Monthly Letter

1. Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.
Zhang L, Li Z, Skrzypczynska KM, Fang Q, Zhang W, O'Brien SA, He Y, Wang L, Zhang Q, Kim A, Gao R, Orf J, Wang T, Sawant D, Kang J, Bhatt D, Lu D, Li CM, Rapaport AS, Perez K, Ye Y, Wang S, Hu X, Ren X, Ouyang W, Shen Z, Egen JG, Zhang Z, Yu X. Cell. 2020 Apr 16;181(2):442-459.e29. doi: 10.1016/j.cell.2020.03.048.

2. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.
Roth TL, Li PJ, Blaeschke F, Nies JF, Apathy R, Mowery C, Yu R, Nguyen MLT, Lee Y, Truong A, Hiatt J, Wu D, Nguyen DN, Goodman D, Bluestone JA, Ye CJ, Roybal K, Shifrut E, Marson A. Cell. 2020 Apr 15:S0092-8674(20)30332-9. doi: 10.1016/j.cell.2020.03.039.

3. Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis.
Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Carmeliet P. Cell Metab. 2020 Apr 7;31(4):862-877.e14. doi: 10.1016/j.cmet.2020.03.009.

4. A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level.
Mair F, Erickson JR, Voillet V, Simoni Y, Bi T, Tyznik AJ, Martin J, Gottardo R, Newell EW, Prlic M. Cell Rep. 2020 Apr 7;31(1):107499. doi: 10.1016/j.celrep.2020.03.063.

5. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis.
Hsiao CJ, Tung P, Blischak JD, Burnett JE, Barr KA, Dey KK, Stephens M, Gilad Y. Genome Res. 2020 Apr;30(4):611-621. doi: 10.1101/gr.247759.118. Epub 2020 Apr 20.

6. Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing.
Cole C, Byrne A, Adams M, Volden R, Vollmers C. Genome Res. 2020 Apr;30(4):589-601. doi: 10.1101/gr.257188.119. Epub 2020 Apr 20.

7. Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity.
Wolbert J, Li X, Heming M, Mausberg AK, Akkermann D, Frydrychowicz C, Fledrich R, Groeneweg L, Schulz C, Stettner M, Alonso Gonzalez N, Wiendl H, Stassart R, Meyer Zu Hörste G. Proc Natl Acad Sci U S A. 2020 Apr 15:201912139. doi: 10.1073/pnas.1912139117.

8. Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA.
Lee SC, Ernst E, Berube B, Borges F, Parent JS, Ledon P, Schorn A, Martienssen RA. Genome Res. 2020 Apr;30(4):576-588. doi: 10.1101/gr.259044.119. Epub 2020 Apr 17.

9. MorphoSeq: Full Single-Cell Transcriptome Dynamics Up to Gastrulation in a Chordate.
Sladitschek HL, Fiuza UM, Pavlinic D, Benes V, Hufnagel L, Neveu PA. Cell. 2020 Apr 13:S0092-8674(20)30348-2. doi: 10.1016/j.cell.2020.03.055.

10. Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors.
Kakebeen AD, Chitsazan AD, Williams MC, Saunders LM, Wills AE. Elife. 2020 Apr 27;9:e52648. doi: 10.7554/eLife.52648.

11. EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes.
Wu D, Dean J. Nucleic Acids Res. 2020 Apr 20:gkaa249. doi: 10.1093/nar/gkaa249.

12. Mechanism of Eccentric Cardiomyocyte Hypertrophy Secondary to Severe Mitral Regurgitation.
Li S, Nguyen NUN, Xiao F, Menendez-Montes I, Nakada Y, Tan WLW, Anene-Nzelu CG, Foo R, Thet S, Cardoso AC, Wang P, Elhelaly WM, Lam NT, Pereira AHM, Hill JA, Sadek HA. Circulation. 2020 Apr 10. doi: 10.1161/CIRCULATIONAHA.119.043939.

13. AntimiR-21 Prevents Myocardial Dysfunction in a Pig Model of Ischemia/Reperfusion Injury.
Hinkel R, Ramanujam D, Kaczmarek V, Howe A, Klett K, Beck C, Dueck A, Thum T, Laugwitz KL, Maegdefessel L, Weber C, Kupatt C, Engelhardt S. J Am Coll Cardiol. 2020 Apr 21;75(15):1788-1800. doi: 10.1016/j.jacc.2020.02.041.

14. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu XD, Graveley BR, Yeo GW. Genome Biol. 2020 Apr 6;21(1):90. doi: 10.1186/s13059-020-01982-9.

15. An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem.
Ram H, Sahadevan S, Gale N, Caggiano MP, Yu X, Ohno C, Heisler MG. PLoS Genet. 2020 Apr 15;16(4):e1008661. doi: 10.1371/journal.pgen.1008661.

16. Consistent RNA sequencing contamination in GTEx and other data sets.
Nieuwenhuis TO, Yang SY, Verma RX, Pillalamarri V, Arking DE, Rosenberg AZ, McCall MN, Halushka MK. Nat Commun. 2020 Apr 22;11(1):1933. doi: 10.1038/s41467-020-15821-9.

17. Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ.
Wu T, Lyu R, You Q, He C. Nat Methods. 2020 Apr 6. doi: 10.1038/s41592-020-0797-9.

18. Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation.
Jia L, Wang Y, Wang C, Du Z, Zhang S, Wen X, Zhou L, Li H, Chen H, Li D, Zhang S, Li W, Xu W, Hoffman AR, Cui J, Hu JF. Nucleic Acids Res. 2020 Apr 17;48(7):3935-3948. doi: 10.1093/nar/gkaa097.

19. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.
Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Vandekerckhove B, Leclercq G, Regev A, Van Vlierberghe P, Guilliams M, Teichmann SA, Saeys Y, Taghon T. Immunity. 2020 Apr 13:S1074-7613(20)30132-1. doi: 10.1016/j.immuni.2020.03.019.

20. Bilateral murine tumor models for characterizing the response to immune checkpoint blockade.
Zemek RM, Fear VS, Forbes C, de Jong E, Casey TH, Boon L, Lassmann T, Bosco A, Millward MJ, Nowak AK, Lake RA, Lesterhuis WJ. Nat Protoc. 2020 Apr 1. doi: 10.1038/s41596-020-0299-3.

21. Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells.
Ma Q, Yang F, Mackintosh C, Jayani RS, Oh S, Jin C, Nair SJ, Merkurjev D, Ma W, Allen S, Wang D, Almenar-Queralt A, Garcia-Bassets I. Cell Rep. 2020 Apr 21;31(3):107532. doi: 10.1016/j.celrep.2020.107532.

22. Prediction of condition-specific regulatory genes using machine learning.
Song Q, Lee J, Akter S, Rogers M, Grene R, Li S. Nucleic Acids Res. 2020 Apr 24:gkaa264. doi: 10.1093/nar/gkaa264.

23. Publisher Correction: Single-cell RNA-seq analysis software providers scramble to offer solutions.
Eisenstein M. Nat Biotechnol. 2020 Apr 15. doi: 10.1038/s41587-020-0510-7.

24. The genomic landscape of undifferentiated embryonal sarcoma of the liver is typified by C19MC structural rearrangement and overexpression combined with TP53 mutation or loss.
Setty BA, Jinesh GG, Arnold M, Pettersson F, Cheng CH, Cen L, Yoder SJ, Teer JK, Flores ER, Reed DR, Brohl AS. PLoS Genet. 2020 Apr 20;16(4):e1008642. doi: 10.1371/journal.pgen.1008642.

25. Translational derepression of Elavl4 isoforms at their alternative 5' UTRs determines neuronal development.
Popovitchenko T, Park Y, Page NF, Luo X, Krsnik Z, Liu Y, Salamon I, Stephenson JD, Kraushar ML, Volk NL, Patel SM, Wijeratne HRS, Li D, Suthar KS, Wach A, Sun M, Arnold SJ, Akamatsu W, Okano H, Paillard L, Zhang H, Buyske S, Kostovic I, De Rubeis S, Hart RP, Rasin MR. Nat Commun. 2020 Apr 3;11(1):1674. doi: 10.1038/s41467-020-15412-8.

26. Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes.
Camunas-Soler J, Dai XQ, Hang Y, Bautista A, Lyon J, Suzuki K, Kim SK, Quake SR, MacDonald PE. Cell Metab. 2020 Apr 13:S1550-4131(20)30187-X. doi: 10.1016/j.cmet.2020.04.005.

27. Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes.
Zhang L, Rube HT, Vakulskas CA, Behlke MA, Bussemaker HJ, Pufall MA. Nucleic Acids Res. 2020 Apr 21:gkaa231. doi: 10.1093/nar/gkaa231.

28. The Sox2 transcription factor binds RNA.
Holmes ZE, Hamilton DJ, Hwang T, Parsonnet NV, Rinn JL, Wuttke DS, Batey RT. Nat Commun. 2020 Apr 14;11(1):1805. doi: 10.1038/s41467-020-15571-8.

29. Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer.
Corona RI, Seo JH, Lin X, Hazelett DJ, Reddy J, Fonseca MAS, Abassi F, Lin YG, Mhawech-Fauceglia PY, Shah SP, Huntsman DG, Gusev A, Karlan BY, Berman BP, Freedman ML, Gayther SA, Lawrenson K. Nat Commun. 2020 Apr 24;11(1):2020. doi: 10.1038/s41467-020-15951-0.

30. Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective.
Pande A, Makalowski W, Brosius J, Raabe CA. Nucleic Acids Res. 2020 Apr 17;48(7):3435-3454. doi: 10.1093/nar/gkaa026.

31. Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption.
Luong XG, Daldello EM, Rajkovic G, Yang CR, Conti M. Nucleic Acids Res. 2020 Apr 6;48(6):3257-3276. doi: 10.1093/nar/gkaa010.

32. Accurate estimation of cell composition in bulk expression through robust integration of single-cell information.
Jew B, Alvarez M, Rahmani E, Miao Z, Ko A, Garske KM, Sul JH, Pietiläinen KH, Pajukanta P, Halperin E. Nat Commun. 2020 Apr 24;11(1):1971. doi: 10.1038/s41467-020-15816-6.

33. Insights into Gonadal Sex Differentiation Provided by Single-Cell Transcriptomics in the Chicken Embryo.
Estermann MA, Williams S, Hirst CE, Roly ZY, Serralbo O, Adhikari D, Powell D, Major AT, Smith CA. Cell Rep. 2020 Apr 7;31(1):107491. doi: 10.1016/j.celrep.2020.03.055.

34. Cell-type diversity and regionalized gene expression in the planarian intestine.
Forsthoefel DJ, Cejda NI, Khan UW, Newmark PA. Elife. 2020 Apr 2;9:e52613. doi: 10.7554/eLife.52613.

35. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4(+) T cells to cytokines.
Cano-Gamez E, Soskic B, Roumeliotis TI, So E, Smyth DJ, Baldrighi M, Willé D, Nakic N, Esparza-Gordillo J, Larminie CGC, Bronson PG, Tough DF, Rowan WC, Choudhary JS, Trynka G. Nat Commun. 2020 Apr 14;11(1):1801. doi: 10.1038/s41467-020-15543-y.

36. Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes.
Werner S, Schmidt L, Marchand V, Kemmer T, Falschlunger C, Sednev MV, Bec G, Ennifar E, Höbartner C, Micura R, Motorin Y, Hildebrandt A, Helm M. Nucleic Acids Res. 2020 Apr 17;48(7):3734-3746. doi: 10.1093/nar/gkaa113.

37. H2A.Z is dispensable for both basal and activated transcription in post-mitotic mouse muscles.
Belotti E, Lacoste N, Simonet T, Papin C, Padmanabhan K, Scionti I, Gangloff YG, Ramos L, Dalkara D, Hamiche A, Dimitrov S, Schaeffer L. Nucleic Acids Res. 2020 Apr 8:gkaa157. doi: 10.1093/nar/gkaa157.

38. Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.
Jones MG, Khodaverdian A, Quinn JJ, Chan MM, Hussmann JA, Wang R, Xu C, Weissman JS, Yosef N. Genome Biol. 2020 Apr 14;21(1):92. doi: 10.1186/s13059-020-02000-8.

39. Dysfunction of Hair Follicle Mesenchymal Progenitors Contributes to Age-Associated Hair Loss.
Shin W, Rosin NL, Sparks H, Sinha S, Rahmani W, Sharma N, Workentine M, Abbasi S, Labit E, Stratton JA, Biernaskie J. Dev Cell. 2020 Apr 20;53(2):185-198.e7. doi: 10.1016/j.devcel.2020.03.019.

40. Antibody-free enzyme-assisted chemical approach for detection of N6-methyladenosine.
Wang Y, Xiao Y, Dong S, Yu Q, Jia G. Nat Chem Biol. 2020 Apr 27. doi: 10.1038/s41589-020-0525-x.

41. A metabolic labeling method detects m6A transcriptome-wide at single base resolution.
Shu X, Cao J, Cheng M, Xiang S, Gao M, Li T, Ying X, Wang F, Yue Y, Lu Z, Dai Q, Cui X, Ma L, Wang Y, He C, Feng X, Liu J. Nat Chem Biol. 2020 Apr 27. doi: 10.1038/s41589-020-0526-9.

42. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements.
Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. PLoS Genet. 2020 Apr 1;16(4):e1008462. doi: 10.1371/journal.pgen.1008462. eCollection 2020 Apr.

43. Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants.
Jackson-Jones LH, Smith P, Portman JR, Magalhaes MS, Mylonas KJ, Vermeren MM, Nixon M, Henderson BEP, Dobie R, Vermeren S, Denby L, Henderson NC, Mole DJ, Bénézech C. Immunity. 2020 Apr 14;52(4):700-715.e6. doi: 10.1016/j.immuni.2020.03.011.