Title (2022년 4월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-04-01
Attached File
Newsletter  Apr. 2022
Recent Papers(RNA-Seq Part)

1. A multiomic study uncovers a bZIP23-PER1A-mediated detoxification pathway to enhance seed vigor in rice
Wang WQ et al. Proc Natl Acad Sci U S A. 2022 Mar 1;119(9):e2026355119. doi: 10.1073/pnas.2026355119.

2. TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
Li D et al. Genome Biol. 2022 Mar 7;23(1):73. doi: 10.1186/s13059-022-02629-7.

3. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62
Yu G et al. Nat Commun. 2022 Mar 25;13(1):1607. doi: 10.1038/s41467-022-29132-8.

4. M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression
Yadav P et al. Cancer Res. 2022 Mar 18:canres.2106.2021. doi: 10.1158/0008-5472.CAN-21-2106. Online ahead of print.

5. Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
Kaminow B et al. Genome Res. 2022 Mar 7:gr.275613.121. doi: 10.1101/gr.275613.121. Online ahead of print.

6. The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages
Trouillon J et al. Nat Commun. 2022 Mar 10;13(1):1258. doi: 10.1038/s41467-022-28849-w.

7. Comprehensive evaluation of deconvolution methods for human brain gene expression
Sutton GJ et al. Nat Commun. 2022 Mar 15;13(1):1358. doi: 10.1038/s41467-022-28655-4.

8. m(6)A RNA modifications are measured at single-base resolution across the mammalian transcriptome
Hu L et al. Nat Biotechnol. 2022 Mar 14. doi: 10.1038/s41587-022-01243-z. Online ahead of print.

9. Grouped-seq for integrated phenotypic and transcriptomic screening of patient-derived tumor organoids
Wu Y et al. Nucleic Acids Res. 2022 Mar 21;50(5):e28. doi: 10.1093/nar/gkab1201.

10. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies
Biancon G et al. Mol Cell. 2022 Mar 17;82(6):1107-1122.e7. doi: 10.1016/j.molcel.2022.02.025.

11. A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell
Ruiz Tejada Segura ML et al. Cell Rep. 2022 Mar 22;38(12):110547. doi: 10.1016/j.celrep.2022.110547.

12. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
Hardwick SA et al. Nat Biotechnol. 2022 Mar 7. doi: 10.1038/s41587-022-01231-3. Online ahead of print.

13. Enhanced protein isoform characterization through long-read proteogenomics
Miller RM et al. Genome Biol. 2022 Mar 3;23(1):69. doi: 10.1186/s13059-022-02624-y.

14. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7
Maldotti M et al. Nucleic Acids Res. 2022 Mar 21;50(5):2587-2602. doi: 10.1093/nar/gkac083.

15. Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
Collora JA et al. Immunity. 2022 Mar 17:S1074-7613(22)00127-3. doi: 10.1016/j.immuni.2022.03.004. Online ahead of print.

16. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum
Hollin T et al. Nat Commun. 2022 Mar 11;13(1):1275. doi: 10.1038/s41467-022-28981-7.

17. Immune Infiltrate and Tumor Microenvironment Transcriptional Programs Stratify Pediatric Osteosarcoma into Prognostic Groups at Diagnosis
Marchais A et al. Cancer Res. 2022 Mar 15;82(6):974-985. doi: 10.1158/0008-5472.CAN-20-4189.

18. Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency
Ivanov IP et al. Proc Natl Acad Sci U S A. 2022 Mar 1;119(9):e2117226119. doi: 10.1073/pnas.2117226119.

19. Concurrent CDX2 cis-deregulation and UBTF-ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL
Passet M et al. Blood. 2022 Mar 22:blood.2021014723. doi: 10.1182/blood.2021014723. Online ahead of print.

20. A PRC2-Kdm5b axis sustains tumorigenicity of acute myeloid leukemia
Ren Z et al. Proc Natl Acad Sci U S A. 2022 Mar 1;119(9):e2122940119. doi: 10.1073/pnas.2122940119.

21. Landscape of adenosine-to-inosine RNA recoding across human tissues
Gabay O et al. Nat Commun. 2022 Mar 4;13(1):1184. doi: 10.1038/s41467-022-28841-4.

