743.

45. piRNA-30473 contributes to tumorigenesis and poor prognosis by regulating m6A RNA methylation in DLBCL.
Han H, Fan G, Song S, Jiang Y, Qian C, Zhang W, Su Q, Xue X, Zhuang W, Li B. Blood. 2020 Sep 23:blood.2019003764. doi: 10.1182/blood.2019003764. Online ahead of print.

46. Phosphorylation control of p53 DNA binding cooperativity balances tumorigenesis and aging.
Timofeev O, Koch L, Niederau C, Tscherne A, Schneikert J, Klimovich M, Elmshäuser S, Zeitlinger M, Mernberger M, Nist A, Osterburg C, Dötsch V, Mouse Clinic Consortium G, Hrabé de Angelis M, Stiewe T. Cancer Res. 2020 Sep 1:canres.2002.2020. doi: 10.1158/0008-5472.CAN-20-2002. Online ahead of print.

47. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.
Liu P, Soukup AA, Bresnick EH, Dewey CN, Keles S. Genome Res. 2020 Sep 21:gr.252445.119. doi: 10.1101/gr.252445.119. Online ahead of print.

48. Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring.
Frost HR. Nucleic Acids Res. 2020 Sep 18;48(16):e94. doi: 10.1093/nar/gkaa582.

49. Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis.
Yang J, McGovern A, Martin P, Duffus K, Ge X, Zarrineh P, Morris AP, Adamson A, Fraser P, Rattray M, Eyre S. Nat Commun. 2020 Sep 2;11(1):4402. doi: 10.1038/s41467-020-18180-7.

50. Comprehensive multi-omics analysis uncovers a group of TGF-β-regulated genes among lncRNA EPR direct transcriptional targets.
Zapparoli E, Briata P, Rossi M, Brondolo L, Bucci G, Gherzi R. Nucleic Acids Res. 2020 Sep 18;48(16):9053-9066. doi: 10.1093/nar/gkaa628.

51. Human norovirus exhibits strain-specific sensitivity to host interferon pathways in human intestinal enteroids.
Lin SC, Qu L, Ettayebi K, Crawford SE, Blutt SE, Robertson MJ, Zeng XL, Tenge VR, Ayyar BV, Karandikar UC, Yu X, Coarfa C, Atmar RL, Ramani S, Estes MK. Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23782-23793. doi: 10.1073/pnas.2010834117. Epub 2020 Sep 9.

52. Sterile Spikelets Contribute to Yield in Sorghum and Related Grasses.
AuBuchon-Elder T, Coneva V, Goad DM, Jenkins LM, Yu Y, Allen DK, Kellogg EA. Plant Cell. 2020 Sep 1:tpc.00424.2020. doi: 10.1105/tpc.20.00424. Online ahead of print.

53. Different lineage contexts direct common pro-neural factors to specify distinct retinal cell subtypes.
Wang M, Du L, Lee AC, Li Y, Qin H, He J. J Cell Biol. 2020 Sep 7;219(9):e202003026. doi: 10.1083/jcb.202003026.

54. Anti-inflammatory functions of the glucocorticoid receptor require DNA binding.
Escoter-Torres L, Greulich F, Quagliarini F, Wierer M, Uhlenhaut NH. Nucleic Acids Res. 2020 Sep 4;48(15):8393-8407. doi: 10.1093/nar/gkaa565.

55. Transcriptome-wide stability analysis uncovers LARP4-mediated NFκB1 mRNA stabilization during T cell activation.
Tian Y, Zeng Z, Li X, Wang Y, Chen R, Mattijssen S, Gaidamakov S, Wu Y, Maraia RJ, Peng W, Zhu J. Nucleic Acids Res. 2020 Sep 4;48(15):8724-8739. doi: 10.1093/nar/gkaa643.

56. Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems.
Carullo NVN, Phillips Iii RA, Simon RC, Soto SAR, Hinds JE, Salisbury AJ, Revanna JS, Bunner KD, Ianov L, Sultan FA, Savell KE, Gersbach CA, Day JJ. Nucleic Acids Res. 2020 Sep 25;48(17):9550-9570. doi: 10.1093/nar/gkaa671.

