Searching journal content for articles similar to Borštnik and Pumpernik 12 (6): 909.

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  1. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    ...(TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. However, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory...
  2. Research: Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
    • Meredith M. Course,
    • Arvis Sulovari,
    • Kathryn Gudsnuk,
    • Evan E. Eichler,
    • and Paul N. Valdmanis
    Genome Res. August 2021 31: 1313-1324; Published in Advance July 9, 2021, doi:10.1101/gr.275560.121
    ...been seen for the VNTRs in ABCA7 (De Roeck et al. 2018, 2019), which is dynamically expanded in non-human primates and has much more internal variability, and in CACNA1A (Song et al. 2018), which has variability primarily in two regions in the middle of the repeat. Some of the earliest studies of VNTR...
  3. Research: Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism
    • Dale J. Annear,
    • Geert Vandeweyer,
    • Alba Sanchis-Juan,
    • F. Lucy Raymond,
    • and R. Frank Kooy
    Genome Res. November/December 2022 32: 1967-1980; Published in Advance November 9, 2022, doi:10.1101/gr.277011.122
    ...present within the 3′-UTR region.View larger version: In this window In a new window Figure 3. A comparison of CGG short tandem repeat characteristics between the specified genetic regions. (A) Distribution of repeat deviation rate of all unusually mutable CGG STR loci within the different genetic regions...
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  4. Research: Large palindromes on the primate X Chromosome are preserved by natural selection
    • Emily K. Jackson,
    • Daniel W. Bellott,
    • Ting-Jan Cho,
    • Helen Skaletsky,
    • Jennifer F. Hughes,
    • Tatyana Pyntikova,
    • and David C. Page
    Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
    ...). Amplicons are long, highly identical repeat units, with lengths that can exceed 100 kb in length and sequence identities >99% (Kuroda-Kawaguchi et al. 2001). Although some amplicons form tandem arrays, the majority comprise large palindromes, with mirrored repeats facing head to head (Skaletsky et al. 2003...
  5. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...Accurate typing of short tandem repeats from genome-wide sequencing data and its applications Arkarachai Fungtammasan 1 , 2 , 3 , 4 , 8 , Guruprasad Ananda 1 , 3 , 4 , 5 , 8 , 9 , Suzanne E. Hile 3 , 6 , Marcia Shu-Wei Su 2 , 3...
  6. Research: The 22q11 low copy repeats are characterized by unprecedented size and structural variability
    • Wolfram Demaerel,
    • Yulia Mostovoy,
    • Feyza Yilmaz,
    • Lisanne Vervoort,
    • Steven Pastor,
    • Matthew S. Hestand,
    • Ann Swillen,
    • Elfi Vergaelen,
    • Elizabeth A. Geiger,
    • Curtis R. Coughlin,
    • Stephen K. Chow,
    • Donna McDonald-McGinn,
    • Bernice Morrow,
    • Pui-Yan Kwok,
    • Ming Xiao,
    • Beverly S. Emanuel,
    • Tamim H. Shaikh,
    • and Joris R. Vermeesch
    Genome Res. September 2019 29: 1389-1401; doi:10.1101/gr.248682.119
    ..., their exact locations have, despite extensive efforts (Guo et al. 2016), remained elusive. We set out to map these repeats to elucidate the LCR22 structures and their variability and to further refine the 22q11DS rearrangement breakpoint regions.ResultsSubunit-resolution LCR assemblies using fiber FISHTo...
  7. Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
    • Leeban Yusuf,
    • Matthew C. Heatley,
    • Joseph P.G. Palmer,
    • Henry J. Barton,
    • Christopher R. Cooney,
    • and Toni I. Gossmann
    Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
    ...undergoing positive selection at branches that show rapid morphological change, we designed a hotspot approach.Binned branch approach for the detection of large-effect genes and regulatory regionsTo detect genes that may be undergoing repeated periods of rapid, possibly adaptive, evolution across multiple...
  8. Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
    • Guillaume Dumas,
    • Simon Malesys,
    • and Thomas Bourgeron
    Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
    ...to the motor cortex in humans is mirrored in the cerebellum by an enlargement of the regions of the cerebellum connected to the prefrontal cortex (Balsters et al. 2010). These anatomic processes of tandem evolution in the brain paralleled the emergence of motor and cognitive abilities, such as bipedalism...
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  9. Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
    • Yi Shao,
    • Chunyan Chen,
    • Hao Shen,
    • Bin Z. He,
    • Daqi Yu,
    • Shuai Jiang,
    • Shilei Zhao,
    • Zhiqiang Gao,
    • Zhenglin Zhu,
    • Xi Chen,
    • Yan Fu,
    • Hua Chen,
    • Ge Gao,
    • Manyuan Long,
    • and Yong E. Zhang
    Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
    ...-wide comparison of the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family–based methods are useful for ancient genes. For SBP-dated primate-specific protein-coding genes (PSGs), we performed manual evaluation based...
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  10. Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
    • Marta Farré,
    • Jaebum Kim,
    • Anastasia A. Proskuryakova,
    • Yang Zhang,
    • Anastasia I. Kulemzina,
    • Qiye Li,
    • Yang Zhou,
    • Yingqi Xiong,
    • Jennifer L. Johnson,
    • Polina L. Perelman,
    • Warren E. Johnson,
    • Wesley C. Warren,
    • Anna V. Kukekova,
    • Guojie Zhang,
    • Stephen J. O'Brien,
    • Oliver A. Ryder,
    • Alexander S. Graphodatsky,
    • Jian Ma,
    • Harris A. Lewin,
    • and Denis M. Larkin
    Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
    ...in msHSBs, repeated the process 2000 times, and found no significant differences in the expression divergence for any pairwise comparisons of different species (P-value = 0.37). Similarly, two subsets of 100 genes were selected from non-EBR regions and the same comparison was performed. After 2000...
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