Searching journal content for articles similar to Erkelenz et al. 28 (12): 1826.

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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...in RNA-seq; note SSU < 1 owing to partial intron retention). In silico mutations confirmed that mutations in the 5′ splice site 2 motif resulted in abrogation of its usage, as one would expect. Importantly, a G > T mutation that restores 5′ splice site 1 in human SOX13 in silico was also predicted...
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Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...by RNA-seq. Wilcoxon rank-sum test P-values are shown.Thus, our computational pipeline took advantage of the two unique features of RAMPAGE technique (TSS identification and connection to the downstream transcripts) and the features of primary Alu elements (unspliced and transcribed past its body...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...). Recently, using samples from postmortem ASD and control brains, several studies have reported a wide range of dysregulation of gene expression (Voineagu et al. 2011; Guan et al. 2016; Parikshak et al. 2016) in ASD. Moreover, epigenetic factors such as alternatively spliced transcripts (Voineagu et al. 2011...
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Research: Pathogenicity and selective constraint on variation near splice sites
- Jenny Lord,
- Giuseppe Gallone,
- Patrick J. Short,
- Jeremy F. McRae,
- Holly Ironfield,
- Elizabeth H. Wynn,
- Sebastian S. Gerety,
- Liu He,
- Bronwyn Kerr,
- Diana S. Johnson,
- Emma McCann,
- Esther Kinning,
- Frances Flinter,
- I. Karen Temple,
- Jill Clayton-Smith,
- Meriel McEntagart,
- Sally Ann Lynch,
- Shelagh Joss,
- Sofia Douzgou,
- Tabib Dabir,
- Virginia Clowes,
- Vivienne P.M. McConnell,
- Wayne Lam,
- Caroline F. Wright,
- David R. FitzPatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. February 2019 29: 159-170; Published in Advance December 26, 2018, doi:10.1101/gr.238444.118
...-associated genes at noncanonical positions in splice sites. We estimate 35%–40% of pathogenic variants in noncanonical splice site positions are missing from public databases.Pre-mRNA splicing in humans is mediated by the major and minor spliceosomes, highly dynamic, metalloenzyme complexes composed of five key...
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Research: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
- Bum-Kyu Lee,
- Akshay A. Bhinge,
- Anna Battenhouse,
- Ryan M. McDaniell,
- Zheng Liu,
- Lingyun Song,
- Yunyun Ni,
- Ewan Birney,
- Jason D. Lieb,
- Terrence S. Furey,
- Gregory E. Crawford,
- and Vishwanath R. Iyer
Genome Res. January 2012 22: 9-24; Published in Advance November 16, 2011, doi:10.1101/gr.127597.111
...Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells Bum-Kyu Lee 1 , Akshay A. Bhinge 1 , Anna Battenhouse 1 , Ryan M. McDaniell 1 , Zheng Liu 1...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...revealed that compared with regular introns, the retained introns of circRNAs (CIRs) are shorter in length, have weaker splice site strength, and have higher GC content. Compared with retained introns in linear RNAs (LIRs), CIRs are more likely to form secondary structures and show greater sequence...
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Research: Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids
- Tülay Karakulak,
- Natalia Zajac,
- Hella Anna Bolck,
- Anna Bratus-Neuenschwander,
- Qin Zhang,
- Weihong Qi,
- Debleena Basu,
- Tamara Carrasco Oltra,
- Hubert Rehrauer,
- Christian von Mering,
- Holger Moch,
- and Abdullah Kahraman
Genome Res. April 2025 35: 698-711; Published in Advance March 19, 2025, doi:10.1101/gr.279345.124
...in capturing the full spectrum of splicing events.Recent advances in single-cell RNA sequencing (scRNA-seq) have revolutionized our understanding of cellular heterogeneity in complex tissues and tumoral environments, revealing unprecedented insights into the transcriptomic variations that define cell types...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...(two isogenic cultures) orangutan, and two rhesus macaque LCLs were processed to produce an average of over 2.3 million circular consensus sequences (CCS) per species (range from 1.9 to 2.9 million CCS). A strict quality control, including base correction and splice junction adjustment with RNA-seq...
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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
..., defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage. Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal–containing transcripts. These results indicate...
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Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
...ribosome occupancy, but when we calculated codon usage levels and identified actively translated noncanonical ORFs, we only used the reads showing strong 3-nt periodicity (typically those around peak sizes) because these analyses require accurate correction of read location to the ribosomal A-site or P-site...

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