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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...Discovery of high-confidence human protein-coding genes and exons by whole- PhyloCSF helps elucidate 118 GWAS loci Jonathan M. Mudge1,9, Irwin Jungreis2,3,9, Toby Hunt1, Jose Manuel Gonzalez1, James C. Wright4, Mike Kay1, Claire Davidson1, Stephen Fitzgerald5, Ruth Seal1,6, Susan Tweedie1, Liang He...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...M Grinder parameters were contained within repeats. Additionally, under high-confidence G4-iM Grinder parameters (score 40 or more; MinNRuns, four or more), an average of 34.2% of lncRNA pG4s were harbored in repeat elements compared with 25.8% for mRNA pG4s. These results may indicate a role for rG4...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...that Gm4665 was highly enriched in genomic regions of the six genes (Fig. 6K). Further binding site analysis showed that the high-confidence Gm4665 ChIRP-seq peaks mapped to the active promoter region and enhancer region of Ip6k1 gene loci and the active promoter region of Akap3 gene loci and were...
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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
...that are consistently expressed or unexpressed based on the RNA-seq from all biological replicates across species (Methods) (Fig. 3A,B; Supplemental Fig. S14; Supplemental Data S9; Supplemental Methods). The number of high-confidence expressed transcripts (H: 14,783; C: 14,602; G: 14,438; O: 14,014; M: 13...
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Research: Regulation of the ESC transcriptome by nuclear long noncoding RNAs
- Jan H. Bergmann,
- Jingjing Li,
- Mélanie A. Eckersley-Maslin,
- Frank Rigo,
- Susan M. Freier,
- and David L. Spector
Genome Res. September 2015 25: 1336-1346; Published in Advance June 5, 2015, doi:10.1101/gr.189027.114
...Regulation of the ESC transcriptome by nuclear long noncoding RNAs Jan H. Bergmann 1 , 3 , Jingjing Li 1 , Mélanie A. Eckersley-Maslin 1 , 4 , Frank Rigo 2 , Susan M. Freier 2 and David L. Spector 1 1Cold Spring...
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Research: Acute depletion of METTL3 implicates N⁶-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
- Guifeng Wei,
- Mafalda Almeida,
- Greta Pintacuda,
- Heather Coker,
- Joseph S. Bowness,
- Jernej Ule,
- and Neil Brockdorff
Genome Res. August 2021 31: 1395-1408; Published in Advance June 15, 2021, doi:10.1101/gr.271635.120
...as “exon” in the nascent transcriptome. Our observations support that high-confidence m6A methylation in constitutive introns is rare, as reported previously (Ke et al. 2017). Based on the assumption that m6A affects splice site usage in cis, we further found that the location of m6A peaks relative...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...Integrated and transcriptome sequencing identifies a noncoding mutation in the replication factor DONSON as the cause of microcephaly-micromelia syndrome Gilad D. Evrony,1,2,3,18 Dwight R. Cordero,4,18 Jun Shen,5,6,18 Jennifer N. Partlow,1,2,3 Timothy W. Yu,1,2,3 Rachel E. Rodin,1,2,3 R. Sean Hill...
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Research: A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
- Pengfei Cai,
- Auke B.C. Otten,
- Binbin Cheng,
- Mitsuhiro A. Ishii,
- Wen Zhang,
- Beibei Huang,
- Kun Qu,
- and Bryan K. Sun
Genome Res. January 2020 30: 22-34; Published in Advance December 4, 2019, doi:10.1101/gr.251561.119
...show variability in lncRNA annotations, and to best address these differences, we combined RefSeq, UCSC, and ENCODE/GENCODE annotations to identify and map lncRNAs. Since the initiation of our work, the FANTOM5 consortium reported a comprehensive atlas of human lncRNA genes with high-confidence 5′ ends...
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Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
.... Here, we leveraged the SMRT platform to study the transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2539 high-confidence novel transcripts that originated from previously unannotated loci and 1835...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...had four or more reads supporting them, indicating that these are high-confidence novel isoforms.Finally, we sought to examine how many of our identified splice isoforms were predicted to be noncoding using the protein coding prediction algorithm CPAT trained on the C. elegans transcriptome annotation...
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