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Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
- Arun B. Dutta,
- Daniel S. Lank,
- Roza K. Przanowska,
- Piotr Przanowski,
- Lixin Wang,
- Bao Nguyen,
- Ninad M. Walavalkar,
- Fabiana M. Duarte,
- and Michael J. Guertin
Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
..., and atherosclerosis. Prior characterizations of the transcriptional network driving adipogenesis have overlooked transiently acting transcription factors (TFs), genes, and regulatory elements that are essential for proper differentiation. Moreover, traditional gene regulatory networks provide neither mechanistic...
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Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
....Overall, both estradiol and testosterone affected genes involved in metabolism, development, and immune function. However, estradiol primarily affected these processes in the adipose tissue, whereas testosterone showed influence in the liver.Genes and pathways affected by gonadal sexIn the liver, 3WA analyses...
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Research: A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort
- Danielle M. Greenawalt,
- Radu Dobrin,
- Eugene Chudin,
- Ida J. Hatoum,
- Christine Suver,
- John Beaulaurier,
- Bin Zhang,
- Victor Castro,
- Jun Zhu,
- Solveig K. Sieberts,
- Susanna Wang,
- Cliona Molony,
- Steven B. Heymsfield,
- Daniel M. Kemp,
- Marc L. Reitman,
- Pek Yee Lum,
- Eric E. Schadt,
- and Lee M. Kaplan
Genome Res. July 2011 21: 1008-1016; Published in Advance May 20, 2011, doi:10.1101/gr.112821.110
...out a genome-wide association analyses for more than 100,000 gene expression traits representing four metabolically relevant tissues: liver, omental adipose, subcutaneous adipose, and stomach. We successfully identified 24,531 eSNPs corresponding to about 10,000 distinct genes. This represents...
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Method: Integrated analysis of motif activity and gene expression changes of transcription factors
- Jesper Grud Skat Madsen,
- Alexander Rauch,
- Elvira Laila Van Hauwaert,
- Søren Fisker Schmidt,
- Marc Winnefeld,
- and Susanne Mandrup
Genome Res. February 2018 28: 243-255; Published in Advance December 12, 2017, doi:10.1101/gr.227231.117
...enriched for transcription factors known to be involved in regulation of fat cell differentiation as defined by gene ontology (Fig. 4B). Furthermore, this group is highly enriched for transcription factors whose expression in adipose tissue correlates with BMI (Supplemental Fig. S1D) and which affect lipid...
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Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
- Hala Al Adhami,
- Brendan Evano,
- Anne Le Digarcher,
- Charlotte Gueydan,
- Emeric Dubois,
- Hugues Parrinello,
- Christelle Dantec,
- Tristan Bouschet,
- Annie Varrault,
- and Laurent Journot
Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
...from proliferation to quiescence and differentiation during fibroblast cell cycle withdrawal, adipogenesis in vitro, and muscle regeneration in vivo. Imprinted gene regulation is not linked to alteration of DNA methylation or to perturbation of monoallelic, parent-of-origin-dependent expression...
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Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
- Anushka Gupta,
- Farnaz Shamsi,
- Nicolas Altemose,
- Gabriel F. Dorlhiac,
- Aaron M. Cypess,
- Andrew P. White,
- Nir Yosef,
- Mary Elizabeth Patti,
- Yu-Hua Tseng,
- and Aaron Streets
Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
...with greater oxidative capacity (Pfeifer and Hoffmann 2015). Therefore, understanding the molecular pathways of adipose tissue expansion (adipogenesis) in humans and identifying resident cell types that regulate adipocyte activity are necessary for understanding the tissue's contribution in the pathology...
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Research: Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers
- Søren Fisker Schmidt,
- Bjørk Ditlev Larsen,
- Anne Loft,
- Ronni Nielsen,
- Jesper Grud Skat Madsen,
- and Susanne Mandrup
Genome Res. September 2015 25: 1281-1294; Published in Advance June 25, 2015, doi:10.1101/gr.188300.114
...4E,F). Interestingly, the basal super-enhancers identified in SGBS cells are enriched in the vicinity of genes suppressed in adipose tissue from obese human subjects compared with lean subjects in three independent studies (Supplemental Fig. S4G). This suggests that these super-enhancers may also...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...with decreased adipogenesis (Braga et al. 2014; Chen et al. 2020) and overexpression of FST promotes white adipose tissue browning (Braga et al. 2014; Tang et al. 2020). Therefore, in addition to the genomic evidence suggesting FST is the target gene at this locus, FST’s established roles in T2D-relevant cell...
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Research: Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes
- Eivind Lund,
- Anja R. Oldenburg,
- Erwan Delbarre,
- Christel T. Freberg,
- Isabelle Duband-Goulet,
- Ragnhild Eskeland,
- Brigitte Buendia,
- and Philippe Collas
Genome Res. October 2013 23: 1580-1589; Published in Advance July 16, 2013, doi:10.1101/gr.159400.113
...interactions with regulatory elements modulate gene expression in different cellular contexts is unknown. We show here that in human adipose tissue stem cells, lamin A/C interacts with distinct spatially restricted subpromoter regions, both within and outside peripheral and intra-nuclear lamin-rich domains...
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Research: Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B
- Torunn Rønningen,
- Akshay Shah,
- Anja R. Oldenburg,
- Kristin Vekterud,
- Erwan Delbarre,
- Jan Øivind Moskaug,
- and Philippe Collas
Genome Res. December 2015 25: 1825-1835; Published in Advance September 10, 2015, doi:10.1101/gr.193748.115
...interact with genes and regulatory regions during embryonic and somatic stem cell differentiation (Peric-Hupkes et al. 2010; Lund et al. 2013). Recent work shows that in adipose tissue stem cells (ASCs), proadipogenic gene promoters are released from lamin A/C after differentiation into adipocytes, whereas...

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