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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...explore the relationship between enriched GOs and tissue-specific gene regulation, we identified transcription factor binding motifs enriched in Up and Down enhancers in either tissue (Fig. 3B; Supplemental Table S9). Up enhancer shifts were enriched for binding motifs of tissue-specific transcription...
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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
...-ALL patients were found to be significantly shallower compared to their normal controls. A reverse trend of change in chromatin structure was observed during early embryo development. We found tissue-specific conservation of hierarchy order in chromatin contact networks. Our findings reveal the top...
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Research: BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies
- Guntram Borck,
- Friederike Hög,
- Maria Lisa Dentici,
- Perciliz L. Tan,
- Nadine Sowada,
- Ana Medeira,
- Lucie Gueneau,
- Holger Thiele,
- Maria Kousi,
- Francesca Lepri,
- Larissa Wenzeck,
- Ian Blumenthal,
- Antonio Radicioni,
- Tito Livio Schwarzenberg,
- Barbara Mandriani,
- Rita Fischetto,
- Deborah J. Morris-Rosendahl,
- Janine Altmüller,
- Alexandre Reymond,
- Peter Nürnberg,
- Giuseppe Merla,
- Bruno Dallapiccola,
- Nicholas Katsanis,
- Patrick Cramer,
- and Christian Kubisch
Genome Res. February 2015 25: 155-166; Published in Advance January 5, 2015, doi:10.1101/gr.176925.114
...substitution p.Trp107Arg (W107R). Extracts from this strain are transcriptionally inactive, but addition of recombinant Brf1 protein restores activity on a template encoding the native SUP4 promoter. When we used purified recombinant Brf1 variants in this assay, we observed significantly less transcription...
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Method: A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1
- Dror Hollander,
- Maya Donyo,
- Nir Atias,
- Keren Mekahel,
- Zeev Melamed,
- Sivan Yannai,
- Galit Lev-Maor,
- Asaf Shilo,
- Schraga Schwartz,
- Iris Barshack,
- Roded Sharan,
- and Gil Ast
Genome Res. April 2016 26: 541-553; Published in Advance February 9, 2016, doi:10.1101/gr.193169.115
...of an alternative splicing factor and the Figure 1. Physical interaction network leading to colon cancer splicing changes. (A) A diagram illustrating the construction of the cancerous splicing interactome connecting transcription factors (TFs) to alternative splicing events (ASEs) exhibiting splicing pattern...
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Method: Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers
- Aleksander Jankowski,
- Ewa Szczurek,
- Ralf Jauch,
- Jerzy Tiuryn,
- and Shyam Prabhakar
Genome Res. August 2013 23: 1307-1318; Published in Advance April 3, 2013, doi:10.1101/gr.154922.113
...extent and tissue specificity of TF dimers in the human . Here we present a method for comprehensively predicting cell-type–specific TF dimerization based on TF affinity motifs and DNase I hypersensitivity profiles in 78 human cell types (The ENCODE Project Consortium 2011). Uniquely, our approach can...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...-content yields poor results, whereas much better results are achieved by accounting for binding motifs. Of the motifs that can be confidently matched to known transcription factor families, our results are consistent with the action of known tissue-specific pioneer factors including SOX2 and POU5F1 in ESCs...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
...elements” (IEs) involved in direct physical interaction with nucleic acids, proteins, or lipids and of “structural elements” (SEs) directing their wiring within the “ncRNA interactor networks” through the emergence of secondary and/or tertiary structures. We suggest that spectrums of “letters” (nc...
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Research: A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA
- Shiyan Wang,
- Jiahuan Chen,
- Sara P. Garcia,
- Xiaodong Liang,
- Fang Zhang,
- Pengyi Yan,
- Huijing Yu,
- Weiting Wei,
- Zixuan Li,
- Jingfang Wang,
- Huangying Le,
- Zeguang Han,
- Xusheng Luo,
- Daniel S. Day,
- Sean M. Stevens,
- Yan Zhang,
- Peter J. Park,
- Zhi-jie Liu,
- Kun Sun,
- Guo-cheng Yuan,
- William T. Pu,
- and Bing Zhang
Genome Res. February 2019 29: 193-207; Published in Advance January 22, 2019, doi:10.1101/gr.239053.118
...of the tested TFs in regulating gene expression downstream from VEGFA signaling.MAFs are master regulators of VEGFA transcriptional responsesTranscriptional regulatory networks play essential roles in many physical and pathological processes. Within these networks, master regulators (MRs) play dominant roles...
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Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
- Stefan Schoenfelder,
- Mayra Furlan-Magaril,
- Borbala Mifsud,
- Filipe Tavares-Cadete,
- Robert Sugar,
- Biola-Maria Javierre,
- Takashi Nagano,
- Yulia Katsman,
- Moorthy Sakthidevi,
- Steven W. Wingett,
- Emilia Dimitrova,
- Andrew Dimond,
- Lucas B. Edelman,
- Sarah Elderkin,
- Kristina Tabbada,
- Elodie Darbo,
- Simon Andrews,
- Bram Herman,
- Andy Higgs,
- Emily LeProust,
- Cameron S. Osborne,
- Jennifer A. Mitchell,
- Nicholas M. Luscombe,
- and Peter Fraser
Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
...types (Fig. 4D; Supplemental Fig. 4A), suggesting that highly connected enhancers represent a class of tissue-specific hub enhancers that coordinate the expression of multiple genes expressed in both cell types. The expression levels of genes interacting with highly connected enhancers are similar...
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Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
- Roger A. Hoskins,
- Joseph W. Carlson,
- Kenneth H. Wan,
- Soo Park,
- Ivonne Mendez,
- Samuel E. Galle,
- Benjamin W. Booth,
- Barret D. Pfeiffer,
- Reed A. George,
- Robert Svirskas,
- Martin Krzywinski,
- Jacqueline Schein,
- Maria Carmela Accardo,
- Elisabetta Damia,
- Giovanni Messina,
- María Méndez-Lago,
- Beatriz de Pablos,
- Olga V. Demakova,
- Evgeniya N. Andreyeva,
- Lidiya V. Boldyreva,
- Marco Marra,
- A. Bernardo Carvalho,
- Patrizio Dimitri,
- Alfredo Villasante,
- Igor F. Zhimulev,
- Gerald M. Rubin,
- Gary H. Karpen,
- and Susan E. Celniker
Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
...sequenced BACs and additional BACs in a redundant tiling path selected from the physical map and BAC end-sequence alignments. For each BAC, fingerprints were produced using five restriction enzymes (ApaLI, BamHI, EcoRI, HindIII, XhoI). For 583 BACs, which had regions of sequence for which none...
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