PMID- 35723254 OWN - NLM STAT- MEDLINE DCOM- 20220630 LR - 20220716 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 11 DP - 2022 Jun 20 TI - An expanded toolkit for Drosophila gene tagging using synthesized homology donor constructs for CRISPR-mediated homologous recombination. LID - 10.7554/eLife.76077 [doi] LID - e76077 AB - Previously, we described a large collection of Drosophila strains that each carry an artificial exon containing a T2AGAL4 cassette inserted in an intron of a target gene based on CRISPR-mediated homologous recombination. These alleles permit numerous applications and have proven to be very useful. Initially, the homologous recombination-based donor constructs had long homology arms (>500 bps) to promote precise integration of large constructs (>5 kb). Recently, we showed that in vivo linearization of the donor constructs enables insertion of large artificial exons in introns using short homology arms (100-200 bps). Shorter homology arms make it feasible to commercially synthesize homology donors and minimize the cloning steps for donor construct generation. Unfortunately, about 58% of Drosophila genes lack a suitable coding intron for integration of artificial exons in all of the annotated isoforms. Here, we report the development of new set of constructs that allow the replacement of the coding region of genes that lack suitable introns with a KozakGAL4 cassette, generating a knock-out/knock-in allele that expresses GAL4 similarly as the targeted gene. We also developed custom vector backbones to further facilitate and improve transgenesis. Synthesis of homology donor constructs in custom plasmid backbones that contain the target gene sgRNA obviates the need to inject a separate sgRNA plasmid and significantly increases the transgenesis efficiency. These upgrades will enable the targeting of nearly every fly gene, regardless of exon-intron structure, with a 70-80% success rate. CI - © 2022, Kanca et al. FAU - Kanca, Oguz AU - Kanca O AUID- ORCID: 0000-0001-5438-0879 AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Zirin, Jonathan AU - Zirin J AD - Department of Genetics, Harvard Medical School, Boston, United States. FAU - Hu, Yanhui AU - Hu Y AD - Department of Genetics, Harvard Medical School, Boston, United States. FAU - Tepe, Burak AU - Tepe B AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Dutta, Debdeep AU - Dutta D AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Lin, Wen-Wen AU - Lin WW AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Ma, Liwen AU - Ma L AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Ge, Ming AU - Ge M AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Zuo, Zhongyuan AU - Zuo Z AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Duncan Neurological Research Institute, Texas Children Hospital, Houston, United States. FAU - Liu, Lu-Ping AU - Liu LP AD - Department of Genetics, Harvard Medical School, Boston, United States. FAU - Levis, Robert W AU - Levis RW AUID- ORCID: 0000-0003-3453-2390 AD - Department of Embryology, Carnegie Institution for Science, Baltimore, United States. FAU - Perrimon, Norbert AU - Perrimon N AUID- ORCID: 0000-0001-7542-472X AD - Department of Genetics, Harvard Medical School, Boston, United States. AD - Howard Hughes Medical Institute, Harvard Medical School, Boston, United States. FAU - Bellen, Hugo J AU - Bellen HJ AUID- ORCID: 0000-0001-5992-5989 AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States. AD - Department of Neuroscience, Baylor College of Medicine, Houston, United States. LA - eng SI - GEO/GSE157202 GR - U54 HD083092/HD/NICHD NIH HHS/United States GR - R01 GM067761/GM/NIGMS NIH HHS/United States GR - R01 GM067858/GM/NIGMS NIH HHS/United States GR - R01 GM084947/GM/NIGMS NIH HHS/United States GR - HHMI/Howard Hughes Medical Institute/United States GR - R24 OD031447/OD/NIH HHS/United States GR - U54 NS093793/NS/NINDS NIH HHS/United