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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...included in one of the two other gene sets. Genes with a TPM of <1 were filtered.KEGG gene annotationsThe annotation of KEGG functional categories was adapted from Dong et al. (2023). We reused their functional category labels but excluded the category “Domain-containing proteins not elsewhere classified...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...TEs as functional regulatory elements of gene expression. Here we show that a subset of KRAB domain–containing zinc-finger proteins (KZFPs), which are highly expressed in mitotically dividing spermatogonia, repress the enhancer function of endogenous retroviruses (ERVs) and that the release from KZFP...
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Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
- Rosario Avolio,
- Ilenia Agliarulo,
- Daniela Criscuolo,
- Daniela Sarnataro,
- Margherita Auriemma,
- Sabrina De Lella,
- Sara Pennacchio,
- Giovanni Calice,
- Martin Y. Ng,
- Carlotta Giorgi,
- Paolo Pinton,
- Barry S. Cooperman,
- Matteo Landriscina,
- Franca Esposito,
- and Danilo Swann Matassa
Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
...function in a stable, inducible HeLa cell system. First of all, we confirmed in this model that modulation of TRAP1 expression levels, by either induction of shRNA-mediated silencing or overexpression of a TRAP1–GFP protein, affected the total cellular protein synthesis rate, as measured by incorporation...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...with the WSD motif suggests that ICOPa and ICOPb are highly divergent relative to other WSD motif–containing proteins (Supplemental Fig. S1). As shown subsequently, the ICOP ohnologs appeared functionally equivalent.ICOP proteins localize to the developing MACs during autogamyWe cotransformed paramecia...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...
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Research: Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance
- Jee Young Chung,
- Qurrat Ul Ain,
- Yoonsung Song,
- Seok-Beom Yong,
- and Yong-Hee Kim
Genome Res. September 2019 29: 1442-1452; Published in Advance August 29, 2019, doi:10.1101/gr.246900.118
...have proven the successful delivery of the CRISPR/Cas9 system in vivo (Ablain et al. 2015; Jiang et al. 2017; Miller et al. 2017), and to this end, carrier systems that can deliver plasmid DNA encoding Cas9, Cas9 mRNA together with sgRNA, or direct delivery of Cas9 protein/sgRNA complexes have been...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
...distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subs: the individual subs show no patterns of functional enrichment, no excess of shared protein–protein or metabolic interactions between their members, and no biases in their likelihood of having...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...containing 28 (TRIM28), also known as KRAB-associated protein 1 (KAP1), which acts as a scaffold for a heterochromatin-inducing complex, repressing transcription over KZFP-bound loci and flanking regions (Urrutia 2003). Older, more conserved KZFPs often harbor variant KRAB domains that display functionally...
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Research: nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
- Valentina Gandin,
- Laia Masvidal,
- Laura Hulea,
- Simon-Pierre Gravel,
- Marie Cargnello,
- Shannon McLaughlan,
- Yutian Cai,
- Preetika Balanathan,
- Masahiro Morita,
- Arjuna Rajakumar,
- Luc Furic,
- Michael Pollak,
- John A. Porco, Jr.,
- Julie St-Pierre,
- Jerry Pelletier,
- Ola Larsson,
- and Ivan Topisirovic
Genome Res. May 2016 26: 636-648; Published in Advance March 16, 2016, doi:10.1101/gr.197566.115
...RNAs encoding proteins with mitochondrial functions (e.g., ATP5O, ATP5G1) (Fig. 3A,B), with one exception, RDH13, which had a long 5′ UTR. These were in stark contrast to cell cycle- and survival-promoting mRNAs with long 5′ UTRs (e.g., CCND3, ODC1, MCL1, BIRC5 [survival] and MYC) (Fig. 3C). mRNAs with short 5...
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Research: Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
- Alex de Mendoza,
- Jahnvi Pflueger,
- and Ryan Lister
Genome Res. August 2019 29: 1277-1286; Published in Advance June 25, 2019, doi:10.1101/gr.243774.118
...most insects and crustaceans (Bewick et al. 2017; Gatzmann et al. 2018).Critical to the function of cytosine DNA methylation are methylation “readers,” proteins capable of binding and interpreting the methylation state and subsequently altering the transcriptional output or chromatin environment (Law...

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