Searching journal content for articles similar to Siepel et al. 15 (8): 1034.

Displaying results 1-10 of 195

For checked items

view abstracts
download to citation manager

Select this article
Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
..., Guelph, ON N1G 2W1, Canada Corresponding author: michael.wilson@sickkids.caAbstractTransposable elements (TEs) provide a source of transcription factor (TF) binding sites that can rewire gene regulatory networks. NF-kB is an evolutionarily conserved TF complex primarily involved in innate immunity...
Select this article
Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...in the sequence conservation of pleiotropic CREs.One of the initial perplexing revelations of the human project was the seemingly limited number of genes, which did not align with the increase in complexity compared with organisms such as yeast, worms, and flies. It became evident that this complexity must stem...
OPEN ACCESS ARTICLE
Select this article
Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
....ji@northwestern.eduAbstract3′-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared with the well-defined regulatory elements in mammals. Here we...
Select this article
Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...as yeasts, plants, worms, flies, and humans. The rDNA locus is an ideal candidate to harbor fundamental and evolutionarily conserved aging mechanisms as well as yield widely applicable markers of aging. In eukaryotes, the array originates the nucleolus, the site of ribosomal RNA (rRNA) transcription...
Select this article
Research: Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes
- Yuvia A. Pérez-Rico,
- Valentina Boeva,
- Allison C. Mallory,
- Angelo Bitetti,
- Sara Majello,
- Emmanuel Barillot,
- and Alena Shkumatava
Genome Res. February 2017 27: 259-268; Published in Advance December 13, 2016, doi:10.1101/gr.203679.115
.... Phylogenetic hidden Markov models. In Statistical methods in molecular evolution (ed. Nielsen R), pp. 325–351. Springer, New York. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate...
Select this article
Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...sequences (Chen et al. 2013; Van Oss and Carvunis 2019). Distinguishing products of gene duplications from de novo genes is often not straightforward, as extensive sequence divergence can prohibit the detection of homologous sequences. Consequently, depending on the taxonomic resolution of available genomic...
Select this article
Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...the fraction of nucleotides overlapped by evolutionarily conserved genomic elements and compared to the equivalent fraction for intronic TEs of the same type. To assess statistical significance, we again used positional randomization (see Fig. 3C, inset). This pipeline was applied independently to the phast...
OPEN ACCESS ARTICLE
Select this article
Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
...enhancers do not exhibit strong evidence of transposon co-option (Emera et al. 2016). Many important questions remain unanswered: To what extent are regulatory elements functionally conserved across primates? Are specific genomic features predictive of CRE conservation? To what extent have TEs driven...
OPEN ACCESS ARTICLE
Select this article
Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
..., University of Washington, Seattle, Washington 98195, USA; 9Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common...
OPEN ACCESS ARTICLE
Select this article
Resource: Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
- Margaret C.W. Ho,
- Porfirio Quintero-Cadena,
- and Paul W. Sternberg
Genome Res. December 2017 27: 2108-2119; Published in Advance October 26, 2017, doi:10.1101/gr.223735.117
...large numbers of developmentally synchronized worms.Traditional approaches to identify CRMs have relied on individually testing conserved sequences in transgenic reporter assays, but these are limited by relatively low throughput. Many enhancers have been found this way in C. elegans, of which most...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Siepel et al. 15 (8): 1034.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: