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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
...of the structure–function relationship in lncRNAs.The discovery of long noncoding RNAs (lncRNAs) has revolutionized scientific understanding of the and has led to an explosion of research into the complex mechanisms that regulate gene expression. Currently, lncRNAs are broadly defined as any RNA >200 nt in length...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...of repetitive sequences to the spermatogenic transcriptome.We set out to create a more complete catalog of genes expressed during postreplicative spermatogenesis by isolating several specific cell types, performing a deep-coverage, paired-end RNA-seq analysis and generating a de novo annotation for genes...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
..., a process known as exaptation (Feschotte 2008; Bourque 2009). This process has contributed to the evolution of diverse features in genomic DNA, including transcriptional regulatory motifs (Johnson et al. 2006; Bourque et al. 2008), microRNAs (Roberts et al. 2014), gene promoters (Faulkner et al. 2009; Huda...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...decided to use the GENCODE consortium genomic annotation. We used the “comprehensive” set which includes the highest number of transcripts associated with protein-coding genes, pseudogenes, long noncoding RNAs and small noncoding RNAs genes (Frankish et al. 2019). Transcripts with “to be experimentally...
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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
..., The Babraham Institute, Babraham Research Campus, Cambridge CB22 AT, UK Abstract Long noncoding (lnc)RNAs have recently emerged as key regulators of gene expression. Here, we performed high-depth poly(A)+ RNA sequencing across multiple clonal populations of mouse embryonic stem cells (ESCs...
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Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...encoding GENCODE lncRNAs were compared to those of our catalogs. A majority (60.37% for GENCODE) were detected in our human lncRNA catalogs (Fig. 7B). Of 8949 GENCODE lncRNAs that were not in our catalogs, 7872 (87.96%) were transcripts that overlapped with annotated genes in RefSeq, GENCODE, Ensembl...
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Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
- Sanjana Pillay,
- Hazuki Takahashi,
- Piero Carninci,
- and Aditi Kanhere
Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
...on their expression pattern, cytosolic nature, and their higher complementarity to the overlapping developmental mRNAs, we speculate that Group 1 NATs function post-transcriptionally to silence spurious expression of developmental genes.Natural antisense transcripts (NATs) are noncoding RNAs that are transcribed...
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Resource: GENCODE: The reference human genome annotation for The ENCODE Project
- Jennifer Harrow,
- Adam Frankish,
- Jose M. Gonzalez,
- Electra Tapanari,
- Mark Diekhans,
- Felix Kokocinski,
- Bronwen L. Aken,
- Daniel Barrell,
- Amonida Zadissa,
- Stephen Searle,
- If Barnes,
- Alexandra Bignell,
- Veronika Boychenko,
- Toby Hunt,
- Mike Kay,
- Gaurab Mukherjee,
- Jeena Rajan,
- Gloria Despacio-Reyes,
- Gary Saunders,
- Charles Steward,
- Rachel Harte,
- Michael Lin,
- Cédric Howald,
- Andrea Tanzer,
- Thomas Derrien,
- Jacqueline Chrast,
- Nathalie Walters,
- Suganthi Balasubramanian,
- Baikang Pei,
- Michael Tress,
- Jose Manuel Rodriguez,
- Iakes Ezkurdia,
- Jeltje van Baren,
- Michael Brent,
- David Haussler,
- Manolis Kellis,
- Alfonso Valencia,
- Alexandre Reymond,
- Mark Gerstein,
- Roderic Guigó,
- and Tim J. Hubbard
Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
.... The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting...
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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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Research: Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- Stefan Washietl,
- Manolis Kellis,
- and Manuel Garber
Genome Res. April 2014 24: 616-628; Published in Advance January 15, 2014, doi:10.1101/gr.165035.113
...an important evolutionary layer to the current annotationof human lincRNAs,which constitutes a rich resource for further experimental and computational studies. Results A reference set of lincRNAs in human The GENCODE catalog is currently the most comprehensive set of manually annotated coding and noncoding...

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