Monthly Letter

1. Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1.
Jen HI, Hill MC, Tao L, Sheng K, Cao W, Zhang H, Yu HV, Llamas J, Zong C, Martin JF, Segil N, Groves AK. Elife. 2019 Apr 29;8. pii: e44328. doi: 10.7554/eLife.44328.

2. Adaptive Immune Resistance Emerges from Tumor-Initiating Stem Cells.
Miao Y, Yang H, Levorse J, Yuan S, Polak L, Sribour M, Singh B, Rosenblum M, Fuchs E. Cell. 2019 Apr 22. pii: S0092-8674(19)30287-9. doi: 10.1016/j.cell.2019.03.025.

3. scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets.
Lin Y, Ghazanfar S, Wang KYX, Gagnon-Bartsch JA, Lo KK, Su X, Han ZG, Ormerod JT, Speed TP, Yang P, Yang JYH. Proc Natl Acad Sci U S A. 2019 Apr 26. pii: 201820006. doi: 10.1073/pnas.1820006116.

4. Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila.
Uyehara CM, McKay DJ. Proc Natl Acad Sci U S A. 2019 Apr 24. pii: 201900343. doi: 10.1073/pnas.1900343116.

5. The Major Risk Factors for Alzheimer's Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques.
Sala Frigerio C, Wolfs L, Fattorelli N, Thrupp N, Voytyuk I, Schmidt I, Mancuso R, Chen WT, Woodbury ME, Srivastava G, Möller T, Hudry E, Das S, Saido T, Karran E, Hyman B, Perry VH, Fiers M, De Strooper B. Cell Rep. 2019 Apr 23;27(4):1293-1306.e6. doi: 10.1016/j.celrep.2019.03.099.

6. Molecular subtyping reveals immune alterations associated with progression of bronchial premalignant lesions.
Beane JE, Mazzilli SA, Campbell JD, Duclos G, Krysan K, Moy C, Perdomo C, Schaffer M, Liu G, Zhang S, Liu H, Vick J, Dhillon SS, Platero SJ, Dubinett SM, Stevenson C, Reid ME, Lenburg ME, Spira AE. Nat Commun. 2019 Apr 23;10(1):1856. doi: 10.1038/s41467-019-09834-2.

7. Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease.
Ferrari Bardile C, Garcia-Miralles M, Caron NS, Rayan NA, Langley SR, Harmston N, Rondelli AM, Teo RTY, Waltl S, Anderson LM, Bae HG, Jung S, Williams A, Prabhakar S, Petretto E, Hayden MR, Pouladi MA. Proc Natl Acad Sci U S A. 2019 Apr 23. pii: 201818042. doi: 10.1073/pnas.1818042116.

8. MicroRNA-92 expression in CD133+ melanoma stem cells regulates immunosuppression in the tumor microenvironment via integrin-dependent activation of TGF-β.
Shidal C, Singh NP, Nagarkatti P, Nagarkatti M. Cancer Res. 2019 Apr 23. pii: canres.2659.2018. doi: 10.1158/0008-5472.CAN-18-2659.

9. TransLiG: a de novo transcriptome assembler that uses line graph iteration.
Liu J, Yu T, Mu Z, Li G. Genome Biol. 2019 Apr 23;20(1):81. doi: 10.1186/s13059-019-1690-7.

10. Destabilization of chromosome structure by histone H3 lysine 27 methylation.
Möller M, Schotanus K, Soyer JL, Haueisen J, Happ K, Stralucke M, Happel P, Smith KM, Connolly LR, Freitag M, Stukenbrock EH. PLoS Genet. 2019 Apr 22;15(4):e1008093. doi: 10.1371/journal.pgen.1008093.

11. Expression estimation and eQTL mapping for HLA genes with a personalized pipeline.
Aguiar VRC, César J, Delaneau O, Dermitzakis ET, Meyer D. PLoS Genet. 2019 Apr 22;15(4):e1008091. doi: 10.1371/journal.pgen.1008091.

12. Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Sarkar AK, Tung PY, Blischak JD, Burnett JE, Li YI, Stephens M, Gilad Y. PLoS Genet. 2019 Apr 19;15(4):e1008045. doi: 10.1371/journal.pgen.1008045. eCollection 2019 Apr.

13. Transcription factors IRF8 and PU.1 are required for follicular B cell development and BCL6-driven germinal center responses.
Wang H, Jain S, Li P, Lin JX, Oh J, Qi C, Gao Y, Sun J, Sakai T, Naghashfar Z, Abbasi S, Kovalchuk AL, Bolland S, Nutt SL, Leonard WJ, Morse HC 3rd. Proc Natl Acad Sci U S A. 2019 Apr 18. pii: 201901258. doi: 10.1073/pnas.1901258116.

14. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.
Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B. Genome Biol. 2019 Apr 19;20(1):71. doi: 10.1186/s13059-019-1671-x.

15. Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development.
Genga RMJ, Kernfeld EM, Parsi KM, Parsons TJ, Ziller MJ, Maehr R. Cell Rep. 2019 Apr 16;27(3):708-718.e10. doi: 10.1016/j.celrep.2019.03.076.

