Title (2022년 7월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-07-01
Attached File
Newsletter  Jul. 2022
Recent Papers(RNA-Seq Part)

1. Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
Replogle JM et al. Cell. 2022 Jun 2:S0092-8674(22)00597-9. doi: 10.1016/j.cell.2022.05.013. Online ahead of print.

2. scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
Zhang Z et al. Genome Biol. 2022 Jun 27;23(1):139. doi: 10.1186/s13059-022-02706-x.

3. Single-cell RNA-seq analysis reveals BHLHE40-driven pro-tumour neutrophils with hyperactivated glycolysis in pancreatic tumour microenvironment
Wang L et al. Gut. 2022 Jun 10:gutjnl-2021-326070. doi: 10.1136/gutjnl-2021-326070. Online ahead of print.

4. The spatiotemporal program of zonal liver regeneration following acute injury
Ben-Moshe S et al. Cell Stem Cell. 2022 Jun 2;29(6):973-989.e10. doi: 10.1016/j.stem.2022.04.008.

5. Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides
Bonté PE et al. Cell Rep. 2022 Jun 7;39(10):110916. doi: 10.1016/j.celrep.2022.110916.

6. Sex-specific variation in R-loop formation in Drosophila melanogaster
Stanek TJ et al. PLoS Genet. 2022 Jun 10;18(6):e1010268. doi: 10.1371/journal.pgen.1010268. eCollection 2022 Jun.

7. Identifying plant genes shaping microbiota composition in the barley rhizosphere
Escudero-Martinez C et al. Nat Commun. 2022 Jun 16;13(1):3443. doi: 10.1038/s41467-022-31022-y.

8. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae
Palos K et al. Plant Cell. 2022 Jun 6:koac166. doi: 10.1093/plcell/koac166. Online ahead of print.

9. Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics
Xu Z et al. Genome Biol. 2022 Jun 23;23(1):135. doi: 10.1186/s13059-022-02698-8.

10. α Cell dysfunction in islets from nondiabetic, glutamic acid decarboxylase autoantibody-positive individuals
Doliba NM et al. J Clin Invest. 2022 Jun 1;132(11):e156243. doi: 10.1172/JCI156243.

11. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
Dimitrov D et al. Nat Commun. 2022 Jun 9;13(1):3224. doi: 10.1038/s41467-022-30755-0.

12. Mapping the single-cell transcriptomic response of murine diabetic kidney disease to therapies
Wu H et al. Cell Metab. 2022 Jun 10:S1550-4131(22)00192-9. doi: 10.1016/j.cmet.2022.05.010. Online ahead of print.

13. Genetic encoding of an esophageal motor circuit
Coverdell TC et al. Cell Rep. 2022 Jun 14;39(11):110962. doi: 10.1016/j.celrep.2022.110962.

14. Deciphering the origins and fates of steroidogenic lineages in the mouse testis
Ademi H et al. Cell Rep. 2022 Jun 14;39(11):110935. doi: 10.1016/j.celrep.2022.110935.

15. TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma
Admoni-Elisha L et al. Nucleic Acids Res. 2022 Jun 13:gkac485. doi: 10.1093/nar/gkac485. Online ahead of print.

16. Inflammatory adipose activates a nutritional immunity pathway leading to retinal dysfunction
Sterling JK et al. Cell Rep. 2022 Jun 14;39(11):110942. doi: 10.1016/j.celrep.2022.110942.

17. HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock
Himanen SV et al. Nucleic Acids Res. 2022 Jun 10;50(11):6102-15. doi: 10.1093/nar/gkac493. Online ahead of print.

18. RIViT-seq enables systematic identification of regulons of transcriptional machineries
Otani H et al. Nat Commun. 2022 Jun 17;13(1):3502. doi: 10.1038/s41467-022-31191-w.

19. Integrated multiomic characterization of congenital heart disease
Hill MC et al. Nature. 2022 Jun 22. doi: 10.1038/s41586-022-04989-3. Online ahead of print.

20. Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing
Katanski CD et al. Nucleic Acids Res. 2022 Jun 17:gkac517. doi: 10.1093/nar/gkac517. Online ahead of print.

21. Cardiac fibroblasts regulate the development of heart failure via Htra3-TGF-β-IGFBP7 axis
Ko T et al. Nat Commun. 2022 Jun 7;13(1):3275. doi: 10.1038/s41467-022-30630-y.

22. Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype
Porter RL et al. J Clin Invest. 2022 Jun 16:e155931. doi: 10.1172/JCI155931. Online ahead of print.

