Monthly Letter

1. Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis.
Liu N, Song J, Xie Y, Wang XL, Rong B, Man N, Zhang MM, Zhang Q, Gao FF, Du MR, Zhang Y, Shen J, Xu CH, Hu CL, Wu JC, Liu P, Zhang YL, Xie YY, Liu P, Huang JY, Huang QH, Lan F, Shen S, Nimer SD, Chen Z, Chen SJ, Roeder RG, Wang L, Sun XJ. Proc Natl Acad Sci U S A. 2018 Dec 28. pii: 201809327. doi: 10.1073/pnas.1809327116.

2. Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination.
Campo JJ, Le TQ, Pablo JV, Hung C, Teng AA, Tettelin H, Tate A, Hanage WP, Alderson MR, Liang X, Malley R, Lipsitch M, Croucher NJ. Elife. 2018 Dec 28;7. pii: e37015. doi: 10.7554/eLife.37015.

3. Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints.
Andor N, Simonds EF, Czerwinski DK, Chen J, Grimes SM, Wood-Bouwens C, Zheng GXY, Kubit MA, Greer S, Weiss WA, Levy R, Ji HP. Blood. 2018 Dec 27. pii: blood-2018-08-862292. doi: 10.1182/blood-2018-08-862292.

4. Long non-coding RNA NEXN-AS1 mitigates atherosclerosis by regulating the actin-binding protein NEXN.
Hu YW, Guo FX, Xu YJ, Li P, Lu ZF, McVey DG, Zheng L, Wang Q, Ye JH, Kang CM, Wu SG, Zhao JJ, Ma X, Yang Z, Fang FC, Qiu YR, Xu BM, Xiao L, Wu Q, Wu LM, Ding L, Webb TR, Samani NJ, Ye S. J Clin Invest. 2018 Dec 27. pii: 98230. doi: 10.1172/JCI98230.

5. Semisoft clustering of single-cell data.
Zhu L, Lei J, Klei L, Devlin B, Roeder K. Proc Natl Acad Sci U S A. 2018 Dec 26. pii: 201817715. doi: 10.1073/pnas.1817715116.

6. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing.
Yuan J, Sheng J, Sims PA. Genome Biol. 2018 Dec 24;19(1):227. doi: 10.1186/s13059-018-1607-x.

7. Single-Cell RNA-Seq of the Pancreatic Islets--a Promise Not yet Fulfilled?
Wang YJ, Kaestner KH. Cell Metab. 2018 Dec 14. pii: S1550-4131(18)30735-6. doi: 10.1016/j.cmet.2018.11.016.

8. RNA element discovery from germ cell to blastocyst.
Estill MS, Hauser R, Krawetz SA. Nucleic Acids Res. 2018 Dec 21. doi: 10.1093/nar/gky1223.

9. The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans.
Davis GM, Tu S, Anderson JWT, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR. Elife. 2018 Dec 21;7. pii: e35478. doi: 10.7554/eLife.35478.

10. A test metric for assessing single-cell RNA-seq batch correction.
Büttner M, Miao Z, Wolf FA, Teichmann SA, Theis FJ. Nat Methods. 2019 Jan;16(1):43-49. doi: 10.1038/s41592-018-0254-1. Epub 2018 Dec 20.

11. Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.
Xu H, Fair BJ, Dwyer ZW, Gildea M, Pleiss JA. Nat Methods. 2019 Jan;16(1):55-58. doi: 10.1038/s41592-018-0258-x. Epub 2018 Dec 20.

12. SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.
Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M, Robson SC, Hermida-Prado F, Yang YH, Babaei-Jadidi R, Garyfallos DA, Ponstingl H, Dias JML, Gallipoli P, Seiler M, Buonamici S, Vick B, Bannister AJ, Rad R, Prinjha RK, Marioni JC, Huntly B, Batson J, Morris JC, Pina C, Bradley A, Jeremias I, Bates DO, Yusa K, Kouzarides T, Vassiliou GS. Nat Commun. 2018 Dec 19;9(1):5378. doi: 10.1038/s41467-018-07620-0.

13. Predicting age from the transcriptome of human dermal fibroblasts.
Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer MW, Navlakha S. Genome Biol. 2018 Dec 20;19(1):221. doi: 10.1186/s13059-018-1599-6.

14. Paired Related Homeobox Protein 1 Regulates Quiescence in Human Oligodendrocyte Progenitors.
Wang J, Saraswat D, Sinha AK, Polanco J, Dietz K, O'Bara MA, Pol SU, Shayya HJ, Sim FJ. Cell Rep. 2018 Dec 18;25(12):3435-3450.e6. doi: 10.1016/j.celrep.2018.11.068.

15. Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle.
Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P. Cell Rep. 2018 Dec 18;25(12):3299-3314.e6. doi: 10.1016/j.celrep.2018.11.077.

