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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...the main transcriptional program may represent a source of transcriptional innovation part of the evolutionary process, and low abundance structural variations may have biological functions, as has been shown for long noncoding RNAs (Mattick et al. 2023). Faithfully identifying these molecules within...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...inhibitor JQ1 (Fig. 4). PRO-seq allows high-resolution mapping of active RNA polymerases across the at both coding and noncoding regions and provides information on both the abundance and directionality of transcripts. Analysis of the transcriptome in LBH589-treated ESCs revealed that the majority of genes...
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Method: Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments
- Ales Varabyou,
- Steven L. Salzberg,
- and Mihaela Pertea
Genome Res. February 2021 31: 301-308; Published in Advance December 23, 2020, doi:10.1101/gr.266213.120
...and transcripts in an RNA sequencing experiment. We show that the inclusion of noise leads to systematic errors in the ability of these programs to measure expression, including systematic underestimates of transcript abundance levels and large increases in the number of false-positive genes and transcripts. Our...
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Research: Global transcriptional activity dynamics reveal functional enhancer RNAs
- Yoon Jung Kim,
- Peng Xie,
- Lian Cao,
- Michael Q. Zhang,
- and Tae Hoon Kim
Genome Res. December 2018 28: 1799-1811; Published in Advance October 23, 2018, doi:10.1101/gr.233486.117
....zhang@utdallas.edu, @utdallas.eduAbstractActive enhancers of the human generate long noncoding transcripts known as enhancer RNAs (eRNAs). How dynamic transcriptional changes of eRNAs are physically and functionally linked with target gene transcription remains unclear. To investigate the dynamic functional relationships among...
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Method: Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication
- Zihao Wang,
- Zhenquan Zhang,
- Songhao Luo,
- Tianshou Zhou,
- and Jiajun Zhang
Genome Res. January 2024 34: 106-118; Published in Advance January 3, 2024, doi:10.1101/gr.278631.123
...). To the best of our knowledge, a comprehensive theory of the information transmission from upstream chromatin organization to downstream transcriptional bursting is still lacking, and important yet fundamental questions such as how E-P communication shapes the observed patterns of mRNA expression and what...
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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: Long noncoding RNAs in C. elegans
- Jin-Wu Nam and
- David P. Bartel
Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
.... elegans might benefit from additional analyses. One potential function of noncoding transcripts is to serve as precursors or templates for the production of endogenous guide RNAs for RNAi or related silencing pathways. For example, the BIC proto-oncogene ncRNA was later reannotated as the primary...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long noncoding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series data...
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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
...mammals compared to almost 90% for protein-coding exons, suggesting that transcript structure and exact splicing patterns are not critical for lincRNA function and that purifying selection is not acting on the linear RNA polymer but more likely on only portions of the molecule or on its folding structure...

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