23. METTL3 inhibits anti-tumor immunity by targeting m(6)A-BHLHE41-CXCL1/CXCR2 axis to promote colorectal cancer
Chen H et al. Gastroenterology. 2022 Jun 11:S0016-5085(22)00629-1. doi: 10.1053/j.gastro.2022.06.024. Online ahead of print.

24. A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex
Fasimoye RY et al. Nucleic Acids Res. 2022 Jun 23:gkac534. doi: 10.1093/nar/gkac534. Online ahead of print.

25. High-throughput total RNA sequencing in single cells using VASA-seq
Salmen F et al. Nat Biotechnol. 2022 Jun 27. doi: 10.1038/s41587-022-01361-8. Online ahead of print.

26. Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia
Kimura S et al. Blood. 2022 Jun 16;139(24):3519-3531. doi: 10.1182/blood.2022015444.

27. SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure
Tang D et al. Genome Biol. 2022 Jun 15;23(1):129. doi: 10.1186/s13059-022-02688-w.

28. Optimal CD8(+) T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape
Karginov TA et al. Nat Commun. 2022 Jun 20;13(1):3540. doi: 10.1038/s41467-022-31228-0.

29. Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder
Lim ET et al. Nat Commun. 2022 Jun 10;13(1):3243. doi: 10.1038/s41467-022-30968-3.

30. Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila
Huang Y et al. Mol Biol Evol. 2022 Jun 10:msac127. doi: 10.1093/molbev/msac127. Online ahead of print.

31. Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states
Jaber M et al. Nat Commun. 2022 Jun 17;13(1):3475. doi: 10.1038/s41467-022-31131-8.

32. Single-cell RNA-seq of a soft-tissue sarcoma model reveals the critical role of tumor-expressed MIF in shaping macrophage heterogeneity
Tessaro FHG et al. Cell Rep. 2022 Jun 21;39(12):110977. doi: 10.1016/j.celrep.2022.110977.

33. Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution
Ma P et al. Cell Rep. 2022 Jun 21;39(12):110979. doi: 10.1016/j.celrep.2022.110979.

34. p57Kip2 regulates embryonic blood stem cells by controlling sympathoadrenal progenitor expansion
Kapeni C et al. Blood. 2022 Jun 2:blood.2021014853. doi: 10.1182/blood.2021014853. Online ahead of print.

35. Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii
Lin G et al. Nat Commun. 2022 Jun 1;13(1):3044. doi: 10.1038/s41467-022-30784-9.

36. EPIC: Inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing
Wang R et al. PLoS Genet. 2022 Jun 16;18(6):e1010251. doi: 10.1371/journal.pgen.1010251. eCollection 2022 Jun.

37. Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing
Wu W et al. Nat Commun. 2022 Jun 10;13(1):3242. doi: 10.1038/s41467-022-30963-8.

38. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma
Chang A et al. Eur Urol. 2022 Jun 16:S0302-2838(22)02395-8. doi: 10.1016/j.eururo.2022.05.021. Online ahead of print.

39. R-SPONDIN2(+) mesenchymal cells form the bud tip progenitor niche during human lung development
Hein RFC et al. Dev Cell. 2022 Jun 7:S1534-5807(22)00367-7. doi: 10.1016/j.devcel.2022.05.010. Online ahead of print.

40. Machine-learning-optimized Cas12a barcoding enables the recovery of single-cell lineages and transcriptional profiles
Hughes NW et al. Mol Cell. 2022 Jun 22:S1097-2765(22)00537-8. doi: 10.1016/j.molcel.2022.06.001. Online ahead of print.

41. Selective ablation of 3' RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts
Gallardo CM et al. Nucleic Acids Res. 2022 Jun 23:gkac516. doi: 10.1093/nar/gkac516. Online ahead of print.

42. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Oh S et al. Nat Commun. 2022 Jun 27;13(1):3695. doi: 10.1038/s41467-022-31411-3.

43. RUV-III-NB: normalization of single cell RNA-seq data
Salim A et al. Nucleic Acids Res. 2022 Jun 27:gkac486. doi: 10.1093/nar/gkac486. Online ahead of print.

44. A programmable in vivo CRISPR activation model elucidates the oncogenic and immunosuppressive functions of MYC in lung adenocarcinoma
Thege FI et al. Cancer Res. 2022 Jun 6:canres.4009.2021. doi: 10.1158/0008-5472.CAN-21-4009. Online ahead of print.

45. Unsupervised cell functional annotation for single-cell RNA-seq
Li D et al. Genome Res. 2022 Jun 28:gr.276609.122. doi: 10.1101/gr.276609.122. Online ahead of print.

46. Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina
Hoang T et al. Cell Rep. 2022 Jun 14;39(11):110849. doi: 10.1016/j.celrep.2022.110849.

