Searching journal content for articles similar to Hammelman et al. 30 (10): 1468.

Displaying results 1-10 of 15

For checked items

view abstracts
download to citation manager

Select this article
Research: SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
- A. Rasim Barutcu,
- Bryan R. Lajoie,
- Andrew J. Fritz,
- Rachel P. McCord,
- Jeffrey A. Nickerson,
- Andre J. van Wijnen,
- Jane B. Lian,
- Janet L. Stein,
- Job Dekker,
- Gary S. Stein,
- and Anthony N. Imbalzano
Genome Res. September 2016 26: 1188-1201; Published in Advance July 19, 2016, doi:10.1101/gr.201624.115
...for this article.] Organization of chromatin is essential formanybiological processes. Packaging of the DNA around the nucleosomes acts to tightly condense the (Cutter and Hayes 2015). At the same time, the cell has to regulate the accessibility of the chromatin to many enzymes for the regulation of gene...
Select this article
Research: Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
...; (HS2) beta-globin hypersensitive site 2 enhancer. (B) Reporter plasmids cotransfected with a plasmid expressing the Sleeping Beauty SB100X transposase for random genomic integration. GFP activity was measured by flow cytometry. A1 and C1 represent previously characterized CTCF-binding insulator...
Select this article
Research: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- Fumitaka Inoue,
- Martin Kircher,
- Beth Martin,
- Gregory M. Cooper,
- Daniela M. Witten,
- Michael T. McManus,
- Nadav Ahituv,
- and Jay Shendure
Genome Res. January 2017 27: 38-52; Published in Advance November 9, 2016, doi:10.1101/gr.212092.116
..., the magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this systematically, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare...
Select this article
Method: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee,
- Qingqing Guo,
- Mijeong Kim,
- Joonhyuk Choi,
- Alia Segura,
- Alper Genceroglu,
- Lucy LeBlanc,
- Nereida Ramirez,
- Yu Jin Jang,
- Yeejin Jang,
- Bum-Kyu Lee,
- Edward M. Marcotte,
- and Jonghwan Kim
Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
...assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). As shown in Figure 6, D and F, we found that the chromatin accessibility of control NANOG binding sites was similar to those in ES cells and the cells without TF induction. However, subsets of GCM1 and OTX2 target...
OPEN ACCESS ARTICLE
Select this article
Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
...–240 aa), and AMTP2. (B) The steady-state kinetics of AMT1 complex on a hemi-methylated substrate (hemi), determined by a 3H-SAM-based MTase assay. The substrate contains a single ApT duplex (underlined), which is hemi-methylated (red). (C) Methylation of the unmodified (un) and hemi-methylated (hemi...
Select this article
Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...expression, we and others have developed massively parallel reporter assays (MPRAs) probing the expression of various regulatory regions (Kwasnieski et al. 2012; Melnikov et al. 2012; Patwardhan et al. 2012; Sharon et al. 2012; Shalem et al. 2015). However, since these measurements are performed using...
Select this article
Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
.... Comparison with chromatin state maps of human ES cells reveals strong conservation of epigenetic makeup and gene regulation between the two systems. Strikingly, genes that are highly expressed in pluripotent cells and in Xenopus embryos but not in differentiated cells exhibit relatively high DNA...
Select this article
Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...of cell fates from single-cell snapshots. However, the study suggested that scRNA-seq fails to capture the heritable properties that guide fate determination, where additional studies such as chromatin accessibility or proteomics information may help to identify the hidden information (VanHorn and Morris...
OPEN ACCESS ARTICLE
Select this article
Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...approaches to gene identification used low-throughput sequencing of cDNA libraries derived from various tissues (Adams et al. 1991). In the context of murine spermatogenesis, these libraries were largely generated from whole adult testes (Kerr et al. 1994). Given the differential duration of various stages...
OPEN ACCESS ARTICLE
Select this article
Research: CG dinucleotides enhance promoter activity independent of DNA methylation
- Dominik Hartl,
- Arnaud R. Krebs,
- Ralph S. Grand,
- Tuncay Baubec,
- Luke Isbel,
- Christiane Wirbelauer,
- Lukas Burger,
- and Dirk Schübeler
Genome Res. April 2019 29: 554-563; Published in Advance February 1, 2019, doi:10.1101/gr.241653.118
...at http://creativecommons.org/licenses/by/4.0/.References ↵Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LFA, van Lohuizen M, van Steensel B. 2013. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154: 914–927. doi:10.1016/j...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Hammelman et al. 30 (10): 1468.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: