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For: Morlan JD, Qu K, Sinicropi DV. Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue. PLoS One 2012;7:e42882. [PMID: 22900061 DOI: 10.1371/journal.pone.0042882] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/13/2012] [Indexed: 11/23/2022]  Open
Number Cited by Other Article(s)
1
Cheslock A, Provencher J, Campeau W, MacMillan HA. The impact of microplastics on tissue-specific gene expression in the tropical house cricket, Gryllodes sigillatus. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025:126475. [PMID: 40383478 DOI: 10.1016/j.envpol.2025.126475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 05/14/2025] [Accepted: 05/15/2025] [Indexed: 05/20/2025]
2
Lee J, Jeon HH, Seo E, Park S, Choe D, Cho BK, Lee JW. Direct mRNA-to-sgRNA conversion generates design-free ultra-dense CRISPRi libraries for systematic phenotypic screening. Metab Eng 2025;89:108-120. [PMID: 39993558 DOI: 10.1016/j.ymben.2025.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 01/16/2025] [Accepted: 02/20/2025] [Indexed: 02/26/2025]
3
Ndione MHD, Ndiaye EH, Dieng M, Diouf B, Sankhé S, Diallo D, Kane M, Sene NM, Mbanne M, Sy FA, Diop SMBS, Doukanda SFM, Sall AA, Faye O, Dia N, Weaver SC, Faye O, Diallo M, Fall G, Gaye A, Diagne MM. Mosquito-Based Detection of Endogenous Jaagsiekte Sheep Retrovirus in Senegal: Expanding the Scope of Xenosurveillance. RESEARCH SQUARE 2025:rs.3.rs-5951454. [PMID: 40313750 PMCID: PMC12045356 DOI: 10.21203/rs.3.rs-5951454/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2025]
4
Hong ZH, Zhu L, Gao LL, Zhu Z, Su T, Krall L, Wu XN, Bock R, Wu GZ. Chloroplast precursor protein preClpD overaccumulation triggers multilevel reprogramming of gene expression and a heat shock-like response. Nat Commun 2025;16:3777. [PMID: 40263324 PMCID: PMC12015282 DOI: 10.1038/s41467-025-59043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 04/07/2025] [Indexed: 04/24/2025]  Open
5
Chen P, Lin L, Lin X, Liao K, Qiang J, Wang Z, Wu J, Li Y, Yang L, Yao N, Song H, Hong Y, Liu WH, Zhang Y, Chang X, Du D, Xiao C. A Csde1-Strap complex regulates plasma cell differentiation by coupling mRNA translation and decay. Nat Commun 2025;16:2906. [PMID: 40133358 PMCID: PMC11937441 DOI: 10.1038/s41467-025-58212-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 03/13/2025] [Indexed: 03/27/2025]  Open
6
Wilson T, Kuch M, Poinar D, Rockarts J, Wainman B, Morgello S, Poinar H. Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues. Biotechniques 2025;77:76-93. [PMID: 40071636 PMCID: PMC12063700 DOI: 10.1080/07366205.2025.2473842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 02/26/2025] [Indexed: 04/10/2025]  Open
7
Lamb E, Pant D, Yang B, Hundley HA. A probe-based capture enrichment method for detection of A-to-I editing in low abundance transcripts. Methods Enzymol 2025;710:55-75. [PMID: 39870451 DOI: 10.1016/bs.mie.2024.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2025]
8
Phelps WA, Ayers TN, Lee MT. Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation. Methods Mol Biol 2025;2923:163-180. [PMID: 40418449 DOI: 10.1007/978-1-0716-4522-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
9
Haile S, Corbett RD, O’Neill K, Xu J, Smailus DE, Pandoh PK, Bayega A, Bala M, Chuah E, Coope RJN, Moore RA, Mungall KL, Zhao Y, Ma Y, Marra MA, Jones SJM, Mungall AJ. Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs. Front Genet 2024;15:1466338. [PMID: 39687742 PMCID: PMC11647301 DOI: 10.3389/fgene.2024.1466338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 11/11/2024] [Indexed: 12/18/2024]  Open
10
Fluke KA, Dai N, Wolf EJ, Fuchs RT, Ho PS, Talbott V, Elkins L, Tsai YL, Schiltz J, Febvre HP, Czarny R, Robb GB, Corrêa IR, Santangelo TJ. A novel N4,N4-dimethylcytidine in the archaeal ribosome enhances hyperthermophily. Proc Natl Acad Sci U S A 2024;121:e2405999121. [PMID: 39471227 PMCID: PMC11551388 DOI: 10.1073/pnas.2405999121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 09/26/2024] [Indexed: 11/01/2024]  Open
11
Vilstrup AP, Gupta A, Rasmussen AJ, Ebert A, Riedelbauch S, Lukassen MV, Hayashi R, Andersen P. A germline PAF1 paralog complex ensures cell type-specific gene expression. Genes Dev 2024;38:866-886. [PMID: 39332828 PMCID: PMC11535153 DOI: 10.1101/gad.351930.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/27/2024] [Indexed: 09/29/2024]
12
Fluke KA, Fuchs RT, Tsai YL, Talbott V, Elkins L, Febvre HP, Dai N, Wolf EJ, Burkhart BW, Schiltz J, Brett Robb G, Corrêa IR, Santangelo TJ. The extensive m5C epitranscriptome of Thermococcus kodakarensis is generated by a suite of RNA methyltransferases that support thermophily. Nat Commun 2024;15:7272. [PMID: 39179532 PMCID: PMC11344067 DOI: 10.1038/s41467-024-51410-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 08/06/2024] [Indexed: 08/26/2024]  Open
13
Liu H, Hu K, O’Connor K, Kelliher MA, Zhu LJ. CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data. BIOTECH 2024;13:30. [PMID: 39189209 PMCID: PMC11348166 DOI: 10.3390/biotech13030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/01/2024] [Accepted: 07/14/2024] [Indexed: 08/28/2024]  Open
14
Zhao J, Huang Y, Liukang C, Yang R, Tang L, Sun L, Zhao Y, Zhang G. Dissecting infectious bronchitis virus-induced host shutoff at the translation level. J Virol 2024;98:e0083024. [PMID: 38940559 PMCID: PMC11265393 DOI: 10.1128/jvi.00830-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024]  Open
15
Zhao H, Xiong Y, Zhou Z, Xu Q, Zi Y, Zheng X, Chen S, Xiao X, Gong L, Xu H, Liu L, Lu H, Cui Y, Shao S, Zhang J, Ma J, Zhou Q, Ma D, Li X. A hidden proteome encoded by circRNAs in human placentas: Implications for uncovering preeclampsia pathogenesis. Clin Transl Med 2024;14:e1759. [PMID: 38997803 PMCID: PMC11245404 DOI: 10.1002/ctm2.1759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]  Open
16
Ura H, Niida Y. Comparison of RNA-Sequencing Methods for Degraded RNA. Int J Mol Sci 2024;25:6143. [PMID: 38892331 PMCID: PMC11172666 DOI: 10.3390/ijms25116143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]  Open
17
Friedländer MR, Gilbert MTP. How ancient RNA survives and what we can learn from it. Nat Rev Mol Cell Biol 2024;25:417-418. [PMID: 38548931 DOI: 10.1038/s41580-024-00726-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
18
Singh A, Xue A, Tai J, Mbadugha F, Obi P, Mascarenhas R, Tyagi A, Siena A, Chen YG. A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations. RNA (NEW YORK, N.Y.) 2024;30:728-738. [PMID: 38485192 PMCID: PMC11098455 DOI: 10.1261/rna.079761.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
19
Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024;15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
20
Zhang L, Ruan J, Gao F, Xin Q, Che LP, Cai L, Liu Z, Kong M, Rochaix JD, Mi H, Peng L. Thylakoid protein FPB1 synergistically cooperates with PAM68 to promote CP47 biogenesis and Photosystem II assembly. Nat Commun 2024;15:3122. [PMID: 38600073 PMCID: PMC11006888 DOI: 10.1038/s41467-024-46863-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024]  Open
21
Zhan J, Jin K, Xie R, Fan J, Tang Y, Chen C, Li H, Wang DW. AGO2 Protects Against Diabetic Cardiomyopathy by Activating Mitochondrial Gene Translation. Circulation 2024;149:1102-1120. [PMID: 38126189 DOI: 10.1161/circulationaha.123.065546] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
22
Samuels TJ, Gui J, Gebert D, Karam Teixeira F. Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation. EMBO J 2024;43:1591-1617. [PMID: 38480936 PMCID: PMC11021484 DOI: 10.1038/s44318-024-00070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/18/2024]  Open
23
Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 2024;15:2425. [PMID: 38499544 PMCID: PMC10948791 DOI: 10.1038/s41467-024-46596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/04/2024] [Indexed: 03/20/2024]  Open
24
He H, Wei Y, Chen Y, Zhao X, Shen X, Zhu Q, Yin H. High expression circRALGPS2 in atretic follicle induces chicken granulosa cell apoptosis and autophagy via encoding a new protein. J Anim Sci Biotechnol 2024;15:42. [PMID: 38468340 PMCID: PMC10926623 DOI: 10.1186/s40104-024-01003-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/29/2024] [Indexed: 03/13/2024]  Open
25
Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024;21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
26
Gosch A, Banemann R, Dørum G, Haas C, Hadrys T, Haenggi N, Kulstein G, Neubauer J, Courts C. Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva. Int J Legal Med 2024;138:401-412. [PMID: 37847308 PMCID: PMC10861700 DOI: 10.1007/s00414-023-03100-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
27
Goraichuk IV, Harden M, Spackman E, Suarez DL. The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing. Front Microbiol 2024;15:1328987. [PMID: 38351914 PMCID: PMC10864109 DOI: 10.3389/fmicb.2024.1328987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]  Open
28
Klein DC, Lardo SM, Hainer SJ. The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9. CANCER RESEARCH COMMUNICATIONS 2024;4:237-252. [PMID: 38126767 PMCID: PMC10831031 DOI: 10.1158/2767-9764.crc-23-0382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
29
Li B, Liu S, Zheng W, Liu A, Yu P, Wu D, Zhou J, Zhang P, Liu C, Lin Q, Ye J, He S, Huang Q, Zhou H, Chen J, Qu L, Yang J. RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators. Nat Biotechnol 2024;42:119-131. [PMID: 37037902 DOI: 10.1038/s41587-023-01749-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/13/2023] [Indexed: 04/12/2023]
30
Tang J, Wang S, Weng M, Guo Q, Ren L, He Y, Cui Z, Cong M, Qin M, Yu J, Su R, Li X. The IGF2BP3-COPS7B Axis Facilitates mRNA Translation to Drive Colorectal Cancer Progression. Cancer Res 2023;83:3593-3610. [PMID: 37560971 DOI: 10.1158/0008-5472.can-23-0557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/21/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023]
31
Bakre A, Kariithi HM, Suarez DL. Alternative probe hybridization buffers for target RNA depletion and viral sequence recovery in NGS for poultry samples. J Virol Methods 2023;321:114793. [PMID: 37604238 DOI: 10.1016/j.jviromet.2023.114793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023]
32
Griesinger AM, Riemondy K, Eswaran N, Donson AM, Willard N, Prince EW, Paine SM, Bowes G, Rheaume J, Chapman RJ, Ramage J, Jackson A, Grundy RG, Foreman NK, Ritzmann TA. Multi-omic approach identifies hypoxic tumor-associated myeloid cells that drive immunobiology of high-risk pediatric ependymoma. iScience 2023;26:107585. [PMID: 37694144 PMCID: PMC10484966 DOI: 10.1016/j.isci.2023.107585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 09/12/2023]  Open
33
VanKuren NW, Doellman MM, Sheikh SI, Palmer Droguett DH, Massardo D, Kronforst MR. Acute and Long-Term Consequences of Co-opted doublesex on the Development of Mimetic Butterfly Color Patterns. Mol Biol Evol 2023;40:msad196. [PMID: 37668300 PMCID: PMC10498343 DOI: 10.1093/molbev/msad196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]  Open
34
Klein DC, Lardo SM, McCannell KN, Hainer SJ. FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells. BMC Biol 2023;21:167. [PMID: 37542287 PMCID: PMC10403911 DOI: 10.1186/s12915-023-01669-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023]  Open
35
Miranda RP, Turrini PCG, Bonadio DT, Zerillo MM, Berselli AP, Creste S, Van Sluys MA. Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness. Microbiol Spectr 2023;11:e0280222. [PMID: 37052486 PMCID: PMC10269729 DOI: 10.1128/spectrum.02802-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 03/03/2023] [Indexed: 04/14/2023]  Open
36
Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K, Du Y, Li S, Yan L, Xie Z, Lyu Y, Shen F, Li Q. Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum. BMC Biol 2023;21:68. [PMID: 37013569 PMCID: PMC10071632 DOI: 10.1186/s12915-023-01564-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023]  Open
37
Tan X, Zheng C, Zhuang Y, Jin P, Wang F. The m6A reader PRRC2A is essential for meiosis I completion during spermatogenesis. Nat Commun 2023;14:1636. [PMID: 36964127 PMCID: PMC10039029 DOI: 10.1038/s41467-023-37252-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/08/2023] [Indexed: 03/26/2023]  Open
38
