Laura Landweber

RNA-mediated epigenetics and genome reorganization during development

Landweber Lab Research description and images

Lu, M.W., Beh, L.Y., Yerlici, V.T., Fang, W., Kulej, K., Garcia, B.A and L.F. Landweber (2023) Exploration of the Nuclear Proteomes in the Ciliate Oxytricha trifallax. Microorganisms 2023, 11, 343. doi.org/10.3390/microorganisms11020343 

Feng, Y., Neme, R., Beh, L.Y., Chen, X., Braun, J., Lu, M., and L.F. Landweber (2022) Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. eLife 11:e82979. doi.org/10.7554/eLife.82979.     

Feng, Y and L.F. Landweber (2021). Transposon debris in ciliate genomes. PLoS Biol. 19(8):e3001354. 

Miller, R.V., Neme, R., Clay, D.M., Pathmanathan, J.S., Lu, M.W., Yerlici, V.T., Khurana, J.S., and L.F. Landweber. (2021).  Transcribed germline-limited coding sequences in Oxytricha trifallax. G3 Genes|Genomes|Genetics  doi.org/10.1093/g3journal/jkab092. 

Feng, Y., Beh, L.Y., Chang, W.J., and L.F. Landweber. (2020). SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping. Genome Biol Evol. doi.org/10.1093/gbe/evaa147. 

Lindblad, K.A., Pathmanathan, J.S., Moreira, S., Bracht, J.R., Sebra, R.P., Hutton, E.R., and L.F. Landweber (2019). Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms. BMC Genomics. 20(1):1037. doi.org/10.1186/s12864-019-6189-9. 

Yerlici, V.T., Lu, M.W., Hoge, C.R., Miller,R.V., Neme, R., Khurana, J.S., Bracht, J.R., and L.F. Landweber (2019). Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. Nucleic Acids Res 47(18):9741–9760. doi.org/10.1093/nar/gkz725. 

Clay, D.M., Yerlici, V.T., Villano, D.J., and L.F. Landweber (2019). Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax. G3 Genes|Genomes|Genetics 9(10):3105–18. doi.org/10.1534/g3.118.200930. 

Clay, D.M., Kim, H., and L.F. Landweber (2019). Transformation with Artificial Chromosomes in Oxytricha trifallax and Their Applications. G3 Genes|Genomes|Genetics 9(10):3119–27. doi.org/10.1534/g3.119.400298. 

Beh, L.Y., Debelouchina, G.T., Clay, D.M., Thompson, R.E., Lindblad, K.A., Hutton, E.R., Bracht, J.R., Sebra, R.P., Muir, T.W., and L.F. Landweber (2019). Identification of a DNA N6-adenine methyltransferase complex and its impact on chromatin organization. Cell 177(7):1781–1796.e25: doi.org/10.1016/j.cell.2019.04.028 

Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax. 
Braun J, Nabergall L, Neme R, Landweber LF, Saito M, Jonoska N. G3. 2018 May 4;8(5):1669-1674. doi.org/10.1534/g3.118.200176.

Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha. 
Khurana JS, Clay DM, Moreira S, Wang X, Landweber LF.
RNA. 2018 Jan;24(1):18-29. doi.org/10.1261/rna.061333.117. Epub 2017 Oct 27.

Non-model model organisms.
Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A.
BMC Biol. 2017 Jun 29;15(1):55. doi.org/10.1186/s12915-017-0391-5.

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development.
Lindblad KA, Bracht JR, Williams AE, Landweber LF.
RNA. 2017 Aug;23(8):1200-1208. doi.org/10.1261/rna.058511.116. 

Chromosome fusions triggered by noncoding RNA.
Bracht JR, Wang X, Shetty K, Chen X, Uttarotai GJ, Callihan EC, McCloud SS, Clay DM, Wang J, Nowacki M, Landweber LF.
RNA Biol. 2017 May 4;14(5):620-631. doi.org/10.1080/15476286.2016.1195940

Goldman AD, Beatty JT, Landweber LF. The TIM Barrel Architecture Facilitated
the Early Evolution of Protein-Mediated Metabolism. J Mol Evol. 2016
Jan;82(1):17-26. doi.org/10.1007/s00239-015-9722-8. Epub 2016 Jan 5. PubMed PMID:
26733481.