16. Rhythmic Food Intake Drives Rhythmic Gene Expression More Potently than the Hepatic Circadian Clock in Mice.
Greenwell BJ, Trott AJ, Beytebiere JR, Pao S, Bosley A, Beach E, Finegan P, Hernandez C, Menet JS. Cell Rep. 2019 Apr 16;27(3):649-657.e5. doi: 10.1016/j.celrep.2019.03.064.

17. DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis.
Xiong B, Yang Y, Fineis FR, Wang JP. Genome Biol. 2019 Apr 16;20(1):75. doi: 10.1186/s13059-019-1682-7.

18. Transcription factor Fra-1 targets arginase-1 to enhance macrophage-mediated inflammation in arthritis.
Hannemann N, Cao S, Eriksson D, Schnelzer A, Jordan J, Eberhardt M, Schleicher U, Rech J, Ramming A, Uebe S, Ekici A, Cañete JD, Chen X, Bäuerle T, Vera J, Bogdan C, Schett G, Bozec A. J Clin Invest. 2019 Apr 16;130. pii: 96832. doi: 10.1172/JCI96832.

19. Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution.
Heng JS, Rattner A, Stein-O'Brien GL, Winer BL, Jones BW, Vernon HJ, Goff LA, Nathans J. Proc Natl Acad Sci U S A. 2019 Apr 15. pii: 201821122. doi: 10.1073/pnas.1821122116.

20. Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells.
Nakanishi M, Mitchell RR, Benoit YD, Orlando L, Reid JC, Shimada K, Davidson KC, Shapovalova Z, Collins TJ, Nagy A, Bhatia M. Cell. 2019 Apr 9. pii: S0092-8674(19)30275-2. doi: 10.1016/j.cell.2019.03.013.

21. Nexilin is a New Component of Junctional Membrane Complexes Required for Cardiac T-Tubule Formation.
Liu C, Spinozzi S, Chen JY, Fang X, Feng W, Perkins G, Cattaneo P, Guimarães-Camboa N, Dalton ND, Peterson KL, Wu T, Ouyang K, Fu XD, Evans SM, Chen J. Circulation. 2019 Apr 15. doi: 10.1161/CIRCULATIONAHA.119.039751.

22. Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of HCV-infected Cells and Liver to Identify Pathways Associated With Disease Development.
Lupberger J, Croonenborghs T, Roca Suarez AA, Van Renne N, Jühling F, Oudot MA, Virzì A, Bandiera S, Jamey C, Meszaros G, Brumaru D, Mukherji A, Durand SC, Heydmann L, Verrier ER, El Saghire H, Hamdane N, Bartenschlager R, Gastroenterology. 2019 Apr 9. pii: S0016-5085(19)35670-7. doi: 10.1053/j.gastro.2019.04.003.

23. Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding.
Li S, Chen K, Zhang Y, Barnes SD, Jaichander P, Zheng Y, Hassan M, Malladi VS, Skapek SX, Xu L, Bassel-Duby R, Olson EN, Liu N. Genes Dev. 2019 Apr 11. doi: 10.1101/gad.324467.119.

24. Shank3 modulates sleep and expression of circadian transcription factors.
Ingiosi AM, Schoch H, Wintler T, Singletary KG, Righelli D, Roser LG, Medina E, Risso D, Frank MG, Peixoto L. Elife. 2019 Apr 11;8. pii: e42819. doi: 10.7554/eLife.42819.

25. Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase.
Sanchez-Vazquez P, Dewey CN, Kitten N, Ross W, Gourse RL. Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8310-8319. doi: 10.1073/pnas.1819682116. Epub 2019 Apr 10.

26. Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies.
Oppel F, Tao T, Shi H, Ross KN, Zimmerman MW, He S, Tong G, Aster JC, Look AT. PLoS Genet. 2019 Apr 10;15(4):e1008039. doi: 10.1371/journal.pgen.1008039. eCollection 2019 Apr.

27. Global identification of functional microRNA-mRNA interactions in Drosophila.
Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U. Nat Commun. 2019 Apr 9;10(1):1626. doi: 10.1038/s41467-019-09586-z.

28. Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration.
Hallberg ZF, Chan CH, Wright TA, Kranzusch PJ, Doxzen KW, Park JJ, Bond DR, Hammond MC. Elife. 2019 Apr 9;8. pii: e43959. doi: 10.7554/eLife.43959.

29. Comparative analysis of sequencing technologies for single-cell transcriptomics.
Natarajan KN, Miao Z, Jiang M, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L, Yang N, Li B, Hou Y, Liu S, Teichmann SA. Genome Biol. 2019 Apr 9;20(1):70. doi: 10.1186/s13059-019-1676-5.

30. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.
Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, Cell. 2019 Apr 18;177(3):572-586.e22. doi: 10.1016/j.cell.2019.03.010. Epub 2019 Apr 4.

31. Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation.
Srinivasan S, Yeri A, Cheah PS, Chung A, Danielson K, De Hoff P, Filant J, Laurent CD, Laurent LD, Magee R, Moeller C, Murthy VL, Nejad P, Paul A, Rigoutsos I, Rodosthenous R, Shah RV, Simonson B, To C, Wong D, Yan IK, Zhang X, Balaj L, Cell. 2019 Apr 4;177(2):446-462.e16. doi: 10.1016/j.cell.2019.03.024.

32. Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation.
Varum S, Baggiolini A, Zurkirchen L, Atak ZK, Cantù C, Marzorati E, Bossart R, Wouters J, Häusel J, Tuncer E, Zingg D, Veen D, John N, Balz M, Levesque MP, Basler K, Aerts S, Zamboni N, Dummer R, Sommer L. Cell Stem Cell. 2019 Apr 4;24(4):637-653.e9. doi: 10.1016/j.stem.2019.03.011.

33. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.
Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. Nat Commun. 2019 Apr 4;10(1):1538. doi: 10.1038/s41467-019-09483-5.

34. HIF-1α regulates IL-1β and IL-17 in sarcoidosis.
Talreja J, Talwar H, Bauerfeld C, Grossman LI, Zhang K, Tranchida P, Samavati L. Elife. 2019 Apr 4;8. pii: e44519. doi: 10.7554/eLife.44519.

35. Intestinal development and homeostasis require activation and apoptosis of diet-reactive T cells.
Visekruna A, Hartmann S, Sillke YR, Glauben R, Fischer F, Raifer H, Mollenkopf H, Bertrams W, Schmeck B, Klein M, Pagenstecher A, Lohoff M, Jacob R, Pabst O, Bland PW, Luu M, Romero R, Siegmund B, Rajalingam K, Steinhoff U. J Clin Invest. 2019 Apr 2;130. pii: 98929. doi: 10.1172/JCI98929. eCollection 2019 Apr 2.

36. Effect of Radiotherapy After Breast-Conserving Surgery Depending on the Presence of Tumor-Infiltrating Lymphocytes: A Long-Term Follow-Up of the SweBCG91RT Randomized Trial.
Kovács A, Stenmark Tullberg A, Werner Rönnerman E, Holmberg E, Hartman L, Sjöström M, Lundstedt D, Malmström P, Fernö M, Karlsson P. J Clin Oncol. 2019 Apr 2:JCO1802157. doi: 10.1200/JCO.18.02157.

37. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.
Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Genome Biol. 2019 Apr 2;20(1):64. doi: 10.1186/s13059-019-1660-0.

38. Ga-Doped and Pt-Loaded Porous TiO2-SiO2 for Photocatalytic Nonoxidative Coupling of Methane.
Wu S, Tan X, Lei J, Chen H, Wang L, Zhang J. J Am Chem Soc. 2019 Apr 24;141(16):6592-6600. doi: 10.1021/jacs.8b13858. Epub 2019 Apr 4.

39. A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities.
Okawa S, Del Sol A. Nucleic Acids Res. 2019 Apr 23;47(7):3333-3343. doi: 10.1093/nar/gkz147.

40. Long noncoding RNA MALAT1 releases epigenetic silencing of HIV-1 replication by displacing the polycomb repressive complex 2 from binding to the LTR promoter.
Qu D, Sun WW, Li L, Ma L, Sun L, Jin X, Li T, Hou W, Wang JH. Nucleic Acids Res. 2019 Apr 8;47(6):3013-3027. doi: 10.1093/nar/gkz117.

41. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development.
Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL. Nucleic Acids Res. 2019 Apr 8;47(6):2856-2870. doi: 10.1093/nar/gkz010.

42. Genome-wide analysis of genomic alterations induced by oxidative DNA damage in yeast.
Zhang K, Zheng DQ, Sui Y, Qi L, Petes TD. Nucleic Acids Res. 2019 Apr 23;47(7):3521-3535. doi: 10.1093/nar/gkz027.

43. NextPBM: a platform to study cell-specific transcription factor binding and cooperativity.
Mohaghegh N, Bray D, Keenan J, Penvose A, Andrilenas KK, Ramlall V, Siggers T. Nucleic Acids Res. 2019 Apr 8;47(6):e31. doi: 10.1093/nar/gkz020.

44. Transcriptome Characterization of Matched Primary Breast and Brain Metastatic Tumors to Detect Novel Actionable Targets.
Varešlija D, Priedigkeit N, Fagan A, Purcell S, Cosgrove N, O'Halloran PJ, Ward E, Cocchiglia S, Hartmaier R, Castro CA, Zhu L, Tseng GC, Lucas PC, Puhalla SL, Brufsky AM, Hamilton RL, Mathew A, Leone JP, Basudan A, Hudson L, Dwyer R, Das S, O'Connor DP, Buckley PG, Farrell M, Hill ADK, Oesterreich S, Lee AV, Young LS. J Natl Cancer Inst. 2019 Apr 1;111(4):388-398. doi: 10.1093/jnci/djy110.