Everaert C, Verwilt J, Verniers K, Vandamme N, Marcos Rubio A, Vandesompele J, Mestdagh P. Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation. Biol Proced Online 2023;25:7. [PMID: 36890441 PMCID: PMC9996952 DOI: 10.1186/s12575-023-00193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/14/2023] [Indexed: 03/10/2023]  Open
39
Koh C, Frangeul L, Blanc H, Ngoagouni C, Boyer S, Dussart P, Grau N, Girod R, Duchemin JB, Saleh MC. Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification. eLife 2023;12:82762. [PMID: 36688360 PMCID: PMC10014081 DOI: 10.7554/elife.82762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023]  Open
40
Lin W, Chen L, Zhang H, Qiu X, Huang Q, Wan F, Le Z, Geng S, Zhang A, Qiu S, Chen L, Kong L, Lu JJ. Tumor-intrinsic YTHDF1 drives immune evasion and resistance to immune checkpoint inhibitors via promoting MHC-I degradation. Nat Commun 2023;14:265. [PMID: 36650153 PMCID: PMC9845301 DOI: 10.1038/s41467-022-35710-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023]  Open
41
Cheng R, Li F, Zhang M, Xia X, Wu J, Gao X, Zhou H, Zhang Z, Huang N, Yang X, Zhang Y, Shen S, Kang T, Liu Z, Xiao F, Yao H, Xu J, Yan C, Zhang N. A novel protein RASON encoded by a lncRNA controls oncogenic RAS signaling in KRAS mutant cancers. Cell Res 2023;33:30-45. [PMID: 36241718 PMCID: PMC9810732 DOI: 10.1038/s41422-022-00726-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/05/2022] [Indexed: 01/07/2023]  Open
42
Yu T, Biasini A, Cecchini K, Saflund M, Mou H, Arif A, Eghbali A, de Rooij D, Weng Z, Zamore PD, Ozata DM. A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals. RNA (NEW YORK, N.Y.) 2022;29:rna.079472.122. [PMID: 36241367 PMCID: PMC9808571 DOI: 10.1261/rna.079472.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
43
Lu W, Zhou Q, Chen Y. Impact of RNA degradation on next-generation sequencing transcriptome data. Genomics 2022;114:110429. [PMID: 35810931 DOI: 10.1016/j.ygeno.2022.110429] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 11/04/2022]
44
Yang L, Ren Z, Yan S, Zhao L, Liu J, Zhao L, Li Z, Ye S, Liu A, Li X, Guo J, Zhao W, Kuang W, Liu H, Chen D. Nsun4 and Mettl3 mediated translational reprogramming of Sox9 promotes BMSC chondrogenic differentiation. Commun Biol 2022;5:495. [PMID: 35614315 PMCID: PMC9133052 DOI: 10.1038/s42003-022-03420-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/27/2022] [Indexed: 11/09/2022]  Open
45
Liu Z, Yang E. circFL-seq, A Full-length circRNA Sequencing Method. Bio Protoc 2022;12:e4384. [PMID: 35800097 PMCID: PMC9081479 DOI: 10.21769/bioprotoc.4384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 12/29/2022]  Open
46
Hu X, Zhang Y, Du M, Yang E. Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei. Mycology 2022;13:106-118. [PMID: 35711330 PMCID: PMC9196791 DOI: 10.1080/21501203.2021.2017045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]  Open
47
Liu Z, Wu A, Wu Z, Wang T, Pan Y, Li B, Zhang X, Yu M. TOX4 facilitates promoter-proximal pausing and C-terminal domain dephosphorylation of RNA polymerase II in human cells. Commun Biol 2022;5:300. [PMID: 35365735 PMCID: PMC8975821 DOI: 10.1038/s42003-022-03214-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]  Open
48
Mubarak G, Zahir FR. Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine. J Pers Med 2022;12:199. [PMID: 35207687 PMCID: PMC8877836 DOI: 10.3390/jpm12020199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/07/2022]  Open
49
Raghavan V, Kraft L, Mesny F, Rigerte L. A simple guide to de novo transcriptome assembly and annotation. Brief Bioinform 2022;23:6514404. [PMID: 35076693 PMCID: PMC8921630 DOI: 10.1093/bib/bbab563] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]  Open
50
Che L, Meng H, Ruan J, Peng L, Zhang L. Rubredoxin 1 Is Required for Formation of the Functional Photosystem II Core Complex in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022;13:824358. [PMID: 35283894 PMCID: PMC8905225 DOI: 10.3389/fpls.2022.824358] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/13/2022] [Indexed: 05/03/2023]
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