Searching journal content for articles similar to Zhu and Landsman 33 (10): 1662.

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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...and time drives the successful development and sustained health of all organisms. To understand the underlying causes of developmental disorders, polygenic diseases, and cancer, we must decipher the code that directs gene expression in diverse cell types and environments. Transcription factors (TFs) bind...
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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
...chromatin may stop the spreading of nearby repressive chromatin. Linear clustering would then reduce the number of interfaces with repressive chromatin and thus stabilize expression. In the second scenario, housekeeping genes may be stimulated by specific enhancers (Zabidi et al. 2015). Clustering around...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...et al. 2019) and impeding the binding of diverse transcription factors (TFs) and RNA polymerase, unlike H3K27me3-marked domains (Becker et al. 2016, 2017).Loss of heterochromatin has been proposed as a potential universal molecular cause of aging, whereby over time, heterochromatin domains lose...
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Method: Characterization of network hierarchy reflects cell state specificity in genome organization
- Jingyao Wang,
- Yue Xue,
- Yueying He,
- Hui Quan,
- Jun Zhang,
- and Yi Qin Gao
Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122
...). A large and diverse set of gene regulatory elements in chromatin are found to regulate transcription through long-range interactions. For example, promoter–enhancer interactions regulate the dynamic activation of genes (Cloney 2016), whereas insulators and repressors play the opposite roles (Yang...
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Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
...research has shown that TAD borders are enriched in housekeeping genes (Li et al. 2015), developmental enhancers (Cubeñs-Potts et al. 2017), and boundaries of highly conserved genomic regulatory blocks (Harmston et al. 2017). In addition, architectural proteins and insulators are enriched at TAD borders...
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Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...; Supplemental Fig. S3). In the hemoglobin subunit beta (HBB) cluster locus, three chromatin accessibility peaks were shared across many different cell types, despite the fact that H3K4me1 and H3K27ac ChIP-seq peaks, RNA-seq transcripts, and 24 DNase-seq peaks were specific to K562 cells (Fig. 1C). We observed...
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Research: Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
- Ryne C. Ramaker,
- Andrew A. Hardigan,
- Say-Tar Goh,
- E. Christopher Partridge,
- Barbara Wold,
- Sara J. Cooper,
- and Richard M. Myers
Genome Res. July 2020 30: 939-950; Published in Advance July 2, 2020, doi:10.1101/gr.260463.119
...contribute to -wide transcriptional regulation.Gene expression networks underlie many cellular processes (Spitz and Furlong 2012). These expression networks are controlled in cis by DNA regulatory elements, such as promoters and enhancers, which can be proximal, can be distal, or can be within their target...
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Method: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
- Nevena Cvetesic,
- Harry G. Leitch,
- Malgorzata Borkowska,
- Ferenc Müller,
- Piero Carninci,
- Petra Hajkova,
- and Boris Lenhard
Genome Res. December 2018 28: 1943-1956; Published in Advance November 7, 2018, doi:10.1101/gr.235937.118
...equivalent transcripts and are generally clustered together and analyzed as a single transcriptional unit termed a tag cluster (Haberle et al. 2015). The CTSS with the highest TPM value within a tag cluster is referred to as the dominant CTSS. Specificity in capturing genuine TSSs can be assessed...
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Research: Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs
- Jake Yeung,
- Jérôme Mermet,
- Céline Jouffe,
- Julien Marquis,
- Aline Charpagne,
- Frédéric Gachon,
- and Felix Naef
Genome Res. February 2018 28: 182-191; Published in Advance December 18, 2017, doi:10.1101/gr.222430.117
...spaced promoters to control rhythmic transcription with spatial precision.View larger version: In this window In a new window Figure 6. Precise promoter-enhancer contacts underlie liver-specific mRNA rhythms. (A,B) 4C-seq profiles for the (A) Slc45a3-short and (B) Slc45a3-long isoforms within ±250 kb...
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Research: Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
- Cai Li,
- Boris Lenhard,
- and Nicholas M. Luscombe
Genome Res. May 2018 28: 676-688; Published in Advance April 4, 2018, doi:10.1101/gr.231449.117
...; (2) new TSSs undergo rapid evolution that reduces the inherent instability of repeat sequences associated with a high propensity of TSS emergence; and (3) once established, the transcriptional competence of surviving TSSs is gradually enhanced, with evolutionary changes subject to temporal (fewer...
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