States GR - R24 OD022005/OD/NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20220620 PL - England TA - Elife JT - eLife JID - 101579614 SB - IM MH - Animals MH - CRISPR-Cas Systems/genetics MH - *Clustered Regularly Interspaced Short Palindromic Repeats/genetics MH - *Drosophila/genetics MH - Exons/genetics MH - Homologous Recombination MH - Plasmids PMC - PMC9239680 OTO - NOTNLM OT - CRISPR OT - D. melanogaster OT - gene trap OT - genetics OT - genomics OT - homologous recombination OT - knock-in OT - knock-out OT - protein trap COIS- OK, JZ, YH, BT, DD, WL, LM, MG, ZZ, LL, RL, NP, HB No competing interests declared EDAT- 2022/06/21 06:00 MHDA- 2022/07/01 06:00 CRDT- 2022/06/20 07:53 PHST- 2021/12/07 00:00 [received] PHST- 2022/06/19 00:00 [accepted] PHST- 2022/06/21 06:00 [pubmed] PHST- 2022/07/01 06:00 [medline] PHST- 2022/06/20 07:53 [entrez] AID - 76077 [pii] AID - 10.7554/eLife.76077 [doi] PST - epublish SO - Elife. 2022 Jun 20;11:e76077. doi: 10.7554/eLife.76077. PMID- 34113007 OWN - NLM STAT- MEDLINE DCOM- 20211025 LR - 20220531 IS - 1530-0366 (Electronic) IS - 1098-3600 (Print) IS - 1098-3600 (Linking) VI - 23 IP - 10 DP - 2021 Oct TI - Heterozygous loss-of-function variants significantly expand the phenotypes associated with loss of GDF11. PG - 1889-1900 LID - 10.1038/s41436-021-01216-8 [doi] AB - PURPOSE: Growth differentiation factor 11 (GDF11) is a key signaling protein required for proper development of many organ systems. Only one prior study has associated an inherited GDF11 variant with a dominant human disease in a family with variable craniofacial and vertebral abnormalities. Here, we expand the phenotypic spectrum associated with GDF11 variants and document the nature of the variants. METHODS: We present a cohort of six probands with de novo and inherited nonsense/frameshift (4/6 patients) and missense (2/6) variants in GDF11. We generated gdf11 mutant zebrafish to model loss of gdf11 phenotypes and used an overexpression screen in Drosophila to test variant functionality. RESULTS: Patients with variants in GDF11 presented with craniofacial (5/6), vertebral (5/6), neurological (6/6), visual (4/6), cardiac (3/6), auditory (3/6), and connective tissue abnormalities (3/6). gdf11 mutant zebrafish show craniofacial abnormalities and body segmentation defects that match some patient phenotypes. Expression of the patients' variants in the fly showed that one nonsense variant in GDF11 is a severe loss-of-function (LOF) allele whereas the missense variants in our cohort are partial LOF variants. CONCLUSION: GDF11 is needed for human development, particularly neuronal development, and LOF GDF11 alleles can affect the development of numerous organs and tissues. CI - © 2021. The Author(s), under exclusive licence to the American College of Medical Genetics and Genomics. FAU - Ravenscroft, Thomas A AU - Ravenscroft TA AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. AD - Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA. FAU - Phillips, Jennifer B AU - Phillips JB AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Fieg, Elizabeth AU - Fieg E AD - Brigham and Women's Hospital, Boston, MA, USA. FAU - Bajikar, Sameer S AU - Bajikar SS AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. AD - Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA. FAU - Peirce, Judy AU - Peirce J AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Wegner, Jeremy AU - Wegner J AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Luna, Alia A AU - Luna AA AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Fox, Eric J AU - Fox EJ AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Yan, Yi-Lin AU - Yan YL AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Rosenfeld, Jill A AU - Rosenfeld JA AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. AD - Baylor Genetics Laboratories, Houston, TX, USA. FAU - Zirin, Jonathan AU - Zirin J AD - Department of Genetics, Harvard Medical School, Boston, MA, USA. FAU - Kanca, Oguz AU - Kanca O AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. AD - Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA. CN - Undiagnosed Diseases Network FAU - Benke, Paul J AU - Benke PJ AD - Joe DiMaggio Children's Hospital, Hollywood, FL, USA. FAU - Cameron, Eric S AU - Cameron ES AD - Joe DiMaggio Children's Hospital, Hollywood, FL, USA. FAU - Strehlow, Vincent AU - Strehlow V AD - Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany. FAU - Platzer, Konrad AU - Platzer K AD - Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany. FAU - Jamra, Rami Abou AU - Jamra RA AD - Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany. FAU - Klöckner, Chiara AU - Klöckner C AD - Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany. FAU - Osmond, Matthew AU - Osmond M AD - Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada. FAU - Licata, Thomas AU - Licata T AD - Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada. FAU - Rojas, Samantha AU - Rojas S AD - Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada. FAU - Dyment, David AU - Dyment D AD - Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada. FAU - Chong, Josephine S C AU - Chong JSC AD - The Chinese University of Hong Kong-Baylor College of Medicine Joint Center of Medical Genetics, Hong Kong Special Administrative Region, The People's Republic of China. FAU - Lincoln, Sharyn AU - Lincoln S AD - Boston Children's Hospital, Boston, MA, USA. FAU - Stoler, Joan M AU - Stoler JM AD - Boston Children's Hospital, Boston, MA, USA. FAU - Postlethwait, John H AU - Postlethwait JH AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Wangler, Michael F AU - Wangler MF AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. AD - Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA. FAU - Yamamoto, Shinya AU - Yamamoto S AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. AD - Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA. AD - Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA. FAU - Krier, Joel AU - Krier J AD - Brigham and Women's Hospital, Boston, MA, USA. FAU - Westerfield, Monte AU - Westerfield M AD - Institute of Neuroscience, University of Oregon, Eugene, OR, USA. FAU - Bellen, Hugo J AU - Bellen HJ AD - Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. hbellen@bcm.edu. AD - Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA. hbellen@bcm.edu. AD - Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA. hbellen@bcm.edu. AD - Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA. hbellen@bcm.edu. LA - eng GR - U01 HG007690/HG/NHGRI NIH HHS/United States GR - P41 GM132087/GM/NIGMS NIH HHS/United States GR - R24 OD031447/OD/NIH HHS/United States GR - F32 HD100048/HD/NICHD NIH HHS/United States GR - U01 HG007942/HG/NHGRI NIH HHS/United States GR - R24 OD026591/OD/NIH HHS/United States GR - U54 NS093793/NS/NINDS NIH HHS/United States GR - R24 OD022005/OD/NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20210610 PL - United States TA - Genet Med JT - Genetics in medicine : official journal of the American College of Medical Genetics JID - 9815831 RN - 0 (Bone Morphogenetic Proteins) RN - 0 (GDF11 protein, human) RN - 0 (Growth Differentiation Factors) SB - IM MH - Animals MH - *Bone Morphogenetic Proteins/genetics MH - Craniofacial Abnormalities/*genetics MH - *Growth Differentiation Factors/genetics MH - Humans MH - Mutation, Missense MH - Phenotype MH - Spine MH - Zebrafish/genetics PMC - PMC8487929 MID - NIHMS1717830 COIS- Declaration of interests The Department of Molecular and Human Genetics at Baylor College of Medicine receives revenue from clinical genetic testing conducted at Baylor Genetics Laboratories. The authors have no other conflicts of interest. FIR - Acosta, Maria T IR - Acosta MT FIR - Adam, Margaret IR - Adam M FIR - Adams, David R IR - Adams DR FIR - Agrawal, Pankaj B IR - Agrawal