22. Genome-wide landscape of ApiAP2 transcription factors reveals a heterochromatin-associated regulatory network during Plasmodium falciparum blood-stage development
Shang X et al. Nucleic Acids Res. 2022 Mar 14:gkac176. doi: 10.1093/nar/gkac176. Online ahead of print.

23. The microprotein Nrs1 rewires the G1/S transcriptional machinery during nitrogen limitation in budding yeast
Tollis S et al. PLoS Biol. 2022 Mar 3;20(3):e3001548. doi: 10.1371/journal.pbio.3001548. eCollection 2022 Mar.

24. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek K et al. Nat Commun. 2022 Mar 22;13(1):1536. doi: 10.1038/s41467-022-28776-w.

25. Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity
LeBlanc VG et al. Cancer Cell. 2022 Mar 14:S1535-6108(22)00068-X. doi: 10.1016/j.ccell.2022.02.016. Online ahead of print.

26. Nuclear hormone receptor NHR-49 acts in parallel with HIF-1 to promote hypoxia adaptation in Caenorhabditis elegans
Doering KRS et al. Elife. 2022 Mar 14;11:e67911. doi: 10.7554/eLife.67911.

27. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms
Zhang Z et al. Cell Rep. 2022 Mar 8;38(10):110467. doi: 10.1016/j.celrep.2022.110467.

28. Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq
Blue SM et al. Nat Protoc. 2022 Mar 23. doi: 10.1038/s41596-022-00680-z. Online ahead of print.

29. Odorant-receptor-mediated regulation of chemosensory gene expression in the malaria mosquito Anopheles gambiae
Maguire SE et al. Cell Rep. 2022 Mar 8;38(10):110494. doi: 10.1016/j.celrep.2022.110494.

30. Low Glucose-Induced Overexpression of HOXC-AS3 Promotes Metabolic Reprogramming of Breast Cancer
Zhu W et al. Cancer Res. 2022 Mar 1;82(5):805-818. doi: 10.1158/0008-5472.CAN-21-1179.

31. Stonewall prevents expression of ectopic genes in the ovary and accumulates at insulator elements in D. melanogaster
Zinshteyn D et al. PLoS Genet. 2022 Mar 24;18(3):e1010110. doi: 10.1371/journal.pgen.1010110. Online ahead of print.

32. mTOR activity is essential for retinal pigment epithelium regeneration in zebrafish
Lu F et al. PLoS Genet. 2022 Mar 10;18(3):e1009628. doi: 10.1371/journal.pgen.1009628. eCollection 2022 Mar.

33. Virus-specific editing identification approach reveals the landscape of A-to-I editing and its impacts on SARS-CoV-2 characteristics and evolution
Song Y et al. Nucleic Acids Res. 2022 Mar 21;50(5):2509-2521. doi: 10.1093/nar/gkac120.

34. Lysosomal exocytosis of HSP70 stimulates monocytic BMP6 expression in Sjögren's syndrome
Mo YQ et al. J Clin Invest. 2022 Mar 15;132(6):e152780. doi: 10.1172/JCI152780.

35. Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor
Miozzo F et al. Nat Commun. 2022 Mar 17;13(1):1426. doi: 10.1038/s41467-022-29075-0.

36. Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading
Liang C et al. Nat Commun. 2022 Mar 8;13(1):1217. doi: 10.1038/s41467-022-28872-x.

37. Global chromosome rearrangement induced by CRISPR-Cas9 reshapes the genome and transcriptome of human cells
Liu Y et al. Nucleic Acids Res. 2022 Mar 4:gkac153. doi: 10.1093/nar/gkac153. Online ahead of print.

38. Nephronectin-integrin α8 signaling is required for proper migration of periocular neural crest cells during chick corneal development
Ma J et al. Elife. 2022 Mar 3;11:e74307. doi: 10.7554/eLife.74307.

39. Transcriptome and chromatin alterations in social fear indicate association of MEG3 with successful extinction of fear
Royer M et al. Mol Psychiatry. 2022 Mar 25. doi: 10.1038/s41380-022-01481-2. Online ahead of print.