57. RNA G-quadruplex structures exist and function in vivo in plants.
Yang X, Cheema J, Zhang Y, Deng H, Duncan S, Umar MI, Zhao J, Liu Q, Cao X, Kwok CK, Ding Y. Genome Biol. 2020 Sep 1;21(1):226. doi: 10.1186/s13059-020-02142-9.

58. 3D model of harlequin ichthyosis reveals inflammatory therapeutic targets.
Enjalbert F, Dewan P, Caley MP, Jones EM, Morse MA, Kelsell DP, Enright AJ, O'Toole EA. J Clin Invest. 2020 Sep 1;130(9):4798-4810. doi: 10.1172/JCI132987.

59. Chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing.
Liu J, Li C, Wang J, Xu D, Wang H, Wang T, Li L, Li H, Nan P, Zhang J, Wang Y, Huang C, Chen D, Zhang Y, Wen T, Zhan Q, Ma F, Qian H. Nat Commun. 2020 Sep 8;11(1):4455. doi: 10.1038/s41467-020-18259-1.

60. Alignment and mapping methodology influence transcript abundance estimation.
Srivastava A, Malik L, Sarkar H, Zakeri M, Almodaresi F, Soneson C, Love MI, Kingsford C, Patro R. Genome Biol. 2020 Sep 7;21(1):239. doi: 10.1186/s13059-020-02151-8.

61. Exhausted CD8(+) T cells exhibit low and strongly inhibited TCR signaling during chronic LCMV infection.
Sandu I, Cerletti D, Claassen M, Oxenius A. Nat Commun. 2020 Sep 8;11(1):4454. doi: 10.1038/s41467-020-18256-4.

62. Dioecy is associated with high genetic diversity and adaptation rates in the plant genus Silene.
Muyle A, Martin H, Zemp N, Mollion M, Gallina S, Tavares R, Silva A, Bataillon T, Widmer A, Glémin S, Touzet P, Marais GAB. Mol Biol Evol. 2020 Sep 14:msaa229. doi: 10.1093/molbev/msaa229. Online ahead of print.

63. Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs.
Park A, Oh S, Jung KL, Choi UY, Lee HR, Rosenfeld MG, Jung JU. Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21618-21627. doi: 10.1073/pnas.1922216117. Epub 2020 Aug 18.

64. Obesity-Linked PPARγ S273 Phosphorylation Promotes Insulin Resistance through Growth Differentiation Factor 3.
Hall JA, Ramachandran D, Roh HC, DiSpirito JR, Belchior T, Zushin PH, Palmer C, Hong S, Mina AI, Liu B, Deng Z, Aryal P, Jacobs C, Tenen D, Brown CW, Charles JF, Shulman GI, Kahn BB, Tsai LTY, Rosen ED, Spiegelman BM, Banks AS. Cell Metab. 2020 Sep 11:S1550-4131(20)30476-9. doi: 10.1016/j.cmet.2020.08.016. Online ahead of print.

65. Genetic mapping of etiologic brain cell types for obesity.
Timshel PN, Thompson JJ, Pers TH. Elife. 2020 Sep 21;9:e55851. doi: 10.7554/eLife.55851.

66. Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution.
Fukushima K, Pollock DD. Nat Commun. 2020 Sep 8;11(1):4459. doi: 10.1038/s41467-020-18090-8.

67. Malic Enzyme Couples Mitochondria with Aerobic Glycolysis in Osteoblasts.
Lee WC, Ji X, Nissim I, Long F. Cell Rep. 2020 Sep 8;32(10):108108. doi: 10.1016/j.celrep.2020.108108.

68. Astrocytic phagocytosis is a compensatory mechanism for microglial dysfunction.
Konishi H, Okamoto T, Hara Y, Komine O, Tamada H, Maeda M, Osako F, Kobayashi M, Nishiyama A, Kataoka Y, Takai T, Udagawa N, Jung S, Ozato K, Tamura T, Tsuda M, Yamanaka K, Ogi T, Sato K, Kiyama H. EMBO J. 2020 Sep 22:e104464. doi: 10.15252/embj.2020104464. Online ahead of print.

69. Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo.
Yang M, Woolfenden HC, Zhang Y, Fang X, Liu Q, Vigh ML, Cheema J, Yang X, Norris M, Yu S, Carbonell A, Brodersen P, Wang J, Ding Y. Nucleic Acids Res. 2020 Sep 4;48(15):8767-8781. doi: 10.1093/nar/gkaa577.