Searching journal content for articles similar to Koterniak et al. 30 (12): 1766.

Displaying results 1-10 of 35

For checked items

view abstracts
download to citation manager

Select this article
Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...also analyze the global data to examine important TF features and relationships, including the correlation of cobinding by TFs at target genes, the frequency of high TF occupancy sites in the , and the impact of underlying sequence motifs and chromatin accessibility on TF binding. Finally, we begin...
Select this article
Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...or in the context of cell culture systems, global studies in complex organisms will be necessary to establish the extent of developmentally regulated zygotic decay.The nematode Caenorhabditis elegans provides an ideal system for the global study of zygotic mRNA decay owing to its invariant cell lineage...
Select this article
Resource: Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
- Nicolas J. Tourasse,
- Jonathan R.M. Millet,
- and Denis Dupuy
Genome Res. December 2017 27: 2120-2128; Published in Advance October 31, 2017, doi:10.1101/gr.224626.117
....0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵Allen MA, Hillier LW, Waterston RH, Blumenthal T. 2011. A global analysis of C. elegans trans-splicing. Genome Res 21: 255–264. ↵Amrane S, Rebora K, Zniber I, Dupuy D, Mackereth CD. 2014. Backbone-independent nucleic acid...
Select this article
Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
..., Finland (Dfc). Colors represent the climate zones according to the Köppen–Geiger climate distribution (Peel et al. 2007). (B) Pipeline to detect chimeric transcripts. (C) Contribution of chimeric gene–TE transcripts to the total transcriptome and the body part–specific transcriptome globally and by strain...
Select this article
Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
- Yang I. Li,
- Luis Sanchez-Pulido,
- Wilfried Haerty,
- and Chris P. Ponting
Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
...and TNS with beta integrin. In light of these findings, we propose that alternate use of micro-exons often alters local binding-site specificities, whereas the inclusion of longer AS exons may more substantially alter global protein structure. Although we show that several AS micro-exons are likely...
OPEN ACCESS ARTICLE
Select this article
Resource: Genome-wide analysis of alternative splicing in Caenorhabditis elegans
- Arun K. Ramani,
- John A. Calarco,
- Qun Pan,
- Sepand Mavandadi,
- Ying Wang,
- Andrew C. Nelson,
- Leo J. Lee,
- Quaid Morris,
- Benjamin J. Blencowe,
- Mei Zhen,
- and Andrew G. Fraser
Genome Res. February 2011 21: 342-348; Published in Advance December 22, 2010, doi:10.1101/gr.114645.110
...switching of mutually exclusive alternative splicing in vivo. Genes Dev 22: 360–374. Pan Q, Shai O,Misquitta C, ZhangW, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, et al. 2004. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform...
OPEN ACCESS ARTICLE
Select this article
Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...efficiency extends the exposure of intronic and exonic sequences to ADAR enzymes. Lack of splicing factors NOVA1 or NOVA2 changes global editing levels, demonstrating that alternative splicing factors can modulate RNA editing. Finally, we show that intron retention rates correlate with editing levels across...
OPEN ACCESS ARTICLE
Select this article
Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
...in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic...
Select this article
Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...into the regulatory network of that factor, as we find that the transcription factor UNC-62 has distinct binding profiles at different stages due to distinct cofactor co-association as well as tissue-specific alternative splicing. Finally, we describe an approach to infer potential regulators of gene expression...
Select this article
Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
...). Each of these features might be explained by the presence of strong regulatory constraints, such as shared enhancers or global control regions (de la Calle-Mustienes et al. 2005; Irimia et al. 2008). Consistently, functional studies in vertebrates and flies have shown that some regulatory elements...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Koterniak et al. 30 (12): 1766.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: