Searching journal content for articles similar to Song et al. 21 (10): 1757.

Displaying results 1-10 of 32

For checked items

view abstracts
download to citation manager

Select this article
Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...are needed to identify tissue-specific genetic effects on regulatory elements, and single-cell studies are needed to identify the relevant cell types for caQTLs in heterogeneous tissues. Our results also show that caQTLs can vary across populations owing to allele frequency differences, but identification...
Select this article
Method: Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
- Seyed Ali Madani Tonekaboni,
- Parisa Mazrooei,
- Victor Kofia,
- Benjamin Haibe-Kains,
- and Mathieu Lupien
Genome Res. October 2019 29: 1733-1743; Published in Advance September 18, 2019, doi:10.1101/gr.248658.119
...lying outside of gene coding regions that harbor functional features, including cis-regulatory elements (CREs) that are important in defining cellular identity by establishing lineage-specific gene expression profiles (Lupien et al. 2008; Heintzman et al. 2009; Ernst et al. 2011). CREs...
OPEN ACCESS ARTICLE
Select this article
Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
- Dongwon Lee,
- Ashish Kapoor,
- Alexias Safi,
- Lingyun Song,
- Marc K. Halushka,
- Gregory E. Crawford,
- and Aravinda Chakravarti
Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
.... We first performed DNase-seq to identify open chromatin regions through DNase I hypersensitive sites (DHSs) as potential CREs in two adult human hearts (left ventricles) together with three publicly available heart DNase-seq data sets (Fig. 1A). Peak calling with MACS2 (Zhang et al. 2008) identified...
OPEN ACCESS ARTICLE
Select this article
Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
- Emily R. Miraldi,
- Maria Pokrovskii,
- Aaron Watters,
- Dayanne M. Castro,
- Nicholas De Veaux,
- Jason A. Hall,
- June-Yong Lee,
- Maria Ciofani,
- Aviv Madar,
- Nick Carriero,
- Dan R. Littman,
- and Richard Bonneau
Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
....Genome-scale inference of TRNs in mammalian settings is an outstanding challenge, given the increased complexity of regulatory mechanisms relative to simpler eukaryotes. Thus, chromatin state data are especially important for mammalian TRN inference. Construction of a -scale TRN for T Helper Cell Type 17 (Th17...
OPEN ACCESS ARTICLE
Select this article
Method: Predicting cell-type–specific gene expression from regions of open chromatin
- Anirudh Natarajan,
- Galip Gürkan Yardımcı,
- Nathan C. Sheffield,
- Gregory E. Crawford,
- and Uwe Ohler
Genome Res. September 2012 22: 1711-1722; doi:10.1101/gr.135129.111
..., this effort reflects the role that sequence plays in determining expression outside of the chromatin context. In contrast, our work attempts to identify cell-type–specific expression from the endogenous accessibility of putative cis-regulatory regions. Second, the investigators defined classification tasks...
OPEN ACCESS ARTICLE
Select this article
Research: Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity
- Sudhir Thakurela,
- Sanjeeb Kumar Sahu,
- Angela Garding,
- and Vijay K. Tiwari
Genome Res. September 2015 25: 1309-1324; Published in Advance July 13, 2015, doi:10.1101/gr.190926.115
..., open chromatin profiling has been widely used to identify regulatory elements that predict cell-type–specific functional behaviors (Thurman et al. 2012). Active regulatory elements such as promoters and enhancers are accessible and are marked by H3K27ac, thereby allowing a study of the activity state...
OPEN ACCESS ARTICLE
Select this article
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
...regions, where TFs can recognize their motifs and regulate gene expression programs. Here, we present motif enrichment in differential elements of accessibility (MEDEA), a computational tool that analyzes high-throughput chromatin accessibility genomic data to identify cell-type-specific accessible...
Select this article
Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
...expression they modulate will be crucial in unlocking the full therapeutic potential of these cells. Here, we use DNase-seq in combination with analysis of histone modifications to identify multiple classes of epigenetically and functionally distinct cis-regulatory elements (CREs). Through motif analysis...
Select this article
Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
...that the genomic location of nucleosome-depleted regions (NDRs) is mostly cell type specific and preferentially found at enhancers in normal cells. In cancer cells, however, we observe a global reconfiguration of NDRs at distal regulatory elements coupled with a substantial reorganization of the cancer methylome...
OPEN ACCESS ARTICLE
Select this article
Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
- Tatsunori Hashimoto,
- Richard I. Sherwood,
- Daniel D. Kang,
- Nisha Rajagopal,
- Amira A. Barkal,
- Haoyang Zeng,
- Bart J.M. Emons,
- Sharanya Srinivasan,
- Tommi Jaakkola,
- and David K. Gifford
Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
...using DNase-seq (Boyle et al. 2008), amethod for identifyingDNase I hypersensitive sites (DHS) (Weintraub and Groudine 1976; Wu 1980). DNase I hypersensitivity is a common feature of most gene regulatory elements, including enhancers and promoters (Thurman et al. 2012), and thus systematic understanding...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Song et al. 21 (10): 1757.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: