Searching journal content for articles similar to Do Kim et al. 16 (7): 901.

Displaying results 1-10 of 22

For checked items

view abstracts
download to citation manager

Select this article
Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...in mice housing the α-globin gene cluster, delineate the chromatin region where enhancers gain access and interact with responsive promoters, which underscored the association of hierarchical TADs with gene-specific regulation. Moreover, several studies have documented a category of partially overlapping...
Select this article
Research: YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
- Jonathan A. Beagan,
- Michael T. Duong,
- Katelyn R. Titus,
- Linda Zhou,
- Zhendong Cao,
- Jingjing Ma,
- Caroline V. Lachanski,
- Daniel R. Gillis,
- and Jennifer E. Phillips-Cremins
Genome Res. July 2017 27: 1139-1152; Published in Advance May 23, 2017, doi:10.1101/gr.215160.116
...(downstream) genes are colored green. (C) Relative gene expression of Nes and Bcan across ES 2i, ES serum, and NPC cellular states. (D) Interaction cluster outlines of the loop boxed in magenta in B. Plot is overlaid with ChIP-seq tracks of H3K27ac, YY1, and CTCF in the ES 2i, ES serum, and NPC conditions...
OPEN ACCESS ARTICLE
Select this article
Method: Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Andrew J. Sharp,
- Eugenia Migliavacca,
- Yann Dupre,
- Elisavet Stathaki,
- Mohammad Reza Sailani,
- Alessandra Baumer,
- Albert Schinzel,
- Deborah J. Mackay,
- David O. Robinson,
- Gilda Cobellis,
- Luigi Cobellis,
- Han G. Brunner,
- Bernhard Steiner,
- and Stylianos E. Antonarakis
Genome Res. September 2010 20: 1271-1278; Published in Advance July 14, 2010, doi:10.1101/gr.108597.110
...modifications that distinguish thematernal and paternal s at these loci (Reik and Walter 2001; Dindot et al. 2009). More than 60 imprinted genes have been identified in humans (http://www.geneimprint.com/), and their clustered nature suggests that many are regulated by regional control mechanisms. To date...
Select this article
LETTER: Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
- Suresh Cuddapah,
- Raja Jothi,
- Dustin E. Schones,
- Tae-Young Roh,
- Kairong Cui,
- and Keji Zhao
Genome Res. January 2009 19: 24-32; Published in Advance December 3, 2008, doi:10.1101/gr.082800.108
....J. ( 2005 ) Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF . Mol. Cell 20 : 483 – 489 . ↵ Donohoe, M.E. , Zhang, L.F. , Xu, N. , Shi, Y. , Lee, J.T. ( 2007 ) Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch . Mol. Cell 25 : 43 – 56...
OPEN ACCESS ARTICLE
Select this article
Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...isolated repetitive regions of the and identified those containing at least one YY1 motif for phylogenetic analysis. This phylogenetic analysis revealed that most of these unannotated repetitive regions from autosomal sequences do not cluster by chromosome. In contrast, sequences derived from the X...
Select this article
Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...transcription factor occupancy. (A) For each transcription factor, the position weight matrix (PWM) of its known motif and its DNA-binding domain (DBD) type are shown. (B) Pairwise comparisons of normalized GABPA, MAX, NRF1, SP1, or YY1 ChIP-seq signal for all identified occupancy peaks. Regions...
OPEN ACCESS ARTICLE
Select this article
Research: Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder
- Przemyslaw Szafranski,
- Avinash V. Dharmadhikari,
- Erwin Brosens,
- Priyatansh Gurha,
- Katarzyna E. Kołodziejska,
- Ou Zhishuo,
- Piotr Dittwald,
- Tadeusz Majewski,
- K. Naga Mohan,
- Bo Chen,
- Richard E. Person,
- Dick Tibboel,
- Annelies de Klein,
- Jason Pinner,
- Maya Chopra,
- Girvan Malcolm,
- Gregory Peters,
- Susan Arbuckle,
- Sixto F. Guiang III,
- Virginia A. Hustead,
- Jose Jessurun,
- Russel Hirsch,
- David P. Witte,
- Isabelle Maystadt,
- Neil Sebire,
- Richard Fisher,
- Claire Langston,
- Partha Sen,
- and Paweł Stankiewicz
Genome Res. January 2013 23: 23-33; Published in Advance October 3, 2012, doi:10.1101/gr.141887.112
...identified and best characterized to date human lncRNA. Recently, lncRNAs have been implicated in imprinting and long-range gene regulation with functional properties of enhancers (Khalil et al. 2009; Mattick 2010;Wang and Chang 2011). Here, we demonstrate that loss of a distant enhancer region in a protein...
Select this article
Chicken Special/Letters: Evolution of the Beckwith-Wiedemann syndrome region in vertebrates
- Martina Paulsen,
- Tarang Khare,
- Christopher Burgard,
- Sascha Tierling,
- and Jörn Walter
Genome Res. January 2005 15: 146-153; Published in Advance December 8, 2004, doi:10.1101/gr.2689805
...is partially recognizable in fish. Identification of paralogous genes in the human Besides the BWS orthologous genes in Fugu and zebrafish we identified a number of paralogs in other chromosomal regions (Supplemental Tables 1, 2). In addition, paralogs have previously been described for a few imprinted BWS...
Select this article
Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- Timothy E. Reddy,
- Jason Gertz,
- Florencia Pauli,
- Katerina S. Kucera,
- Katherine E. Varley,
- Kimberly M. Newberry,
- Georgi K. Marinov,
- Ali Mortazavi,
- Brian A. Williams,
- Lingyun Song,
- Gregory E. Crawford,
- Barbara Wold,
- Huntington F. Willard,
- and Richard M. Myers
Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
...by TFs. Ultimately, targeting intergenic regions shown to have functional consequence may improve future microarray- and sequencing-based association studies by increasing coverage with only a modest effect on statistical power. Results Transcription factors often cluster together on the same alleles...
Select this article
LETTER: A Large Imprinted microRNA Gene Cluster at the Mouse Dlk1-Gtl2 Domain
- Hervé Seitz,
- Hélène Royo,
- Marie-Line Bortolin,
- Shau-Ping Lin,
- Anne C. Ferguson-Smith,
- and Jérôme Cavaillé
Genome Res. September 2004 14: 1741-1748; Published in Advance August 12, 2004, doi:10.1101/gr.2743304
...)—map within an intron of Ev1 and between Yy1 and Wars genes, respectively. Imprinting status of mir-342 remains unsolved as we failed to detect it in embryos. An intergenic germ-line derived differentially methylated region (IG-DMR) located between Dlk1 and Gtl2 genes is represented by circles (filled...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Do Kim et al. 16 (7): 901.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: