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Research: Alu insertion variants alter gene transcript levels
- Lindsay M. Payer,
- Jared P. Steranka,
- Maria S. Kryatova,
- Giacomo Grillo,
- Mathieu Lupien,
- Pedro P. Rocha,
- and Kathleen H. Burns
Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
.... Some Alu elements that have accumulated point mutations over time have become enhancers (e.g., Norris et al. 1995; Gombart et al. 2009; Jacobsen et al. 2009; Zhang et al. 2019). In general, these evolutionarily older Alu elements that are “fixed” in the , homozygous present in all individuals, can...
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Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- Brian S. Roberts,
- E. Christopher Partridge,
- Bryan A. Moyers,
- Vikram Agarwal,
- Kimberly M. Newberry,
- Beth K. Martin,
- Jay Shendure,
- Richard M. Myers,
- and Gregory M. Cooper
Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
...strand, suggesting that function related to endogenous transcription is driving the phenomenon. Similarly, we find that within Alu mobile element insertions, strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements...
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Resource: Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types
- Jill E. Moore,
- Xiao-Ou Zhang,
- Shaimae I. Elhajjajy,
- Kaili Fan,
- Henry E. Pratt,
- Fairlie Reese,
- Ali Mortazavi,
- and Zhiping Weng
Genome Res. February 2022 32: 389-402; Published in Advance December 23, 2021, doi:10.1101/gr.275723.121
...gene expression.Although public RNA-seq data are accumulating across a wide array of tissues and cells types, many of which are from coordinated efforts such as the Genotype-Tissue Expression (GTEx) (The GTEx Consortium 2020) and Encyclopedia of DNA Elements (ENCODE) (The ENCODE Project Consortium et...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...enhancers among ChIP peaks, whereas remaining peaks have no obvious regulatory function and may represent crosslinking artifacts. Genome-wide TP53 responsive enhancers are invariably used across cell types Unsophisticated enhancer logic, with only a single high-scoring TP53 binding site being necessary...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...are characteristic of the tissue type Principal component analysis (PCA) and cluster analysis of the unmethylated Alu repeats revealed specific signatures of each cell type (blood, normal colon, and tumor cells) ( Supplemental Fig. S16 ). Analysis of the remaining genomic elements also classified the samples...
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Research: Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites
- Daniel Savic,
- Brian S. Roberts,
- Julia B. Carleton,
- E. Christopher Partridge,
- Michael A. White,
- Barak A. Cohen,
- Gregory M. Cooper,
- Jason Gertz,
- and Richard M. Myers
Genome Res. December 2015 25: 1791-1800; Published in Advance October 20, 2015, doi:10.1101/gr.191593.115
...= 0.00321), consistent with a recent finding that most human Alus lack epigenetic features of active enhancers (Su et al. 2014). We also detected significant differences in sequence conservation between active and inactive sequences (GERP scores for active and inactive elements P = 4.069 × 10−5). We...
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Resource: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- Lingyun Song,
- Zhancheng Zhang,
- Linda L. Grasfeder,
- Alan P. Boyle,
- Paul G. Giresi,
- Bum-Kyu Lee,
- Nathan C. Sheffield,
- Stefan Gräf,
- Mikael Huss,
- Damian Keefe,
- Zheng Liu,
- Darin London,
- Ryan M. McDaniell,
- Yoichiro Shibata,
- Kimberly A. Showers,
- Jeremy M. Simon,
- Teresa Vales,
- Tianyuan Wang,
- Deborah Winter,
- Zhuzhu Zhang,
- Neil D. Clarke,
- Ewan Birney,
- Vishwanath R. Iyer,
- Gregory E. Crawford,
- Jason D. Lieb,
- and Terrence S. Furey
Genome Res. October 2011 21: 1757-1767; Published in Advance July 12, 2011, doi:10.1101/gr.121541.111
...cells, a core sequence in Alu repeats. We repeated the above motif analyses in distal FAIRE-only or DNase-only sites and found biologically relevant motifs. For example, DNase-only sites are most enriched for the same motifs as the combined open chromatin set in K562, GM12878, NHEK, and HepG2 (GATA1...
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ARTICLE: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes
- Liora Z. Strichman-Almashanu,
- Richard S. Lee,
- Patrick O. Onyango,
- Elizabeth Perlman,
- Folke Flam,
- Matthew B. Frieman,
- and Andrew P. Feinberg
Genome Res. April 1, 2002 12: 543-554; Published in Advance March 20, 2002, doi:10.1101/gr.224102
...to be methylated. The little-known SVA retroposon contains a GC-rich VNTR region, which embodies a CpG island between an Alu-derived region and an LTR-derived region. Only three such elements had previously been described ( Kawajiri et al. 1986 ; Zhu et al. 1992 ; Shen 1994 ), although their methylation has...
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Research: Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
- Angel Carlos Román,
- Francisco J. González-Rico,
- Eduardo Moltó,
- Henar Hernando,
- Ana Neto,
- Cristina Vicente-Garcia,
- Esteban Ballestar,
- José L. Gómez-Skarmeta,
- Jana Vavrova-Anderson,
- Robert J. White,
- Lluís Montoliu,
- and Pedro M. Fernández-Salguero
Genome Res. March 2011 21: 422-432; Published in Advance February 3, 2011, doi:10.1101/gr.111203.110
...flanking human Alu repeats are implicated in ependymomas (Xie et al. 2010). In addition, we have shown that the insulator activity of B1-X35S involves binding of parylated CTCF, an established insulator-binding protein involved in loop formation and the recruitment of repressive complexes to chromatin (Han...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...of CRS/repeat overlaps, including 1572 CRSs that overlap Alu elements. Evolutionary constraints on RNA structure do not necessarily coincide with evolutionary constraints on sequence. In particular, ∼50% of CRSs fall outside of conserved elements identified by phastCons (Siepel et al. 2005) in the 100...
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