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Karger, Amir

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Karger

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Amir

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Karger, Amir

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2012 - 20163

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Author's Publications: search.filters.isAuthorOfPublication.b59ef980-87d7-40b6-8697-93bc6b3cd01e

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Now showing 1 - 3 of 3
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    Peptidomic discovery of short open reading frame-encoded peptides in human cells
    (2013) Slavoff, Sarah A.; Mitchell, Andrew J.; Schwaid, Adam G.; Cabili, Moran N.; Ma, Jiao; Levin, Joshua Z.; Karger, Amir; Budnik, Bogdan A.; Rinn, John; Saghatelian, Alan
    The amount of the transcriptome that is translated into polypeptides is of fundamental importance. We developed a peptidomic strategy to detect short ORF (sORF)-encoded polypeptides (SEPs) in human cells. We identified 90 SEPs, 86 of which are novel, the largest number of human SEPs ever reported. SEP abundances range from 10-1000 molecules per cell, identical to known proteins. SEPs arise from sORFs in non-coding RNAs as well as multi-cistronic mRNAs, and many SEPs initiate with non-AUG start codons, indicating that non-canonical translation may be more widespread in mammals than previously thought. In addition, coding sORFs are present in a small fraction (8/1866) of long intergenic non-coding RNAs (lincRNAs). Together, these results provide the strongest evidence to date that the human proteome is more complex than previously appreciated.
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    The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity
    (Nature Publishing Group, 2016) Hanschen, Erik R.; Marriage, Tara N.; Ferris, Patrick J.; Hamaji, Takashi; Toyoda, Atsushi; Fujiyama, Asao; Neme, Rafik; Noguchi, Hideki; Minakuchi, Yohei; Suzuki, Masahiro; Kawai-Toyooka, Hiroko; Smith, David R.; Sparks, Halle; Anderson, Jaden; Bakarić, Robert; Luria, Victor; Karger, Amir; Kirschner, Marc; Durand, Pierre M.; Michod, Richard E.; Nozaki, Hisayoshi; Olson, Bradley J. S. C.
    The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.
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    Deep Annotation of Populus trichocarpa MicroRNAs from Diverse Tissue Sets
    (Public Library of Science, 2012) Puzey, Joshua; Karger, Amir; Axtell, Michael; Kramer, Elena
    Populus trichocarpa is an important woody model organism whose entire genome has been sequenced. This resource has facilitated the annotation of microRNAs (miRNAs), which are short non-coding RNAs with critical regulatory functions. However, despite their developmental importance, P. trichocarpa miRNAs have yet to be annotated from numerous important tissues. Here we significantly expand the breadth of tissue sampling and sequencing depth for miRNA annotation in P. trichocarpa using high-throughput smallRNA (sRNA) sequencing. miRNA annotation was performed using three individual next-generation sRNA sequencing runs from separate leaves, xylem, and mechanically treated xylem, as well as a fourth run using a pooled sample containing vegetative apices, male flowers, female flowers, female apical buds, and male apical and lateral buds. A total of 276 miRNAs were identified from these datasets, including 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Importantly, we identified several xylem-enriched miRNAs predicted to target genes known to be important in secondary growth, including the critical reaction wood enzyme xyloglucan endo-transglycosylase/hydrolase and vascular-related transcription factors. This study provides a thorough genome-wide annotation of miRNAs in P. trichocarpathrough deep sRNA sequencing from diverse tissue sets. Our data significantly expands the P. trichocarpa miRNA repertoire, which will facilitate a broad range of research in this major model system.