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Research: Genomic insights into metabolic flux in hummingbirds
- Ariel Gershman,
- Quinn Hauck,
- Morag Dick,
- Jerrica M. Jamison,
- Michael Tassia,
- Xabier Agirrezabala,
- Saad Muhammad,
- Raafay Ali,
- Rachael E. Workman,
- Mikel Valle,
- G. William Wong,
- Kenneth C. Welch, Jr.,
- and Winston Timp
Genome Res. May 2023 33: 703-714; Published in Advance May 8, 2023, doi:10.1101/gr.276779.122
...and annotation. Our genomic and transcriptomic data found positive selection of key metabolic genes in nectivorous avian species and deletion of critical genes (SLC2A4, GCK) involved in glucostasis in other vertebrates. We found expression of a fructose-specific version of SLC2A5 putatively in place of insulin...
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Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...core promoter element cannot be inferred solely by observing native genomic sequences. To achieve this goal, a large number of designed sequences in which specific elements are systematically varied in a highly controlled setting should be assayed.Other pivotal components of functional promoters are TF...
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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
...by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/17; www..org Genome Research 1153 www..org Results TRIP with Drosophila housekeeping promoters Drosophila housekeeping genes form clusters of consecutive genes, which are themselves densely packed in the (Fig. 1A). To understand whether...
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Research: The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
- Daniel C. Kraushaar,
- Zuozhou Chen,
- Qingsong Tang,
- Kairong Cui,
- Junfang Zhang,
- and Keji Zhao
Genome Res. November 2018 28: 1646-1655; Published in Advance September 25, 2018, doi:10.1101/gr.236224.118
...–1432. ↵Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human . Genome Biol 10: R25. ↵Lewis PW, Elsaesser SJ, Noh KM, Stadler SC, Allis CD. 2010. Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication...
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Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Keyi Geng,
- Lara G. Merino,
- Linda Wedemann,
- Aniek Martens,
- Małgorzata Sobota,
- Yerma P. Sanchez,
- Jonas Nørskov Søndergaard,
- Robert J. White,
- and Claudia Kutter
Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
...but instead were actively transcribed.View larger version: In this window In a new window Figure 5. Adverse on-target genomic alterations affected cell growth, promoted active transcription, and varied in abundance among deletion clones. (A) Illustration of the different CRISPR-Cas9 vector sequences (fragment...
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Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
- Stefan Schoenfelder,
- Mayra Furlan-Magaril,
- Borbala Mifsud,
- Filipe Tavares-Cadete,
- Robert Sugar,
- Biola-Maria Javierre,
- Takashi Nagano,
- Yulia Katsman,
- Moorthy Sakthidevi,
- Steven W. Wingett,
- Emilia Dimitrova,
- Andrew Dimond,
- Lucas B. Edelman,
- Sarah Elderkin,
- Kristina Tabbada,
- Elodie Darbo,
- Simon Andrews,
- Bram Herman,
- Andy Higgs,
- Emily LeProust,
- Cameron S. Osborne,
- Jennifer A. Mitchell,
- Nicholas M. Luscombe,
- and Peter Fraser
Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
...genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for &gt;22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment...
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Research: Recurrent epimutations activate gene body promoters in primary glioblastoma
- Raman P. Nagarajan,
- Bo Zhang,
- Robert J.A. Bell,
- Brett E. Johnson,
- Adam B. Olshen,
- Vasavi Sundaram,
- Daofeng Li,
- Ashley E. Graham,
- Aaron Diaz,
- Shaun D. Fouse,
- Ivan Smirnov,
- Jun Song,
- Pamela L. Paris,
- Ting Wang,
- and Joseph F. Costello
Genome Res. May 2014 24: 761-774; Published in Advance April 7, 2014, doi:10.1101/gr.164707.113
...in detection of hydroxymethylation by these two methods. We further validated several individual loci by the ‘‘gold standard’’ of bisulfite PCR, cloning and Sanger sequencing. We chose a hypomethylated locus within the TRPM5 gene body and a hypermethylated locus at the BCL2L11 promoter and in both cases...
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Method: High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
- Marie-Odile Baudement,
- Axel Cournac,
- Franck Court,
- Marie Seveno,
- Hugues Parrinello,
- Christelle Reynes,
- Robert Sabatier,
- Tristan Bouschet,
- Zhou Yi,
- Sephora Sallis,
- Mathilde Tancelin,
- Cosette Rebouissou,
- Guy Cathala,
- Annick Lesne,
- Julien Mozziconacci,
- Laurent Journot,
- and Thierry Forné
Genome Res. November 2018 28: 1733-1746; Published in Advance October 4, 2018, doi:10.1101/gr.237073.118
...isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. By using mouse embryonic stem cells (ESCs), we showed that these regions essentially correspond to the most highly expressed genes, and to cis-regulatory sequences like super-enhancers, that belong to the active...
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LETTER: Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
- Kouichi Kimura,
- Ai Wakamatsu,
- Yutaka Suzuki,
- Toshio Ota,
- Tetsuo Nishikawa,
- Riu Yamashita,
- Jun-ichi Yamamoto,
- Mitsuo Sekine,
- Katsuki Tsuritani,
- Hiroyuki Wakaguri,
- Shizuko Ishii,
- Tomoyasu Sugiyama,
- Kaoru Saito,
- Yuko Isono,
- Ryotaro Irie,
- Norihiro Kushida,
- Takahiro Yoneyama,
- Rie Otsuka,
- Katsuhiro Kanda,
- Takahide Yokoi,
- Hiroshi Kondo,
- Masako Wagatsuma,
- Katsuji Murakawa,
- Shinichi Ishida,
- Tadashi Ishibashi,
- Asako Takahashi-Fujii,
- Tomoo Tanase,
- Keiichi Nagai,
- Hisashi Kikuchi,
- Kenta Nakai,
- Takao Isogai,
- and Sumio Sugano
Genome Res. January 2006 16: 55-65; Published in Advance December 12, 2005, doi:10.1101/gr.4039406
...have also demonstrated that the exact positions of the TSSs and the adjacent putative promoters could be retrieved from the human genomic sequences in a high-throughput manner ( Suzuki et al. 2001b ). Our human full-length cDNA data accumulated so far and the retrieved adjacent upstream PPR information...
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Research: CBX3 regulates efficient RNA processing genome-wide
- Andrea Smallwood,
- Gary C. Hon,
- Fulai Jin,
- Ryan E. Henry,
- Joaquín M. Espinosa,
- and Bing Ren
Genome Res. August 2012 22: 1426-1436; Published in Advance June 8, 2012, doi:10.1101/gr.124818.111
...CBX3 regulates efficient RNA processing genome-wide Andrea Smallwood 1 , Gary C. Hon 1 , Fulai Jin 1 , Ryan E. Henry 2 , Joaquín M. Espinosa 2 and Bing Ren 1 , 3 , 4 1 Ludwig Institute for Cancer Research, La...

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