40. ZFP541 maintains the repression of pre-pachytene transcriptional programs and promotes male meiosis progression
Xu J et al. Cell Rep. 2022 Mar 22;38(12):110540. doi: 10.1016/j.celrep.2022.110540.

41. AP-2α and AP-2β cooperatively function in the craniofacial surface ectoderm to regulate chromatin and gene expression dynamics during facial development
Van Otterloo E et al. Elife. 2022 Mar 25;11:e70511. doi: 10.7554/eLife.70511. Online ahead of print.

42. Exaggerated false positives by popular differential expression methods when analyzing human population samples
Li Y et al. Genome Biol. 2022 Mar 15;23(1):79. doi: 10.1186/s13059-022-02648-4.

43. Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data
Liu W et al. Nucleic Acids Res. 2022 Mar 29:gkac219. doi: 10.1093/nar/gkac219. Online ahead of print.

44. The Arabidopsis cyclophilin CYP18-1 facilitates PRP18 dephosphorylation and the splicing of introns retained under heat stress
Jo SH et al. Plant Cell. 2022 Mar 9:koac084. doi: 10.1093/plcell/koac084. Online ahead of print.

45. PhOxi-Seq: Single-Nucleotide Resolution Sequencing of N(2)-Methylation at Guanosine in RNA by Photoredox Catalysis
Chung Kim Chung K et al. J Am Chem Soc. 2022 Mar 22. doi: 10.1021/jacs.2c00670. Online ahead of print.

46. Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging
Ye L et al. Nat Struct Mol Biol. 2022 Mar 28. doi: 10.1038/s41594-022-00746-2. Online ahead of print.

47. Unique molecular features and cellular responses differentiate two populations of motor cortical layer 5b neurons in a preclinical model of ALS
Moya MV et al. Cell Rep. 2022 Mar 22;38(12):110556. doi: 10.1016/j.celrep.2022.110556.

48. Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology
Sajuthi SP et al. Nat Commun. 2022 Mar 28;13(1):1632. doi: 10.1038/s41467-022-28973-7.

49. Single-cell transcriptomic landscapes of the otic neuronal lineage at multiple early embryonic ages
Sun Y et al. Cell Rep. 2022 Mar 22;38(12):110542. doi: 10.1016/j.celrep.2022.110542.

50. NOGOB receptor deficiency increases cerebrovascular permeability and hemorrhage via impairing histone acetylation mediated CCM1/2 expression
Fang Z et al. J Clin Invest. 2022 Mar 22:e151382. doi: 10.1172/JCI151382. Online ahead of print.

51. Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified using scRNA-seq
Ulrich ND et al. Dev Cell. 2022 Mar 10:S1534-5807(22)00119-8. doi: 10.1016/j.devcel.2022.02.017. Online ahead of print.

52. ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3
Wei W et al. Cell Rep. 2022 Mar 22;38(12):110546. doi: 10.1016/j.celrep.2022.110546.

53. Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids
Thomas ED et al. Dev Cell. 2022 Mar 28;57(6):820-836.e6. doi: 10.1016/j.devcel.2022.02.018. Epub 2022 Mar 17.

54. Systematic reconstruction of cellular trajectories across mouse embryogenesis
Qiu C et al. Nat Genet. 2022 Mar;54(3):328-341. doi: 10.1038/s41588-022-01018-x. Epub 2022 Mar 14.

55. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
He D et al. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11.

56. Prediction of histone post-translational modification patterns based on nascent transcription data
Wang Z et al. Nat Genet. 2022 Mar;54(3):295-305. doi: 10.1038/s41588-022-01026-x. Epub 2022 Mar 10.

57. A single factor elicits multilineage reprogramming of astrocytes in the adult mouse striatum
Zhang Y et al. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2107339119. doi: 10.1073/pnas.2107339119. Epub 2022 Mar 7.

58. Single-cell transcriptome analysis reveals three sequential phases of gene expression during zebrafish sensory hair cell regeneration
Baek S et al. Dev Cell. 2022 Mar 28;57(6):799-819.e6. doi: 10.1016/j.devcel.2022.03.001. Epub 2022 Mar 21.

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