Chen X, Jung S, Beh LY, Eddy SR, Landweber LF. Combinatorial DNA Rearrangement
Facilitates the Origin of New Genes in Ciliates. Genome Biol Evol. 2015 Sep
2;7(10):2859-70. doi.org/10.1093/gbe/evv172. PubMed PMID: 26338187; PubMed Central
PMCID: PMC4684698.
 
Beh LY, Müller MM, Muir TW, Kaplan N, Landweber LF. DNA-guided establishment
of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res.
2015 Nov;25(11):1727-38. doi.org/10.1101/gr.188516.114. Epub 2015 Sep 1. PubMed
PMID: 26330564; PubMed Central PMCID: PMC4617968.
 
Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis
ER, Snyder M, McVean G. Where Next for Genetics and Genomics? PLoS Biol. 2015 Jul
30;13(7):e1002216. doi.org/10.1371/journal.pbio.1002216. eCollection 2015 Jul.
PubMed PMID: 26225775; PubMed Central PMCID: PMC4520474.
 
Yerlici VT, Landweber LF. Programmed Genome Rearrangements in the Ciliate
Oxytricha. Microbiol Spectr. 2014 Dec;2(6). doi.org/10.1128/microbiolspec.MDNA3-0025-2014. PubMed PMID: 26104449; PubMed Central
PMCID: PMC4480583.
 
Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH,
Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. The architecture of a
scrambled genome reveals massive levels of genomic rearrangement during
development. Cell. 2014 Aug 28;158(5):1187-98. doi.org/10.1016/j.cell.2014.07.034.
PubMed PMID: 25171416; PubMed Central PMCID: PMC4199391.
 
Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman
AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins
JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA,
Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. The Oxytricha
trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny
chromosomes. PLoS Biol. 2013;11(1):e1001473. doi.org/10.1371/journal.pbio.1001473.
Epub 2013 Jan 29. PubMed PMID: 23382650; PubMed Central PMCID: PMC3558436.
 
Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF. Genomes on
the edge: programmed genome instability in ciliates. Cell. 2013 Jan
31;152(3):406-16. doi.org/10.1016/j.cell.2013.01.005. PubMed PMID: 23374338;
PubMed Central PMCID: PMC3725814.
 
Fang W, Landweber LF. RNA-mediated genome rearrangement: hypotheses and
evidence. Bioessays. 2013 Feb;35(2):84-7. doi.org/10.1002/bies.201200140. Epub 2012
Dec 20. PubMed PMID: 23281134; PubMed Central PMCID: PMC3821980.
 
Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. Piwi-interacting RNAs
protect DNA against loss during Oxytricha genome rearrangement. Cell. 2012 Dec
7;151(6):1243-55. doi.org/10.1016/j.cell.2012.10.045. PubMed PMID: 23217708; PubMed
Central PMCID: PMC3678556.
 
Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of
Genome Rearrangements. Annu Rev Genomics Hum Genet. 2011;12:367-89. doi.org/10.1146/annurev-genom-082410-101420. Review. PubMed PMID: 21801022; PubMed
Central PMCID: PMC3518427.
 
Nowacki M, Haye JE, Fang W, Vijayan V, Landweber LF. RNA-mediated epigenetic
regulation of DNA copy number. Proc Natl Acad Sci U S A. 2010 Dec
21;107(51):22140-4. doi.org/10.1073/pnas.1012236107. Epub 2010 Nov 15. PubMed PMID:
21078984; PubMed Central PMCID: PMC3009799.
 
Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, Landweber LF. A
functional role for transposases in a large eukaryotic genome. Science. 2009 May
15;324(5929):935-8. doi.org/10.1126/science.1170023. Epub 2009 Apr 16. PubMed PMID:
19372392; PubMed Central PMCID: PMC3491810.
 
Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF.
RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature.
2008 Jan 10;451(7175):153-8. Epub 2007 Nov 28. PubMed PMID: 18046331; PubMed
Central PMCID: PMC2647009.
 
Landweber LF. Why genomes in pieces? Science. 2007 Oct
19;318(5849):405-7. PubMed PMID: 17947572.