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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...proximity-based DNA ligation with high-throughput sequencing to measure the geographical proximity of any pair of genomic loci. Techniques such as Hi-C are widely employed to characterize the 3D structure of the and uncover folding principles of chromatin, such as A/B compartments, topologically associating...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
...persist until a polyadenylation signal or a new exon is encountered. For 5′ truncations, a promoter unlike that of the ancestral gene must be used if such duplicates are to be transcribed. Specific examples of known human-specific genes by type are indicated.Duplicated genomic segments of high sequence...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
.... In contrast, Category 3 showed lower DNA constraint that was comparable to the DNA constraint observed for human-specific RELA binding. To investigate this further, we extracted and realigned all human RELA-bound sequences (±500 bp from the summit) that had conserved orthologous RELA binding in at least one...
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Research: Human-specific features of spatial gene expression and regulation in eight brain regions
- Chuan Xu,
- Qian Li,
- Olga Efimova,
- Liu He,
- Shoji Tatsumoto,
- Vita Stepanova,
- Takao Oishi,
- Toshifumi Udono,
- Katsushi Yamaguchi,
- Shuji Shigenobu,
- Akiyoshi Kakita,
- Hiroyuki Nawa,
- Philipp Khaitovich,
- and Yasuhiro Go
Genome Res. August 2018 28: 1097-1110; Published in Advance June 13, 2018, doi:10.1101/gr.231357.117
...investigated the regulatory mechanisms driving human-specific changes in gene expression. Analyses of transcription factors (TFs) revealed predicted TF regulatory networks and individual TFs driving gene expression differences between human and chimpanzee brains (Nowick et al. 2009; Liu et al. 2012). Analyses...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...-regulated in human LCLs (SYNRG, DUSP14, TADA2A, ACACA, MYO19, and DDX52) are comprised in the same topologically associating domain in Chr17q12 (Rao et al. 2015) and display human-specific exon usage changes (Fig. 5C). Genomic rearrangements in this locus have been extensively studied given their evolutionary...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
...variation mainly due to the lack of high-throughput techniques for detecting them. Most inversions described to date between human and nonhuman primate s result from laborious and target-based chromosomal studies in cytogenetics that led to the identification of several large inversion variants (Ventura et...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...al. 2016; Wu and Knudson 2018). Some genes that emerge de novo not only provide new functions, but have even become essential to the species in which they emerged. For example, the human-specific de novo gene ESRG is required for the maintenance of pluripotency in human naive stem cells (Wang et al...
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Research: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
- Jennifer Y. Tan,
- Tamara Sirey,
- Frantisek Honti,
- Bryony Graham,
- Allison Piovesan,
- Matthias Merkenschlager,
- Caleb Webber,
- Chris P. Ponting,
- and Ana C. Marques
Genome Res. May 2015 25: 655-666; Published in Advance March 19, 2015, doi:10.1101/gr.181974.114
...JY Tan Merkenschlager Matthias Tan, JY Chris Matthias Jennifer Ponting, C.P Merkenschlager Ana C Marques, AC Honti, F 1549-5469 10.1101/gr.181974.114 1088-9051 genome;gr.181974.114 Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells Tan et al. mi...
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Research: Extensive somatic L1 retrotransposition in colorectal tumors
- Szilvia Solyom,
- Adam D. Ewing,
- Eric P. Rahrmann,
- Tara Doucet,
- Heather H. Nelson,
- Michael B. Burns,
- Reuben S. Harris,
- David F. Sigmon,
- Alex Casella,
- Bracha Erlanger,
- Sarah Wheelan,
- Kyle R. Upton,
- Ruchi Shukla,
- Geoffrey J. Faulkner,
- David A. Largaespada,
- and Haig H. Kazazian, Jr.
Genome Res. December 2012 22: 2328-2338; Published in Advance September 11, 2012, doi:10.1101/gr.145235.112
...). Although there are about half a million L1s in the human , only the human-specific L1s (L1Hs) are currently active, represented in each individual by about 800 germline copies (Ewing and Kazazian 2010), including;200 full-length sequences (Boissinot et al. 2000). According to conservative estimates...
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Research: Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia
- Paul W. Hook and
- Andrew S. McCallion
Genome Res. April 2020 30: 528-539; Published in Advance April 17, 2020, doi:10.1101/gr.256578.119
...open chromatin profileWe lifted over all mouse OCR profiles to syntenic sequences in the human (hg19). We compared three methods, seeking to retain the maximum number of peaks while ensuring human profiles resembled mouse profiles. First, peaks were lifted over “as is” including 250-bp extensions...

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