47. The novel FGFR inhibitor F1-7 induces DNA damage and cell death in colon cells
Liu Y et al. Br J Cancer. 2022 Jun 17. doi: 10.1038/s41416-022-01878-4. Online ahead of print.

48. Results of the phase IIa RADICAL trial of the FGFR inhibitor AZD4547 in endocrine resistant breast cancer
Coombes RC et al. Nat Commun. 2022 Jun 10;13(1):3246. doi: 10.1038/s41467-022-30666-0.

49. The retrograde signalling regulator ANAC017 recruits the MKK9-MPK3/6, ethylene, and auxin signalling pathways to balance mitochondrial dysfunction with growth
He C et al. Plant Cell. 2022 Jun 16:koac177. doi: 10.1093/plcell/koac177. Online ahead of print.

50. Somatic retrotransposition in the developing rhesus macaque brain
Billon V et al. Genome Res. 2022 Jun 21:gr.276451.121. doi: 10.1101/gr.276451.121. Online ahead of print.

51. Author Correction: Detection of aberrant splicing events in RNA-seq data using FRASER
Mertes C et al. Nat Commun. 2022 Jun 16;13(1):3474. doi: 10.1038/s41467-022-31242-2.

52. The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis
Lakey BD et al. PLoS Genet. 2022 Jun 29;18(6):e1010270. doi: 10.1371/journal.pgen.1010270. Online ahead of print.

53. High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighbouring protein-coding genes
Muskovic W et al. Genome Res. 2022 Jun 27:gr.276818.122. doi: 10.1101/gr.276818.122. Online ahead of print.

54. Macrophage-derived CCL23 upregulates expression of T-cell exhaustion markers in ovarian cancer
Kamat K et al. Br J Cancer. 2022 Jun 24. doi: 10.1038/s41416-022-01887-3. Online ahead of print.

55. Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation
Fontaine E et al. Nucleic Acids Res. 2022 Jun 29:gkac541. doi: 10.1093/nar/gkac541. Online ahead of print.

56. An oncogenic JMJD6-DGAT1 axis tunes the epigenetic regulation of lipid droplet formation in clear cell renal cell carcinoma
Zhou J et al. Mol Cell. 2022 Jun 15:S1097-2765(22)00539-1. doi: 10.1016/j.molcel.2022.06.003. Online ahead of print.

57. Embigin is a fibronectin receptor that affects sebaceous gland differentiation and metabolism
Sipilä K et al. Dev Cell. 2022 Jun 20;57(12):1453-1465.e7. doi: 10.1016/j.devcel.2022.05.011. Epub 2022 Jun 6.

58. Isotype-specific plasma cells express divergent transcriptional programs
Higgins BW et al. Proc Natl Acad Sci U S A. 2022 Jun 21;119(25):e2121260119. doi: 10.1073/pnas.2121260119. Epub 2022 Jun 15.

59. Epigenetic reactivation of transcriptional programs orchestrating fetal lung development in human pulmonary hypertension
Chelladurai P et al. Sci Transl Med. 2022 Jun 8;14(648):eabe5407. doi: 10.1126/scitranslmed.abe5407. Epub 2022 Jun 8.

60. Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing
Xu J et al. Proc Natl Acad Sci U S A. 2022 Jun 21;119(25):e2203179119. doi: 10.1073/pnas.2203179119. Epub 2022 Jun 13.

61. Granzyme K(+) CD8 T cells form a core population in inflamed human tissue
Jonsson AH et al. Sci Transl Med. 2022 Jun 15;14(649):eabo0686. doi: 10.1126/scitranslmed.abo0686. Epub 2022 Jun 15.

62. Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress
Yamagami R et al. Proc Natl Acad Sci U S A. 2022 Jun 21;119(25):e2201237119. doi: 10.1073/pnas.2201237119. Epub 2022 Jun 13.

63. Single-cell analyses highlight the proinflammatory contribution of C1q-high monocytes to Behçet's disease
Zheng W et al. Proc Natl Acad Sci U S A. 2022 Jun 28;119(26):e2204289119. doi: 10.1073/pnas.2204289119. Epub 2022 Jun 21.

64. Molecularly defined circuits for cardiovascular and cardiopulmonary control
Veerakumar A et al. Nature. 2022 Jun;606(7915):739-746. doi: 10.1038/s41586-022-04760-8. Epub 2022 Jun 1.

65. Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development
Xiong Z et al. Nat Cell Biol. 2022 Jun;24(6):968-980. doi: 10.1038/s41556-022-00928-6. Epub 2022 Jun 13.

66. Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential
Vlaming H et al. Nat Struct Mol Biol. 2022 Jun;29(6):613-620. doi: 10.1038/s41594-022-00785-9. Epub 2022 Jun 9.

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