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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...for chromosome-scale assembly. PLoS Comput Biol 15: e1007273. doi:10.1371/journal.pcbi.1007273 ↵Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...downregulation, which was regulated by miR-216b. PLCB2, coexpressed with taste receptors in rat taste bud cells, forms a taste transduction pathway consisting of Gi2 and PLCB2 that occurs in a subset of taste cells (Asano-Miyoshi et al. 2000; Miyoshi et al. 2001). The significantly downregulated plcb2...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...not show any consistent pattern (Fig. 2B; Supplemental Fig. S10). This finding suggests that elevated mtDNA gene expression after birth is conserved across mammalian and terrestrial nonmammalian vertebrates.Expression of postnatal nuclear DNA–encoded OXPHOS gene is elevated across evolutionAs mt...
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Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
- Alexander Xi Fu,
- Kathy Nga-Chu Lui,
- Clara Sze-Man Tang,
- Ray Kit Ng,
- Frank Pui-Ling Lai,
- Sin-Ting Lau,
- Zhixin Li,
- Maria-Mercè Garcia-Barcelo,
- Pak-Chung Sham,
- Paul Kwong-Hang Tam,
- Elly Sau-Wai Ngan,
- and Kevin Y. Yip
Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
...behind it not fully known.Damaging rare variants at protein-coding sequences associated with HSCR have been found in many genes involved in ENS development. Among them, RET, encoding a receptor tyrosine kinase, is responsible for ∼50% of familial cases and 10%–20% of sporadic cases (Chakravarti et al...
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Research: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha
- James M. Davison,
- Colin R. Lickwar,
- Lingyun Song,
- Ghislain Breton,
- Gregory E. Crawford,
- and John F. Rawls
Genome Res. July 2017 27: 1195-1206; Published in Advance April 6, 2017, doi:10.1101/gr.220111.116
...nuclear factor 4 (HNF4) is the most ancient family of nuclear receptor transcription factors with important roles in human metabolic and inflammatory bowel diseases, but a role in host response to microbes is unknown. Using an unbiased screening strategy, we found that zebrafish Hnf4a specifically binds...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...with unknown function (33 genes), genes encoding ribosomal proteins (11 genes), or olfactory receptors (one gene), 15 of the genes have been assigned distinct rat gene symbols for which there is at least a partial functional characterization. Of these 15 genes, although some may be incorrectly annotated...
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Research: Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Xianzhi Lin,
- Tak-Ming Chan,
- Rena Wang,
- and Xinshu Xiao
Genome Res. April 2016 26: 440-450; Published in Advance February 17, 2016, doi:10.1101/gr.193359.115
.... 2012).We examined the ASE patterns of single-nucleotide variants (SNVs) and analyzed nuclear and cytosolic RNA contents comparatively. Our analyses identified more than 600 GMAS exons and associated SNVs, which enabled a detailed examination of the global features of these events.We observed that cis...
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LETTER: A Genomic Analysis of Rat Proteases and Protease Inhibitors
- Xose S. Puente and
- Carlos López-Otín
Genome Res. April 2004 14: 609-622; doi:10.1101/gr.1946304
...that facilitate their interaction with substrates, inhibitors, or receptors, or play some kind of regulatory role. Analysis of ancillary domains present in the annotated rat proteases has shown that ∼50% of these enzymes are associated with at least one recognizable domain among those present in the Pfam database...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...with the general structural conservatism exhibited by metatherian chromosomes in general (see following section). Chromosome structure and evolution Comparison of synteny relationships in the opossum with those of human, dog, mouse, rat, and chicken enabled construction of a five-way multispecies synteny map...
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Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
- Piotr J. Balwierz,
- Mikhail Pachkov,
- Phil Arnold,
- Andreas J. Gruber,
- Mihaela Zavolan,
- and Erik van Nimwegen
Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
...Figs. 5, 6). The associated transcription factor hepatocyte nuclear factor 1 homeoboxA (HNF1A) is relativelywell-studied and indeedknown to be mainly expressed in liver, kidney, stomach, and intestine (Kuo et al. 1990; Serfas and Tyner 1993), where it is essential for organ function (Pontoglio et al...
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