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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...of operative transcription factors (TFs). However, identification of conserved CRMs is often 61 confounded by rearrangement and substitution of TFBSs, leading to similar functional 62 capabilities without deep sequence conservation (reviewed in (Nelson and Wardle 2013; Long 63 et al. 2016; Jindal and Farley...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...ORFs, results from the altered ribosome footprint length at the codon preceding the stop codon (Wu et al. 2024a).Third example: translation of noncoding RNATAS3 is an annotated noncoding RNA, encoding the primary transcript of trans-acting short-interfering RNA (tasiRNA). A small ORF is known to be translated...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...studies have provided insights into the complexity of alternative isoforms at a deep evolutionary timescale. However, the diversity and pattern of the alternative isoform landscape within natural populations remain largely unexplored (Verta and Jacobs 2022).Owing to its well-defined evolutionary history...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...proband contigs was 29.05 Mb (Table 1).View this table: In this window In a new window Table 1. Demographics, and sequencing and assembly metrics for the cohortHiFi reads were aligned to hg38, and variant calling was performed using DeepVariant (Poplin et al. 2018) and pbsv (https...
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Research: Widespread formation of double-stranded RNAs in testis
- Andreas Werner,
- James E. Clark,
- Calum Samaranayake,
- John Casement,
- Hany S. Zinad,
- Shaymaa Sadeq,
- Surar Al-Hashimi,
- Martin Smith,
- Noora Kotaja,
- and John S. Mattick
Genome Res. July 2021 31: 1174-1186; Published in Advance June 22, 2021, doi:10.1101/gr.265603.120
...transcriptome is highly complex and includes RNAs that potentially hybridize to form double-stranded RNA (dsRNA). We isolated dsRNA using the monoclonal J2 antibody and deep-sequenced the enriched samples from testes of juvenile Dicer1 knockout mice, age-matched controls, and adult animals. Comparison of our...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...concordant with TSS peaks called by RAMPAGE, CAGE-seq, and GRO-cap signals using human cancer cell lines. In addition, robust long-read full-length RNA-seq has the advantage of trivially identifying alternative transcripts. Previous studies have also shown that long-read sequencing can identify thousands...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...” and “UACUCC” IRES elements, and novel short C/U-related sequences (such as “CCCUCUU” and “UUCCUU) that can base pair with 18S rRNAs within a scanning ribosome to enhance cap-independent translation (Weingarten-Gabbay et al. 2016). However, much less evidence is available for their regulatory roles in plant mRNA...
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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
...d of continuous proliferation (Fig. 1A). Deep sequencing was used to quantify sgRNA representation at each time point. After normalization and mean-variance modeling, we determined enriched and depleted sgRNAs (Fig. 1B). The experiment was performed in technical and biological duplicates, which both...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...were generated using deepTools (Ramírez et al. 2016). The ATAC-inferred CTCF-bound sites per tissue were used to calculate LOR for TE subfamily enrichment. To test the significance of TE subfamily enrichment in a specific tissue for certain epigenetic states, we binned the reference into 100-bp...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...transcripts. Although the heterogeneity of pre-mRNA 3′ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3′ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3′ end sequencing data sets, we have...
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