PB FIR - Alejandro, Mercedes E IR - Alejandro ME FIR - Alvey, Justin IR - Alvey J FIR - Amendola, Laura IR - Amendola L FIR - Andrews, Ashley IR - Andrews A FIR - Ashley, Euan A IR - Ashley EA FIR - Azamian, Mahshid S IR - Azamian MS FIR - Bacino, Carlos A IR - Bacino CA FIR - Bademci, Guney IR - Bademci G FIR - Baker, Eva IR - Baker E FIR - Balasubramanya, Ashok IR - Balasubramanya A FIR - Baldridge, Dustin IR - Baldridge D FIR - Bale, Jim IR - Bale J FIR - Bamshad, Michael IR - Bamshad M FIR - Barbouth, Deborah IR - Barbouth D FIR - Bayrak-Toydemir, Pinar IR - Bayrak-Toydemir P FIR - Beck, Anita IR - Beck A FIR - Beggs, Alan H IR - Beggs AH FIR - Behrens, Edward IR - Behrens E FIR - Bejerano, Gill IR - Bejerano G FIR - Bennet, Jimmy IR - Bennet J FIR - Berg-Rood, Beverly IR - Berg-Rood B FIR - Bernstein, Jonathan A IR - Bernstein JA FIR - Berry, Gerard T IR - 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Sacco, Ralph IR - Sacco R FIR - Sampson, Jacinda B IR - Sampson JB FIR - Samson, Susan L IR - Samson SL FIR - Saporta, Mario IR - Saporta M FIR - Scott, C Ron IR - Scott CR FIR - Schaechter, Judy IR - Schaechter J FIR - Schedl, Timothy IR - Schedl T FIR - Schoch, Kelly IR - Schoch K FIR - Scott, Daryl A IR - Scott DA FIR - Shashi, Vandana IR - Shashi V FIR - Shin, Jimann IR - Shin J FIR - Signer, Rebecca IR - Signer R FIR - Silverman, Edwin K IR - Silverman EK FIR - Sinsheimer, Janet S IR - Sinsheimer JS FIR - Sisco, Kathy IR - Sisco K FIR - Smith, Edward C IR - Smith EC FIR - Smith, Kevin S IR - Smith KS FIR - Solem, Emily IR - Solem E FIR - Solnica-Krezel, Lilianna IR - Solnica-Krezel L FIR - Solomon, Ben IR - Solomon B FIR - Spillmann, Rebecca C IR - Spillmann RC FIR - Stoler, Joan M IR - Stoler JM FIR - Sullivan, Jennifer A IR - Sullivan JA FIR - Sullivan, Kathleen IR - Sullivan K FIR - Sun, Angela IR - Sun A FIR - Sutton, Shirley IR - Sutton S FIR - Sweetser, David A IR - Sweetser DA FIR - Sybert, Virginia IR - Sybert V FIR - Tabor, Holly K IR - Tabor HK FIR - Tan, Amelia L M IR - Tan ALM FIR - Tan, Queenie K-G IR - Tan QK FIR - Tekin, Mustafa IR - Tekin M FIR - Telischi, Fred IR - Telischi F FIR - Thorson, Willa IR - Thorson W FIR - Thurm, Audrey IR - Thurm A FIR - Tifft, Cynthia J IR - Tifft CJ FIR - Toro, Camilo IR - Toro C FIR - Tran, Alyssa A IR - Tran AA FIR - Tucker, Brianna M IR - Tucker BM FIR - Urv, Tiina K IR - Urv TK FIR - Vanderver, Adeline IR - Vanderver A FIR - Velinder, Matt IR - Velinder M FIR - Viskochil, Dave IR - Viskochil D FIR - Vogel, Tiphanie P IR - Vogel TP FIR - Wahl, Colleen E IR - Wahl CE FIR - Wallace, Stephanie IR - Wallace S FIR - Walley, Nicole M IR - Walley NM FIR - Walsh, Chris A IR - Walsh CA FIR - Walker, Melissa IR - Walker M FIR - Wambach, Jennifer IR - Wambach J FIR - Wan, Jijun IR - Wan J FIR - Wang, Lee-Kai IR - Wang LK FIR - Wangler, Michael F IR - Wangler MF FIR - Ward, Patricia A IR - Ward PA FIR - Wegner, Daniel IR - Wegner D FIR - Wener, Mark IR - Wener M FIR - Wenger, Tara IR - Wenger T FIR - Perry, Katherine Wesseling IR - Perry KW FIR - Westerfield, Monte IR - Westerfield M FIR - Wheeler, Matthew T IR - Wheeler MT FIR - Whitlock, Jordan IR - Whitlock J FIR - Wolfe, Lynne A IR - Wolfe LA FIR - Woods, Jeremy D IR - Woods JD FIR - Yamamoto, Shinya IR - Yamamoto S FIR - Yang, John IR - Yang J FIR - Yousef, Muhammad IR - Yousef M FIR - Zastrow, Diane B IR - Zastrow DB FIR - Zein, Wadih IR - Zein W FIR - Zhao, Chunli IR - Zhao C FIR - Zuchner, Stephan IR - Zuchner S EDAT- 2021/06/12 06:00 MHDA- 2021/10/26 06:00 CRDT- 2021/06/11 06:36 PHST- 2021/01/25 00:00 [received] PHST- 2021/05/05 00:00 [accepted] PHST- 2021/05/04 00:00 [revised] PHST- 2021/06/12 06:00 [pubmed] PHST- 2021/10/26 06:00 [medline] PHST- 2021/06/11 06:36 [entrez] AID - S1098-3600(21)05130-3 [pii] AID - 10.1038/s41436-021-01216-8 [doi] PST - ppublish SO - Genet Med. 2021 Oct;23(10):1889-1900. doi: 10.1038/s41436-021-01216-8. Epub 2021 Jun 10.