Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 4월)
Writer Admin
Date 2024-04-01
Attached File
Newsletter | Apr. 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. N-Acetyltransferase 10 represses Uqcr11 and Uqcrb independently of ac4C modification to promote heart regeneration
Ma W et al. Nat Commun. 2024 Mar 8;15(1):2137. doi: 10.1038/s41467-024-46458-7.

2. Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis
Murthy D et al. Nat Cell Biol. 2024 Mar 1. doi: 10.1038/s41556-024-01372-4. Online ahead of print.

3. Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance
Xiang X et al. Nat Commun. 2024 Mar 9;15(1):2164. doi: 10.1038/s41467-024-46480-9.

4. N(6)-methyladenosine modification is not a general trait of viral RNA genomes
Baquero-Pérez B et al. Nat Commun. 2024 Mar 11;15(1):1964. doi: 10.1038/s41467-024-46278-9.

5. A single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification
Li Y et al. Nat Commun. 2024 Mar 6;15(1):2019. doi: 10.1038/s41467-024-46455-w.

6. Metabolic targeting of cancer associated fibroblasts overcomes T-cell exclusion and chemoresistance in soft-tissue sarcomas
Broz MT et al. Nat Commun. 2024 Mar 20;15(1):2498. doi: 10.1038/s41467-024-46504-4.

7. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy
Tan CL et al. Nat Biotechnol. 2024 Mar 7. doi: 10.1038/s41587-024-02161-y. Online ahead of print.

8. Neuronal miR-9 promotes HSV-1 epigenetic silencing and latency by repressing Oct-1 and Onecut family genes
Deng Y et al. Nat Commun. 2024 Mar 5;15(1):1991. doi: 10.1038/s41467-024-46057-6.

9. Evolution of a Restriction Factor by Domestication of a Yeast Retrotransposon
Hannon-Hatfield JA et al. Mol Biol Evol. 2024 Mar 1;41(3):msae050. doi: 10.1093/molbev/msae050.

10. Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release
Tufan T et al. Nature. 2024 Mar 13. doi: 10.1038/s41586-024-07172-y. Online ahead of print.

11. Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system
Spisak S et al. Nat Commun. 2024 Mar 12;15(1):2230. doi: 10.1038/s41467-024-46285-w.

12. Genetic and transcriptomic landscape of colonic diverticulosis
Seo J et al. Gut. 2024 Mar 4:gutjnl-2023-331267. doi: 10.1136/gutjnl-2023-331267. Online ahead of print.

13. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration
Advani J et al. Nat Commun. 2024 Mar 4;15(1):1972. doi: 10.1038/s41467-024-46063-8.

14. Targeting ESE3/EHF with Nifurtimox inhibits CXCR2+ neutrophil infiltration and overcomes pancreatic cancer resistance to chemotherapy and immunotherapy
Xie Y et al. Gastroenterology. 2024 Mar 14:S0016-5085(24)00291-9. doi: 10.1053/j.gastro.2024.02.046. Online ahead of print.

15. Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity
Robertson HE et al. Nat Commun. 2024 Mar 19;15(1):2469. doi: 10.1038/s41467-024-45956-y.

16. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy
Li H et al. Cell Metab. 2024 Mar 13:S1550-4131(24)00061-5. doi: 10.1016/j.cmet.2024.02.015. Online ahead of print.

17. miR-430 regulates zygotic mRNA during zebrafish embryogenesis
Baia Amaral D et al. Genome Biol. 2024 Mar 19;25(1):74. doi: 10.1186/s13059-024-03197-8.

18. A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution
Nardone S et al. Nat Commun. 2024 Mar 4;15(1):1966. doi: 10.1038/s41467-024-45907-7.

19. InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data
Liu X et al. Nat Commun. 2024 Mar 22;15(1):2583. doi: 10.1038/s41467-024-46875-8.

20. INSIDER: Interpretable sparse matrix decomposition for RNA expression data analysis
Zhao K et al. PLoS Genet. 2024 Mar 14;20(3):e1011189. doi: 10.1371/journal.pgen.1011189. eCollection 2024 Mar.

21. Long noncoding RNA GATA2AS influences human erythropoiesis by transcription factor and chromatin landscape regulation
Liu G et al. Blood. 2024 Mar 6:blood.2023021287. doi: 10.1182/blood.2023021287. Online ahead of print.

22. txtools: an R package facilitating analysis of RNA modifications, structures, and interactions
Garcia-Campos MA et al. Nucleic Acids Res. 2024 Mar 21:gkae203. doi: 10.1093/nar/gkae203. Online ahead of print.

23. Amphiregulin switches progenitor cell fate for lineage commitment during gastric mucosal regeneration
Lee SH et al. Gastroenterology. 2024 Mar 14:S0016-5085(24)00290-7. doi: 10.1053/j.gastro.2024.03.009. Online ahead of print.

24. Autophagy regulates the maturation of hematopoietic precursors in the embryo
Liu Y et al. Nat Commun. 2024 Mar 15;15(1):2255. doi: 10.1038/s41467-024-46453-y.

25. Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6A) modified RNA
Li Y et al. Nucleic Acids Res. 2024 Mar 1:gkae150. doi: 10.1093/nar/gkae150. Online ahead of print.

26. A cellular model provides insights into the pathogenicity of the oncogenic FOXL2 somatic variant p.Cys134Trp
Herman L et al. Br J Cancer. 2024 Mar 1. doi: 10.1038/s41416-024-02613-x. Online ahead of print.

27. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions
Liu S et al. Nat Commun. 2024 Mar 18;15(1):2425. doi: 10.1038/s41467-024-46596-y.

