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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
....05.003 ↵Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. 2013. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23: 169–180. doi:10.1101/gr.139618.112 ↵Bell AC, West AG, Felsenfeld G. 1999. The protein CTCF...
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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
...and validating the quantitative aspects of our data, we proceeded to evaluate the use of alternative promoters across tissues and the composition of each network module. Expression profiles from alternative TSCs of the same gene across the data set were generally independent, as evidenced by the low correlation...
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Resource: Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types
- Jill E. Moore,
- Xiao-Ou Zhang,
- Shaimae I. Elhajjajy,
- Kaili Fan,
- Henry E. Pratt,
- Fairlie Reese,
- Ali Mortazavi,
- and Zhiping Weng
Genome Res. February 2022 32: 389-402; Published in Advance December 23, 2021, doi:10.1101/gr.275723.121
...with TSSs that were exclusively proximal to CAGE peaks (CAGE-only genes) (Supplemental Table S2A) or were exclusively proximal to RAMPAGE rPeaks (RAMPAGE-only genes) (Supplemental Table S2B). Gene Ontology analysis revealed that the 6932 CAGE-only genes were enriched in terms such as T-cell receptor complex...
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Method: Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome
- Hagen Tilgner,
- Fereshteh Jahanbani,
- Ishaan Gupta,
- Paul Collier,
- Eric Wei,
- Morten Rasmussen,
- and Michael Snyder
Genome Res. February 2018 28: 231-242; Published in Advance December 1, 2017, doi:10.1101/gr.230516.117
....5% of protein-coding genes contain two nonconstitutive exons that are separated by one or more constitutive exons. The question of coordination of multiple distant alternative sites is therefore relevant for many genes. We recently revealed a limited number of exon pairs that are distant in mRNAs but show...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...start sites (TSSs) and coregulated clusters of TSSs, commonly referred to as transcription start regions (TSRs). Usage of alternative TSSs is widespread (Davuluri et al. 2008; Reyes and Huber 2018) and results in mRNAs with shortened or lengthened 5′ untranslated regions (5′ UTRs), which can lead...
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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
...% verified protein-coding genes. We corrected misannotation of translation start codon for 122 genes and suggested an alternative start codon for 57 genes. We found that 56% of yeast genes are controlled by multiple core promoters, and alternative core promoter usage by a gene is widespread in response...
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Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...of transcripts (Pan et al. 2008; Barash et al. 2010; Brown et al. 2014; Söllner et al. 2017). The complexity and diversity of the transcriptome arises from the combinatorial usage of alternative promoters, exons and introns, and polyadenylation sites. A single gene can, therefore, encode a rich repertoire...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...al. 2011; The ENCODE Project Consortium 2012; Lu and Lin 2019). Transcription can be initiated from multiple TSSs in most genes, and alternative usage of TSSs in different cell types or growth conditions is prevalent in mammals, the fruit fly, and yeast (Davuluri et al. 2008; Batut et al. 2013; Lu...
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Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...biosamples, and our results revealed that although the human-specific Alu elements are transcriptionally repressed, the older, expressed Alu elements may be exapted by the human host to function as cell-type–specific enhancers for their nearby protein-coding genes.Transposable elements and other repeats...
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Method: Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
- Peng Liu,
- Rajendran Sanalkumar,
- Emery H. Bresnick,
- Sündüz Keleş,
- and Colin N. Dewey
Genome Res. August 2016 26: 1124-1133; Published in Advance July 12, 2016, doi:10.1101/gr.199174.115
...by fragmentation, reverse transcription, and high-throughput sequencing. Millions of reads from sequencing are mapped back to a reference or transcriptome and quantified to estimate the expression of isoforms and genes (Mortazavi et al. 2008). Due to alternative splicing and the repetitiveness of genomic sequence...
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