Monthly Letter

1. Differential m(6)A RNA landscapes across hematopoiesis reveal a role for IGF2BP2 in preserving hematopoietic stem cell function.
Yin R et al. Cell Stem Cell. 2021 Oct 13:S1934-5909(21)00390-8. doi: 10.1016/j.stem.2021.09.014. Online ahead of print.

2. Capture of the newly transcribed RNA interactome using click chemistry.
Guo X et al. Nat Protoc. 2021 Oct 25. doi: 10.1038/s41596-021-00609-y. Online ahead of print.

3. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation.
Shah A et al. Genome Biol. 2021 Oct 14;22(1):291. doi: 10.1186/s13059-021-02502-z.

4. Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.
Rebboah E et al. Genome Biol. 2021 Oct 7;22(1):286. doi: 10.1186/s13059-021-02505-w.

5. The autoimmune signature of hyperinflammatory multisystem inflammatory syndrome in children.
Porritt RA et al. J Clin Invest. 2021 Oct 15;131(20):e151520. doi: 10.1172/JCI151520.

6. Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility.
Wang K et al. Mol Cell. 2021 Oct 21;81(20):4319-4332.e10. doi: 10.1016/j.molcel.2021.09.026.

7. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses.
Janissen R et al. Mol Cell. 2021 Oct 19:S1097-2765(21)00832-7. doi: 10.1016/j.molcel.2021.10.003. Online ahead of print.

8. A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation.
Ren Y et al. Genome Biol. 2021 Oct 14;22(1):290. doi: 10.1186/s13059-021-02508-7.

9. Single-cell transcriptomics reveals a conserved metaplasia program in pancreatic injury.
Ma Z et al. Gastroenterology. 2021 Oct 22:S0016-5085(21)03665-9. doi: 10.1053/j.gastro.2021.10.027. Online ahead of print.

10. The translatome of neuronal cell bodies, dendrites, and axons.
Glock C et al. Proc Natl Acad Sci U S A. 2021 Oct 26;118(43):e2113929118. doi: 10.1073/pnas.2113929118.

11. The chromatin remodeler Ino80 mediates RNAPII pausing site determination.
Cheon Y et al. Genome Biol. 2021 Oct 18;22(1):294. doi: 10.1186/s13059-021-02500-1.

12. CeDR Atlas: a knowledgebase of cellular drug response.
Wang YY et al. Nucleic Acids Res. 2021 Oct 11:gkab897. doi: 10.1093/nar/gkab897. Online ahead of print.

13. RGD v2.0: a major update of the ruminant functional and evolutionary genomics database.
Fu W et al. Nucleic Acids Res. 2021 Oct 13:gkab887. doi: 10.1093/nar/gkab887. Online ahead of print.

14. CancerSCEM: a database of single-cell expression map across various human cancers.
Zeng J et al. Nucleic Acids Res. 2021 Oct 13:gkab905. doi: 10.1093/nar/gkab905. Online ahead of print.

15. ZFP91 disturbs metabolic fitness and antitumor activity of tumor-infiltrating T cells.
Wang F et al. J Clin Invest. 2021 Oct 1;131(19):e144318. doi: 10.1172/JCI144318.

16. Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells.
Witkowski M et al. Nature. 2021 Oct 25. doi: 10.1038/s41586-021-04142-6. Online ahead of print.

17. ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms.
Zhou Q et al. Nucleic Acids Res. 2021 Oct 19:gkab937. doi: 10.1093/nar/gkab937. Online ahead of print.

18. Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci.
Perrin HJ et al. PLoS Genet. 2021 Oct 26;17(10):e1009865. doi: 10.1371/journal.pgen.1009865. Online ahead of print.

19. A sex-specific evolutionary interaction between ADCY9 and CETP.
Gamache I et al. Elife. 2021 Oct 5;10:e69198. doi: 10.7554/eLife.69198. Online ahead of print.

20. Dystonia-specific mutations in THAP1 alter transcription of genes associated with neurodevelopment and myelin.
Domingo A et al. Am J Hum Genet. 2021 Oct 15:S0002-9297(21)00353-0. doi: 10.1016/j.ajhg.2021.09.017. Online ahead of print.

21. circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing.
Liu Z et al. Elife. 2021 Oct 14;10:e69457. doi: 10.7554/eLife.69457.

22. Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data.
Nakajima N et al. Nucleic Acids Res. 2021 Oct 11;49(18):e104. doi: 10.1093/nar/gkab601.

23. Determinants of renal cell carcinoma invasion and metastatic competence.
Kim K et al. Nat Commun. 2021 Oct 4;12(1):5760. doi: 10.1038/s41467-021-25918-4.

24. VThunter: a database for single-cell screening of virus target cells in the animal kingdom.
Chen D et al. Nucleic Acids Res. 2021 Oct 11:gkab894. doi: 10.1093/nar/gkab894. Online ahead of print.

25. MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.
Cmero M et al. Genome Biol. 2021 Oct 22;22(1):296. doi: 10.1186/s13059-021-02507-8.

26. Modifying the m(6)A brain methylome by ALKBH5-mediated demethylation: a new contender for synaptic tagging.
Martinez De La Cruz B et al. Mol Psychiatry. 2021 Oct 19. doi: 10.1038/s41380-021-01282-z. Online ahead of print.

27. scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse.
Yang X et al. Nucleic Acids Res. 2021 Oct 13:gkab917. doi: 10.1093/nar/gkab917. Online ahead of print.

28. Microglia and their LAG3 checkpoint underlie the antidepressant and neurogenesis-enhancing effects of electroconvulsive stimulation.
Rimmerman N et al. Mol Psychiatry. 2021 Oct 14. doi: 10.1038/s41380-021-01338-0. Online ahead of print.

29. TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles.
Han M et al. Nucleic Acids Res. 2021 Oct 11;49(18):e108. doi: 10.1093/nar/gkab629.

30. Intrathymic differentiation of natural antibody-producing plasma cells in human neonates.
Cordero H et al. Nat Commun. 2021 Oct 1;12(1):5761. doi: 10.1038/s41467-021-26069-2.

31. Antisense RNAs influence promoter usage of their counterpart sense genes in cancer.
Bellido Molias et al. Cancer Res. 2021 Oct 14:canres.1859.2021. doi: 10.1158/0008-5472.CAN-21-1859. Online ahead of print.

32. Toxicity after AAV delivery of RNAi expression constructs into nonhuman primate brain.
Keiser MS et al. Nat Med. 2021 Oct 18. doi: 10.1038/s41591-021-01522-3. Online ahead of print.

33. Enhancer-associated H3K4 methylation safeguards in vitro germline competence.
Bleckwehl T et al. Nat Commun. 2021 Oct 1;12(1):5771. doi: 10.1038/s41467-021-26065-6.

34. The SUMO ligase MMS21 profoundly influences maize development through its impact on genome activity and stability.
Zhang J et al. PLoS Genet. 2021 Oct 25;17(10):e1009830. doi: 10.1371/journal.pgen.1009830. Online ahead of print.

35. CARMN is an Evolutionarily Conserved Smooth Muscle Cell-specific LncRNA that Maintains Contractile Phenotype by Binding Myocardin.
Dong K et al. Circulation. 2021 Oct 25. doi: 10.1161/CIRCULATIONAHA.121.055949. Online ahead of print.

36. G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities.
He X et al. Nucleic Acids Res. 2021 Oct 6:gkab873. doi: 10.1093/nar/gkab873. Online ahead of print.

37. Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation.
Cirnaru MD et al. Elife. 2021 Oct 5;10:e65979. doi: 10.7554/eLife.65979.

38. Cholecystokinin 1 receptor activation restores normal mTORC1 signaling and is protective to Purkinje cells of SCA mice.
Wozniak EAL et al. Cell Rep. 2021 Oct 12;37(2):109831. doi: 10.1016/j.celrep.2021.109831.

39. Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer.
Zhang Y et al. Cancer Cell. 2021 Oct 5:S1535-6108(21)00499-2. doi: 10.1016/j.ccell.2021.09.010. Online ahead of print.

40. ADGRG1 enriches for functional human hematopoietic stem cells following ex vivo expansion-induced mitochondrial oxidative stress.
Chen Y et al. J Clin Invest. 2021 Oct 15;131(20):e148329. doi: 10.1172/JCI148329.

41. CstF64-induced shortening of the BID 3'UTR promotes esophageal squamous cell carcinoma progression by disrupting ceRNA crosstalk with ZFP36L2.
Lin A et al. Cancer Res. 2021 Oct 4:canres.1201.2021. doi: 10.1158/0008-5472.CAN-21-1201. Online ahead of print.

42. Single-cell profiling reveals the importance of CXCL13/CXCR5 axis biology in lymphocyte-rich classic Hodgkin lymphoma.
Aoki T et al. Proc Natl Acad Sci U S A. 2021 Oct 12;118(41):e2105822118. doi: 10.1073/pnas.2105822118.

43. Stage-resolved Hi-C analyses reveal meiotic chromosome organizational features influencing homolog alignment.
Zuo W et al. Nat Commun. 2021 Oct 8;12(1):5827. doi: 10.1038/s41467-021-26033-0.

44. TIGER: The gene expression regulatory variation landscape of human pancreatic islets.
Alonso L et al. Cell Rep. 2021 Oct 12;37(2):109807. doi: 10.1016/j.celrep.2021.109807.

45. Inherent hepatocytic heterogeneity determines expression and retention of edited F9 alleles post-AAV/CRISPR infusion.
Wang Q et al. Proc Natl Acad Sci U S A. 2021 Oct 19;118(42):e2110887118. doi: 10.1073/pnas.2110887118.

46. Neurofibromin 1 in mushroom body neurons mediates circadian wake drive through activating cAMP-PKA signaling.
Machado Almeida P et al. Nat Commun. 2021 Oct 1;12(1):5758. doi: 10.1038/s41467-021-26031-2.

47. Efficient stimulation of retinal regeneration from Müller glia in adult mice using combinations of proneural bHLH transcription factors.
Todd L et al. Cell Rep. 2021 Oct 19;37(3):109857. doi: 10.1016/j.celrep.2021.109857.

48. Recurrent rewiring of the adult hippocampal mossy fiber system by a single transcriptional regulator, Id2.
Luo W et al. Proc Natl Acad Sci U S A. 2021 Oct 5;118(40):e2108239118. doi: 10.1073/pnas.2108239118.