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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
...repeats drive expression of nonrepetitive sequences in a cell type–specific manner. Finally, we observe many fairly long antisense transcripts originating from canonical gene promoters, pointing to pervasive bidirectional promoter activity during spermatogenesis that is distinct and more frequent compared...
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Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
- Boning Chen,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
...et al. 2008; Doris et al. 2018). There is also evidence for antisense transcription initiating from the nucleosome-free region (NFR) of transcribed genes, indicating that some promoters may be bidirectional (Xu et al. 2009). In the case of CAC1 deletion, we found that the increase in antisense...
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Research: Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast
- Wu Wei,
- Bianca P. Hennig,
- Jingwen Wang,
- Yujie Zhang,
- Ilaria Piazza,
- Yerma Pareja Sanchez,
- Christophe D. Chabbert,
- Sophie H. Adjalley,
- Lars M. Steinmetz,
- and Vicent Pelechano
Genome Res. December 2019 29: 1974-1984; Published in Advance November 18, 2019, doi:10.1101/gr.243378.118
...polypeptides by reanalyzing N-terminal proteomic data sets. Our work suggests that a fraction of chromatin-sensitive internal cryptic promoters initiates the transcription of alternative truncated mRNA isoforms. The expression of these chromatin-sensitive isoforms is conserved from yeast to human, expanding...
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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
..., given that distal CGIs can display transcriptional activity similar to promoters, it is likely that they also harbor histone modifications reflective of their activity status. To this end, we contrasted the ChIP-seq signal of two active (H3K4me3, H3K9ac) and two repressive (H3K27me3, H3K9me3) histone...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...RNA 3′ ends and maps transcriptionally engaged Pol II. G4 signals overlapped with the TSSs and Pol II pausing sites at promoter regions (Fig. 1I,J), indicating that G4s may participate in the early stages of transcription.Because G4-CUT&Tag could detect the G4 signals at enhancers (Fig. 1E), we...
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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
...bound by ZFX were down-regulated upon ZFX knockdown, supporting the hypothesis that ZFX acts as a transcriptional activator. Surprisingly, ZFX binds at +240 bp downstream from the TSS of the responsive promoters. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds...
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Resource: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
- Daniel E. Goszczynski,
- Michelle M. Halstead,
- Alma D. Islas-Trejo,
- Huaijun Zhou,
- and Pablo J. Ross
Genome Res. April 2021 31: 732-744; Published in Advance March 15, 2021, doi:10.1101/gr.267336.120
...transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE to produce a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-seq. Coexpression networks revealed considerable use...
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Research: Enhancer RNA profiling predicts transcription factor activity
- Joseph G. Azofeifa,
- Mary A. Allen,
- Josephina R. Hendrix,
- Timothy Read,
- Jonathan D. Rubin,
- and Robin D. Dowell
Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
...polymerase II (RNAP) to identify individual transcripts within nascent transcription data (Azofeifa and Dowell 2017). Although Tfit does not implicitly assume polymerase initiation will be bidirectional, we observed bidirectional transcription at both promoters and enhancers (Azofeifa and Dowell 2017...
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Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
...activity (Jiang and Pugh 2009; Nocetti and Whitehouse 2016). The eukaryotic DNA is coiled around a core of histones that form nucleosomes. If nucleosomes are present in the core promoter region, it becomes an obstacle for transcription initiation. Thus, the activation of transcription from such core...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...association patternsIn yeast, in which many RNAPII genes are transcriptionally regulated, a group of chromatin regulators are enriched specifically at promoters, where they assist in transcription initiation, whereas others travel with RNAPII into gene bodies, aiding transcription elongation, splicing...
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