Title (2022년 9월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-09-01
Attached File
Newsletter  Sep. 2022
Recent Papers(RNA-Seq Part)

1. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis
Biermann J et al. Cell. 2022 Jul 7;185(14):2591-2608.e30. doi: 10.1016/j.cell.2022.06.007.

2. Identifying cell state-associated alternative splicing events and their coregulation
Buen Abad Najar CF et al. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276109.121. Online ahead of print.

3. A single-cell analysis of thymopoiesis and thymic iNKT cell development in pigs
Gu W et al. Cell Rep. 2022 Jul 5;40(1):111050. doi: 10.1016/j.celrep.2022.111050.

4. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
Zhang R et al. Genome Biol. 2022 Jul 7;23(1):149. doi: 10.1186/s13059-022-02711-0.

5. Cancer type classification using plasma cell-free RNAs derived from human and microbes
Chen S et al. Elife. 2022 Jul 11;11:e75181. doi: 10.7554/eLife.75181.

6. scSTEM: clustering pseudotime ordered single-cell data
Song Q et al. Genome Biol. 2022 Jul 7;23(1):150. doi: 10.1186/s13059-022-02716-9.

7. Mesenchymal-epithelial interaction regulates gastrointestinal tract development in mouse embryos
Zhao L et al. Cell Rep. 2022 Jul 12;40(2):111053. doi: 10.1016/j.celrep.2022.111053.

8. Massively targeted evaluation of therapeutic CRISPR off-targets in cells
Pan X et al. Nat Commun. 2022 Jul 13;13(1):4049. doi: 10.1038/s41467-022-31543-6.

9. Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data
Liu W et al. Nucleic Acids Res. 2022 Jul 8;50(12):e72. doi: 10.1093/nar/gkac219.

10. Genetic dissection of the RNA polymerase II transcription cycle
Chou SP et al. Elife. 2022 Jul 1;11:e78458. doi: 10.7554/eLife.78458.

11. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato
Ma L et al. Plant Cell. 2022 Jul 4;34(7):2747-2764. doi: 10.1093/plcell/koac104.

12. Notch-dependent and -independent functions of transcription factor RBPJ
Friedrich T et al. Nucleic Acids Res. 2022 Jul 15:gkac601. doi: 10.1093/nar/gkac601. Online ahead of print.

13. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis
Romano LM et al. Blood. 2022 Jul 21:blood.2022015724. doi: 10.1182/blood.2022015724. Online ahead of print.

14. A human adipose tissue cell-type transcriptome atlas
Norreen-Thorsen M et al. Cell Rep. 2022 Jul 12;40(2):111046. doi: 10.1016/j.celrep.2022.111046.

15. Hijacking of transcriptional condensates by endogenous retroviruses
Asimi V et al. Nat Genet. 2022 Jul 21. doi: 10.1038/s41588-022-01132-w. Online ahead of print.

16. Donor T cell DNMT3a regulates alloreactivity in mouse models of hematopoietic stem cell transplantation
Ktena YP et al. J Clin Invest. 2022 Jul 1;132(13):e158047. doi: 10.1172/JCI158047.

17. MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering
Kim C et al. Nucleic Acids Res. 2022 Jul 8;50(12):e71. doi: 10.1093/nar/gkac216.

18. A high-resolution map of human RNA translation
Chothani SP et al. Mol Cell. 2022 Jul 7:S1097-2765(22)00606-2. doi: 10.1016/j.molcel.2022.06.023. Online ahead of print.

19. Bromodomain factor 5 is an essential regulator of transcription in Leishmania
Jones NG et al. Nat Commun. 2022 Jul 13;13(1):4071. doi: 10.1038/s41467-022-31742-1.

20. Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells
Luan Y et al. Nucleic Acids Res. 2022 Jul 8;50(12):6601-6617. doi: 10.1093/nar/gkac053.

21. Deconstructing cold-induced brown adipocyte neogenesis in mice
Burl RB et al. Elife. 2022 Jul 18;11:e80167. doi: 10.7554/eLife.80167. Online ahead of print.

22. Renal organoid modeling of tuberous sclerosis complex reveals lesion features arise from diverse developmental processes
Pietrobon A et al. Cell Rep. 2022 Jul 5;40(1):111048. doi: 10.1016/j.celrep.2022.111048.

23. A time-resolved, multi-symbol molecular recorder via sequential genome editing
Choi J et al. Nature. 2022 Jul 6. doi: 10.1038/s41586-022-04922-8. 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 Jul 22;50(13):7591-7607. doi: 10.1093/nar/gkac534.

25. Base editing in bovine embryos reveals a species-specific role of SOX2 in regulation of pluripotency
Luo L et al. PLoS Genet. 2022 Jul 5;18(7):e1010307. doi: 10.1371/journal.pgen.1010307. eCollection 2022 Jul.

26. DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk
Kalita CA et al. Genome Biol. 2022 Jul 8;23(1):152. doi: 10.1186/s13059-022-02708-9.

27. 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 Jul 2;39(7):msac127. doi: 10.1093/molbev/msac127.

28. Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq
Liu Y et al. Nat Protoc. 2022 Jul 13. doi: 10.1038/s41596-022-00704-8. Online ahead of print.

29. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks
Freimer JW et al. Nat Genet. 2022 Jul 11. doi: 10.1038/s41588-022-01106-y. Online ahead of print.

30. Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin
Chakraborty A et al. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276192.121. Online ahead of print.

31. Regulatory enhancer profiling of mesenchymal-type gastric cancer reveals subtype-specific epigenomic landscapes and targetable vulnerabilities
Ho SWT et al. Gut. 2022 Jul 11:gutjnl-2021-326483. doi: 10.1136/gutjnl-2021-326483. Online ahead of print.

32. Lymph node fibroblastic reticular cells preserve a tolerogenic niche in allograft transplantation through laminin α4
Li L et al. J Clin Invest. 2022 Jul 1;132(13):e156994. doi: 10.1172/JCI156994.

33. Distinct histopathological phenotypes of severe alcoholic hepatitis suggest different mechanisms driving liver injury and failure
Ma J et al. J Clin Invest. 2022 Jul 15;132(14):e157780. doi: 10.1172/JCI157780.

34. Exploring the expression patterns of palmitoylating and de-palmitoylating enzymes in the mouse brain using the curated RNA-seq database BrainPalmSeq
Wild AR et al. Elife. 2022 Jul 12;11:e75804. doi: 10.7554/eLife.75804. Online ahead of print.

35. Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome
Dantas Machado AC et al. Cell Rep. 2022 Jul 5;40(1):111008. doi: 10.1016/j.celrep.2022.111008.

36. Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control
Wagner S et al. Nat Protoc. 2022 Jul 22. doi: 10.1038/s41596-022-00708-4. Online ahead of print.

37. Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure
Yu B et al. Nat Commun. 2022 Jul 22;13(1):4227. doi: 10.1038/s41467-022-31875-3.

38. Transcriptional Repression by FoxM1 Suppresses Tumor Differentiation and Promotes Metastasis of Breast Cancer
Kopanja D et al. Cancer Res. 2022 Jul 5;82(13):2458-2471. doi: 10.1158/0008-5472.CAN-22-0410.

39. ZnT8 loss-of-function accelerates functional maturation of hESC-derived β cells and resists metabolic stress in diabetes
Ma Q et al. Nat Commun. 2022 Jul 16;13(1):4142. doi: 10.1038/s41467-022-31829-9.

40. HLA-B∗46 associates with rapid HIV disease progression in Asian cohorts and prominent differences in NK cell phenotype
Li SS et al. Cell Host Microbe. 2022 Jul 15:S1931-3128(22)00310-9. doi: 10.1016/j.chom.2022.06.005. Online ahead of print.

41. 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 Jul 22;50(13):7350-7366. doi: 10.1093/nar/gkac541.

42. Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer's disease
Otero-Garcia M et al. Neuron. 2022 Jul 21:S0896-6273(22)00600-6. doi: 10.1016/j.neuron.2022.06.021. Online ahead of print.

43. Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1(st) and 2(nd) chemical steps
Gildea MA et al. Mol Cell. 2022 Jul 8:S1097-2765(22)00603-7. doi: 10.1016/j.molcel.2022.06.020. Online ahead of print.

44. TransMeta simultaneously assembles multisample RNA-seq reads
Yu T et al. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276434.121. Online ahead of print.

45. ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics
Hao Y et al. Genome Biol. 2022 Jul 25;23(1):162. doi: 10.1186/s13059-022-02729-4.

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