Noteworthy Publications 2019
Director's Highlights
Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates.
Liu XM, Zhou J, Mao Y, Ji Q, Qian SB.
Nat Chem Biol. 2019 Sep;15(9):865-871. doi: 10.1038/s41589-019-0327-1. Epub 2019 Aug 5.
In this seminal work, Shu-Bing Qian (DNS) and colleagues develop a novel method for ‘m6A editing’. This approach allows researchers to assess for the first time the biological effects of individual m6A modifications. Shu-Bing is one of the 2020 CVG Seed Grant awardees.
Transmission of human-associated microbiota along family and social networks.
Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ.
Nature microbiology 2019 Jun;4(6):964.
How does our social network influence our microbiome and health? In this study of almost 300 people from the Fiji Islands, led by Ilana Brito (BME), the authors provide an unprecedented glimpse into how interpersonal contacts shape gut and oral microbiome composition.
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, Keinan A, Schimenti JC, Clark AG, Yu H.
Nat Commun. 2019 Sep 12;10(1):4141. doi: 10.1038/s41467-019-11959-3.
This study, on which Haiyuan Yu (CB) serves as senior author, represents an exciting collaboration among CVG members from several departments including CB (Keinan, Yu, Clark), BMS (Schimenti), and MBG (Clark). A key notable claim of this study is that possibly ~10% of missense variants in each individual disrupt protein interactions.
Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing
Therkildsen NO, Wilder AP, Conover DO, Munch SB, Baumann H, Palumbi SR.
Science. 2019 Aug 2;365(6452):487-90.
In this study, led by Nina Therkildsen (Natural Resources), the authors study rapid adaptation of fish populations to selection induced by human fishing activity. This study is a collaboration across five different institutions. Nina was one of the invited speakers at the 2018 CVG symposium.
A cell-free DNA metagenomic sequencing assay that integrates the damage response to infection
Cheng AP, Burnham P, Lee JR, Cheng MP, Suthanthiran M, Dadhania D, De Vlaminck I
PNAS September 10, 2019 116 (37) 18738-18744
This study from the lab of Iwijn De Vlaminck (BME) describes a new method for metagenomic sequencing that integrates information about the host, providing greater biological insight into the type and origin of infection or infectious disease. Iwijn is one of our newest members, as of December 2019.
Summer and Fall 2019
Fluorescent Reporter Zebrafish Line for Estrogenic Compound Screening Generated Using a CRISPR/Cas9-Mediated Knock-in System
Abdelmoneim A, Clark CL, Mukai M
Toxicological Sciences. 2019 Nov 5
Evolution of the new head by gradual acquisition of neural crest regulatory circuits.
Martik ML, Gandhi S, Uy BR, Gillis JA, Green SA, Simoes-Costa M, Bronner ME.
Nature. 2019 Oct;574(7780):675-8.
CDK2 kinase activity is a regulator of male germ cell fate.
Singh P, Patel RK, Palmer N, Grenier JK, Paduch D, Kaldis P, Grimson A, Schimenti JC.
Development. 2019 Oct 3. pii: dev.180273. doi: 10.1242/dev.180273. [Epub ahead of print]
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.
Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT.
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19431-19439. doi: 10.1073/pnas.1901244116. Epub 2019 Sep 10.
Unexpected roles for ADH1 and SORD in catalyzing the final step of erythritol biosynthesis
Schlicker L, Szebenyi DM, Ortiz SR, Heinz A, Hiller K, Field MS.
Journal of Biological Chemistry. 2019 Sep 11:jbc-RA119.
Unexpected species diversity in electric eels with a description of the strongest living bioelectricity generator
de Santana CD, Crampton WG, Dillman CB, Frederico RG, Sabaj MH, Covain R, Ready J, Zuanon J, de Oliveira RR, Mendes-Júnior RN, Bastos DA.
Nature communications. 2019 Sep 10;10(1):1-0.
Host-transposon interactions: conflict, cooperation, and cooption.
Cosby RL, Chang NC, Feschotte C.
Genes Dev. 2019 Sep 1;33(17-18):1098-1116. doi: 10.1101/gad.327312.119. Review.
Sex-specific hepatic lipid and bile acid metabolism alterations in Fancd2-deficient mice following dietary challenge.
Moore ES, Daugherity EK, Karambizi DI, Cummings BP, Behling-Kelly E, Schaefer DMW, Southard TL, McFadden JW, Weiss RS.
J Biol Chem. 2019 Aug 21. pii: jbc.RA118.005729. doi: 10.1074/jbc.RA118.005729. [Epub ahead of print]
Taste loss with obesity in mice and men
Kaufman A, Kim J, Noel C, Dando R.
International Journal of Obesity. 2019 Aug 6:1-5.
January - June 2019
methyl-ATAC-seq measures DNA methylation at accessible chromatin.
Spektor R, Tippens ND, Mimoso CA, Soloway PD
Genome research. 2019 Jun 1;29(6):969-77.
Retinoic acid and 6-formylindolo(3,2-b)carbazole (FICZ) combinatin therapy reveals putative targets for enhancing response in non-APL AML.
Bunaciu RP, MacDonald RJ, Jensen HA, Gao F, Wang X, Johnson L, Varner JD, Yen A.
Leukemia & lymphoma. 2019 Jun 7;60(7):1697-708.
A mutation in the endonuclease domain of mouse MLH3 reveals novel roles for MutLγ during crossover formation in meiotic prophase I.
Toledo M, Sun X, Brieño-Enríquez MA, Raghavan V, Gray S, Pea J, Milano CR, Venkatesh A, Patel L, Borst PL, Alani E, Cohen PE.
PLoS Genet. 2019 Jun 6;15(6):e1008177. doi: 10.1371/journal.pgen.1008177. eCollection 2019 Jun.
Redefining the IBDs using genome-scale molecular phenotyping.
Furey TS, Sethupathy P, Sheikh SZ.
Nat Rev Gastroenterol Hepatol. 2019 May;16(5):296-311. doi: 10.1038/s41575-019-0118-x. Review.
TGR5 Protects Against Colitis in Mice, but Vertical Sleeve Gastrectomy Increases Colitis Severity.
Garibay D, Zaborska KE, Shanahan M, Zheng Q, Kelly KM, Montrose DC, Dannenberg AJ, Miller AD, Sethupathy P, Cummings BP.
Obes Surg. 2019 May;29(5):1593-1601. doi: 10.1007/s11695-019-03707-9.
Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.
Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG, Ley RE.
Cell Host Microbe. 2019 Apr 10;25(4):553-564.e7. doi: 10.1016/j.chom.2019.03.001.
Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing.
Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A.
Genes (Basel). 2019 Apr 2;10(4). pii: E269. doi: 10.3390/genes10040269.
MicroRNA-375 Suppresses the Growth and Invasion of Fibrolamellar Carcinoma.
Dinh TA, Jewell ML, Kanke M, Francisco A, Sritharan R, Turnham RE, Lee S, Kastenhuber ER, Wauthier E, Guy CD, Yeung RS, Lowe SW, Reid LM, Scott JD, Diehl AM, Sethupathy P.
Cell Mol Gastroenterol Hepatol. 2019;7(4):803-817. doi: 10.1016/j.jcmgh.2019.01.008. Epub 2019 Feb 11.