Searching journal content for articles similar to Abewe et al. 35 (3): 393.

Displaying results 1-10 of 10

For checked items

view abstracts
download to citation manager

Select this article
Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...integrative analysis of human and mouse regulatory landscapes across progenitor and mature blood cell types. The features included chromatin accessibility, which is a hallmark of almost all regulatory elements, occupancy by the structural protein CTCF, and histone modifications associated with gene activation...
OPEN ACCESS ARTICLE
Select this article
Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...of ESR1 chromatin occupancy, the transcriptional program converges in the estrogen response owing to a redundancy of distal regulatory element binding by ESR1.ERE strength weakly associates with the level of inter-tumor conservation of ESR1 sitesFrom cell lines, ESR1 DNA binding is known to be enriched...
Select this article
Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
...impact of genetic variants within regulatory regions. In summary, TOP offers a cost-effective strategy for profiling the quantitative occupancy of hundreds of TF motifs using only a single chromatin accessibility experiment, markedly enhancing our ability to explore quantitative changes in TF occupancy...
Select this article
Methods: Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
- Mathieu Blanchette,
- Alain R. Bataille,
- Xiaoyu Chen,
- Christian Poitras,
- Josée Laganière,
- Céline Lefèbvre,
- Geneviève Deblois,
- Vincent Giguère,
- Vincent Ferretti,
- Dominique Bergeron,
- Benoit Coulombe,
- and François Robert
Genome Res. May 2006 16: 656-668; Published in Advance April 10, 2006, doi:10.1101/gr.4866006
.... Alternatively, these regions may actually be depleted for regulatory elements. This could be due to constraints imposed by the chromatin structure of the nuclear architecture, making it more difficult for the DNA of these regions to come in physical proximity to the TSS. After the first 50 kb upstream...
Select this article
Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
- Wendy A. Kellner,
- Joshua S.K. Bell,
- and Paula M. Vertino
Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
...-acting regulatory elements that control transcription from a distance through the formation of contacts between the enhancer-bound transcription factors and promoter-bound Pol II and the looping out of intervening chromatin (Kagey et al. 2010b). BRD4 and components of the P-TEFb complex have been shown...
Select this article
Research: GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility
- Vasiliki Theodorou,
- Rory Stark,
- Suraj Menon,
- and Jason S. Carroll
Genome Res. January 2013 23: 12-22; Published in Advance November 21, 2012, doi:10.1101/gr.139469.112
.... 2011). We find that in cells with intact GATA3 (siControl), EP300 is redistributed upon estrogen stimulation from regions not bound by ESR1 to regions co-occupied by ESR1–EP300, showing that estrogen induces recruitment of EP300 only to a subset of cis-regulatory elements (Supplemental Fig. 3A...
Select this article
Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- Yong Cheng,
- Weisheng Wu,
- Swathi Ashok Kumar,
- Duonan Yu,
- Wulan Deng,
- Tamara Tripic,
- David C. King,
- Kuan-Bei Chen,
- Ying Zhang,
- Daniela Drautz,
- Belinda Giardine,
- Stephan C. Schuster,
- Webb Miller,
- Francesca Chiaromonte,
- Yu Zhang,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
...to recruitment of large enzymatic complexes that lead to activation or repression by altering histone modifications or chromatin structure (Maston et al. 2006; Jiang and Pugh 2009). Some cis-regulatory modules (CRMs), containing clusters of binding sites for transcription factors (Maniatis et al. 1987...
OPEN ACCESS ARTICLE
Select this article
LETTER: Defining the mammalian CArGome
- Qiang Sun,
- Guang Chen,
- Jeffrey W. Streb,
- Xiaochun Long,
- Yumei Yang,
- Christian J. Stoeckert, Jr.,
- and Joseph M. Miano
Genome Res. February 2006 16: 197-207; Published in Advance December 19, 2005, doi:10.1101/gr.4108706
...IP-chip”) have been instrumental in defining regulatory sequences in yeast and mammals ( Horak et al. 2002 ; Lee et al. 2002 ; Blais et al. 2005 ). A related technique called serial analysis of chromatin occupancy has recently been reported for the definition of the cyclic AMP response element binding protein...
Select this article
Method: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases
- László Halász,
- Zsolt Karányi,
- Beáta Boros-Oláh,
- Tímea Kuik-Rózsa,
- Éva Sipos,
- Éva Nagy,
- Ágnes Mosolygó-L,
- Anett Mázló,
- Éva Rajnavölgyi,
- Gábor Halmos,
- and Lóránt Székvölgyi
Genome Res. June 2017 27: 1063-1073; Published in Advance March 24, 2017, doi:10.1101/gr.219394.116
...%–8% of the and impacting many cellular processes (Sanz et al. 2016; Wahba et al. 2016). For instance, R-loops (1) drive embryonic stem cell differentiation via modulating the chromosomal binding of chromatin-regulatory complexes (Chen et al. 2015), (2) ensure the optimal binding of transcriptional activators...
Select this article
Research: A CTCF-independent role for cohesin in tissue-specific transcription
- Dominic Schmidt,
- Petra C. Schwalie,
- Caryn S. Ross-Innes,
- Antoni Hurtado,
- Gordon D. Brown,
- Jason S. Carroll,
- Paul Flicek,
- and Duncan T. Odom
Genome Res. May 2010 20: 578-588; Published in Advance March 10, 2010, doi:10.1101/gr.100479.109
...proceeds via activation of the ER-regulated gene expression program that mediates re-entry into cell cycle. The functional effect of RNAimediated removal of candidate regulators on estrogen-induced proliferation can be used to determine whether cofactors are required for ER-driven transcription (Prall et...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Abewe et al. 35 (3): 393.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: