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Research: Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
- Cui Du,
- Jing Jiang,
- Yuzhuo Li,
- Miao Yu,
- Jian Jin,
- Shuai Chen,
- Hairui Fan,
- Todd S. Macfarlan,
- Bin Cao,
- and Ming-an Sun
Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122
...other ERV families — indicating their broad impact on ERV-derived enhancers. Functionally, the derepression of many syncytiotrophoblast genes after MSX2 knockdown is likely to be mediated by regulatory elements derived from ERVs — suggesting ERVs are also important for mediating transcriptional...
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Resource: Modeling transcriptional regulation of model species with deep learning
- Evan M. Cofer,
- João Raimundo,
- Alicja Tadych,
- Yuji Yamazaki,
- Aaron K. Wong,
- Chandra L. Theesfeld,
- Michael S. Levine,
- and Olga G. Troyanskaya
Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
...allow for the detection of constrained noncoding sequences in the absence of regulatory assays, but they are only a proxy for regulatory function and their interpretation can be confounded. For instance, some regulatory elements are enriched for recent evolution (Moon et al. 2019), whereas other highly...
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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
.... However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
...; Maricic et al. 2013; Becker et al. 2015; Torres-Ruiz et al. 2019). The majority of ARs in the FOXP2-containing hotspot were located between the FOXP2 and TFEC transcription factors (Fig. 4D), a region known to contain FOXP2 regulatory elements (Becker et al. 2015; Torres-Ruiz et al. 2019). NEUROD6 is one...
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Research: Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
- Phil Arnold,
- Anne Schöler,
- Mikhail Pachkov,
- Piotr J. Balwierz,
- Helle Jørgensen,
- Michael B. Stadler,
- Erik van Nimwegen,
- and Dirk Schübeler
Genome Res. January 2013 23: 60-73; Published in Advance September 10, 2012, doi:10.1101/gr.142661.112
.... The analysis of such data has predominantly focused on characterizing the different kinds of chromatin domains that exist and associating these domains with functional features such as active or inactive promoters or distal regulatory elements (Suzuki and Bird 2008; Meissner 2010; Ernst et al. 2011; Zhou et al...
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