28. Gene networks and systems biology in Alzheimer's disease: Insights from multi-omics approaches
Rahimzadeh N et al. Alzheimers Dement. 2024 Mar 27. doi: 10.1002/alz.13790. Online ahead of print.

29. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis
Mitra S et al. Nat Genet. 2024 Mar 21. doi: 10.1038/s41588-024-01689-8. Online ahead of print.

30. Perirenal adipose tissue contains a subpopulation of cold-inducible adipocytes derived from brown-to-white conversion
Zhang H et al. Elife. 2024 Mar 12;13:RP93151. doi: 10.7554/eLife.93151.

31. Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis
Hou W et al. Nat Methods. 2024 Mar 25. doi: 10.1038/s41592-024-02235-4. Online ahead of print.

32. Expanding the repertoire reveals recurrent, cryptic and hematopoietic HLA class I minor histocompatibility antigens
Fuchs KJ et al. Blood. 2024 Mar 1:blood.2023022343. doi: 10.1182/blood.2023022343. Online ahead of print.

33. Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study
Li Y et al. Nat Commun. 2024 Mar 19;15(1):2444. doi: 10.1038/s41467-024-46692-z.

34. PRRX1-TOP2A interaction is a malignancy-promoting factor in human malignant peripheral nerve sheath tumours
Takihira S et al. Br J Cancer. 2024 Mar 6. doi: 10.1038/s41416-024-02632-8. Online ahead of print.

35. Determinant of m6A regional preference by transcriptional dynamics
Wang Y et al. Nucleic Acids Res. 2024 Mar 7:gkae169. doi: 10.1093/nar/gkae169. Online ahead of print.

36. Pirfenidone alleviates fibrosis by acting on tumour-stroma interplay in pancreatic cancer
Lei Y et al. Br J Cancer. 2024 Mar 7. doi: 10.1038/s41416-024-02631-9. Online ahead of print.

37. Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data
Lee G et al. Genome Biol. 2024 Mar 11;25(1):66. doi: 10.1186/s13059-024-03208-8.

38. Transcriptomic dysregulation and autistic-like behaviors in Kmt2c haploinsufficient mice rescued by an LSD1 inhibitor
Nakamura T et al. Mol Psychiatry. 2024 Mar 26. doi: 10.1038/s41380-024-02479-8. Online ahead of print.

39. Tyrosine 1-phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
Ajit K et al. Genome Res. 2024 Mar 20;34(2):201-216. doi: 10.1101/gr.278644.123.

40. Villus myofibroblasts are developmental and adult progenitors of mammalian gut lymphatic musculature
Sanketi BD et al. Dev Cell. 2024 Mar 19:S1534-5807(24)00146-1. doi: 10.1016/j.devcel.2024.03.005. Online ahead of print.

41. Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells
Qian C et al. Nat Commun. 2024 Mar 11;15(1):2206. doi: 10.1038/s41467-024-46428-z.

42. A specific enterotype derived from gut microbiome of older individuals enables favorable responses to immune checkpoint blockade therapy
Zhu X et al. Cell Host Microbe. 2024 Mar 18:S1931-3128(24)00075-1. doi: 10.1016/j.chom.2024.03.002. Online ahead of print.

43. Supermultipotency and unpredictability in the developing superior colliculus
Rudenko A et al. Trends Neurosci. 2024 Mar 20:S0166-2236(24)00038-9. doi: 10.1016/j.tins.2024.03.001. Online ahead of print.

44. Metaplastic regeneration in the mouse stomach requires a reactive oxygen species pathway
Miao ZF et al. Dev Cell. 2024 Mar 19:S1534-5807(24)00142-4. doi: 10.1016/j.devcel.2024.03.002. Online ahead of print.

45. Correction to 'Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data'
et al. Nucleic Acids Res. 2024 Mar 23:gkae218. doi: 10.1093/nar/gkae218. Online ahead of print.

46. Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements
Colombi E et al. Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2309263121. doi: 10.1073/pnas.2309263121. Epub 2024 Mar 8.

47. RN7SL1 may be translated under oncogenic conditions
Hara T et al. Proc Natl Acad Sci U S A. 2024 Mar 19;121(12):e2312322121. doi: 10.1073/pnas.2312322121. Epub 2024 Mar 13.

48. Cationic cholesterol-dependent LNP delivery to lung stem cells, the liver, and heart
Radmand A et al. Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2307801120. doi: 10.1073/pnas.2307801120. Epub 2024 Mar 4.

49. Regulatory activity is the default DNA state in eukaryotes
Luthra I et al. Nat Struct Mol Biol. 2024 Mar;31(3):559-567. doi: 10.1038/s41594-024-01235-4. Epub 2024 Mar 6.

50. SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination
Iram T et al. Proc Natl Acad Sci U S A. 2024 Mar 19;121(12):e2307250121. doi: 10.1073/pnas.2307250121. Epub 2024 Mar 14.

51. Attenuation of fibroblast activation and fibrosis by adropin in systemic sclerosis
Liang M et al. Sci Transl Med. 2024 Mar 27;16(740):eadd6570. doi: 10.1126/scitranslmed.add6570. Epub 2024 Mar 27.

52. Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives
Jenniches L et al. Proc Natl Acad Sci U S A. 2024 Apr 2;121(14):e2308814121. doi: 10.1073/pnas.2308814121. Epub 2024 Mar 25.

53. NSUN5/TET2-directed chromatin-associated RNA modification of 5-methylcytosine to 5-hydroxymethylcytosine governs glioma immune evasion
Wu R et al. Proc Natl Acad Sci U S A. 2024 Apr 2;121(14):e2321611121. doi: 10.1073/pnas.2321611121. Epub 2024 Mar 28.

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