16. Early loss of Histone H2B monoubiquitylation alters chromatin accessibility and activates key immune pathways that facilitate progression of ovarian cancer.
Hooda J, Novak M, Salomon MP, Matsuba C, Ramos RI, MacDuffie E, Song M, Hirsch MS, Lester J, Parkash V, Karlan BY, Oren M, Hoon DS, Drapkin R. Cancer Res. 2018 Dec 18. pii: canres.2297.2018. doi: 10.1158/0008-5472.CAN-18-2297.

17. Personalised Transcriptomics Reveals Heterogeneous Immunophenotypes in Children with Viral Bronchiolitis.
Jones AC, Anderson D, Galbraith S, Fantino E, Gutierrez Cardenas D, Read JF, Serralha M, Holt BJ, Strickland DH, Sly PD, Bosco A, Holt PG. Am J Respir Crit Care Med. 2018 Dec 18. doi: 10.1164/rccm.201804-0715OC.

18. Local and global chromatin interactions are altered by large genomic deletions associated with human brain development.
Zhang X, Zhang Y, Zhu X, Purmann C, Haney MS, Ward T, Khechaduri A, Yao J, Weissman SM, Urban AE. Nat Commun. 2018 Dec 17;9(1):5356. doi: 10.1038/s41467-018-07766-x.

19. Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA. Nat Commun. 2018 Dec 17;9(1):5346. doi: 10.1038/s41467-018-07779-6.

20. miR-3607-3p suppresses non-small cell lung cancer (NSCLC) by targeting TGFBR1 and CCNE2.
Gao P, Wang H, Yu J, Zhang J, Yang Z, Liu M, Niu Y, Wei X, Wang W, Li H, Wang Y, Sun G. PLoS Genet. 2018 Dec 17;14(12):e1007790. doi: 10.1371/journal.pgen.1007790.

21. β-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming.
Xie X, Jankauskas R, Mazari AMA, Drou N, Percipalle P. PLoS Genet. 2018 Dec 17;14(12):e1007846. doi: 10.1371/journal.pgen.1007846.

22. A quantitative framework for characterizing the evolutionary history of mammalian gene expression.
Chen J, Swofford R, Johnson J, Cummings BB, Rogel N, Lindblad-Toh K, Haerty W, di Palma F, Regev A. Genome Res. 2018 Dec 14. doi: 10.1101/gr.237636.118.

23. Organoid Modeling of the Tumor Immune Microenvironment.
Neal JT, Li X, Zhu J, Giangarra V, Grzeskowiak CL, Ju J, Liu IH, Chiou SH, Salahudeen AA, Smith AR, Deutsch BC, Liao L, Zemek AJ, Zhao F, Karlsson K, Schultz LM, Metzner TJ, Nadauld LD, Tseng YY, Alkhairy S, Oh C, Keskula P, Mendoza-Villanueva D, De La Vega FM, Kunz PL, Liao JC, Leppert JT, Sunwoo JB, Sabatti C, Boehm JS, Hahn WC, Zheng GXY, Davis MM, Kuo CJ. Cell. 2018 Dec 13;175(7):1972-1988.e16. doi: 10.1016/j.cell.2018.11.021.

24. Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories.
Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L, Assenov Y, Heckmann D, Sidiropoulos N, Waszak SM, Hübschmann D, Urbanucci A, Girma EG, Kuryshev V, Klimczak LJ, Saini N, Stütz AM, Weichenhan D, Böttcher LM, Toth R, Hendriksen JD, Koop C, Lutsik P, Matzk S, Warnatz HJ, Amstislavskiy V, Feuerstein C, Raeder B, Bogatyrova O, Schmitz EM, Hube-Magg C, Kluth M, Huland H, Graefen M, Lawerenz C, Henry GH, Yamaguchi TN, Malewska A, Meiners J, Schilling D, Reisinger E, Eils R, Schlesner M, Strand DW, Bristow RG, Boutros PC, von Kalle C, Gordenin D, Sültmann H, Brors B, Sauter G, Plass C, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J. Cancer Cell. 2018 Dec 10;34(6):996-1011.e8. doi: 10.1016/j.ccell.2018.10.016.

25. Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo.
Zeidan Q, He F, Zhang F, Zhang H, Jacobson A, Hinnebusch AG. PLoS Genet. 2018 Dec 7;14(12):e1007806. doi: 10.1371/journal.pgen.1007806. eCollection 2018 Dec.

26. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue.
Zanini F, Robinson ML, Croote D, Sahoo MK, Sanz AM, Ortiz-Lasso E, Albornoz LL, Rosso F, Montoya JG, Goo L, Pinsky BA, Quake SR, Einav S. Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12363-E12369. doi: 10.1073/pnas.1813819115. Epub 2018 Dec 7.

27. Phosphorylated RB Promotes Cancer Immunity by Inhibiting NF-κB Activation and PD-L1 Expression.
Jin X, Ding D, Yan Y, Li H, Wang B, Ma L, Ye Z, Ma T, Wu Q, Rodrigues DN, Kohli M, Jimenez R, Wang L, Goodrich DW, de Bono J, Dong H, Wu H, Zhu R, Huang H. Mol Cell. 2018 Dec 3. pii: S1097-2765(18)30894-3. doi: 10.1016/j.molcel.2018.10.034.

28. Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism.
Stephen J, Maddirevula S, Nampoothiri S, Burke JD, Herzog M, Shukla A, Steindl K, Eskin A, Patil SJ, Joset P, Lee H, Garrett LJ, Yokoyama T, Balanda N, Bodine SP, Tolman NJ, Zerfas PM, Zheng A, Ramantani G, Girisha KM, Rivas C, Suresh PV, Elkahloun A, Alsaif HS, Wakil SM, Mahmoud L, Ali R, Prochazkova M; Undiagnosed Diseases Network members, Kulkarni AB, Ben-Omran T, Colak D, Morris HD, Rauch A, Martinez-Agosto JA, Nelson SF, Alkuraya FS, Gahl WA, Malicdan MCV. Am J Hum Genet. 2018 Dec 6;103(6):948-967. doi: 10.1016/j.ajhg.2018.11.001.

29. Small Heterodimer Partner and Fibroblast Growth Factor 19 Inhibit Expression of NPC1L1 in Mouse Intestine and Cholesterol Absorption.
Kim YC, Byun S, Seok S, Guo G, Xu HE, Kemper B, Kemper JK. Gastroenterology. 2018 Dec 3. pii: S0016-5085(18)35371-X. doi: 10.1053/j.gastro.2018.11.061.

30. The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage.
Jeong E, Brady OA, Martina JA, Pirooznia M, Tunc I, Puertollano R. Elife. 2018 Dec 6;7. pii: e40856. doi: 10.7554/eLife.40856.

31. Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons.
Tepe B, Hill MC, Pekarek BT, Hunt PJ, Martin TJ, Martin JF, Arenkiel BR. Cell Rep. 2018 Dec 4;25(10):2689-2703.e3. doi: 10.1016/j.celrep.2018.11.034.

32. Shortening the Half-Life of Cas9 Maintains Its Gene Editing Ability and Reduces Neuronal Toxicity.
Yang S, Li S, Li XJ. Cell Rep. 2018 Dec 4;25(10):2653-2659.e3. doi: 10.1016/j.celrep.2018.11.019.

33. A map of direct TF-DNA interactions in the human genome.
Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A. Nucleic Acids Res. 2018 Dec 4. doi: 10.1093/nar/gky1210.

34. Wnt11 directs nephron progenitor polarity and motile behavior ultimately determining nephron endowment.
O'Brien LL, Combes AN, Short KM, Lindström NO, Whitney PH, Cullen-McEwen LA, Ju A, Abdelhalim A, Michos O, Bertram JF, Smyth IM, Little MH, McMahon AP. Elife. 2018 Dec 5;7. pii: e40392. doi: 10.7554/eLife.40392.

35. Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression.
Song B, Park SH, Zhao JC, Fong KW, Li S, Lee Y, Yang YA, Sridhar S, Lu X, Abdulkadir SA, Vessella RL, Morrissey C, Kuzel TM, Catalona W, Yang X, Yu J. J Clin Invest. 2018 Dec 18. pii: 122367. doi: 10.1172/JCI122367.

36. APC-activated long non-coding RNA inhibits colorectal carcinoma pathogenesis through reducing exosome production.
Wang FW, Cao CH, Han K, Zhao YX, Cai MY, Xiang ZC, Zhang JX, Chen JW, Zhong LP, Huang Y, Zhou SF, Jin XH, Guan XY, Xu RH, Xie D. J Clin Invest. 2018 Dec 4. pii: 122478. doi: 10.1172/JCI122478.

37. Autocrine regulation of mesenchymal progenitor cell fates orchestrates tooth eruption.
Takahashi A, Nagata M, Gupta A, Matsushita Y, Yamaguchi T, Mizuhashi K, Maki K, Ruellas AC, Cevidanes LS, Kronenberg HM, Ono N, Ono W. Proc Natl Acad Sci U S A. 2018 Dec 3. pii: 201810200. doi: 10.1073/pnas.1810200115.

38. Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis.
Glenfield C, McLysaght A. Mol Biol Evol. 2018 Dec 1;35(12):2886-2899. doi: 10.1093/molbev/msy183.

39. Integrating Embryonic Development and Evolutionary History to Characterize Tentacle-Specific Cell Types in a Ctenophore.
Babonis LS, DeBiasse MB, Francis WR, Christianson LM, Moss AG, Haddock SHD, Martindale MQ, Ryan JF. Mol Biol Evol. 2018 Dec 1;35(12):2940-2956. doi: 10.1093/molbev/msy171.

40. Ambient Pollution-related Reprogramming of the Human Small Airway Epithelial Transcriptome.
O'Beirne SL, Shenoy SA, Salit J, Strulovici-Barel Y, Kaner RJ, Visvanathan S, Fine JS, Mezey JG, Crystal RG. Am J Respir Crit Care Med. 2018 Dec 1;198(11):1413-1422. doi: 10.1164/rccm.201712-2526OC.