Ildar Gainetdinov

Genomics & Systems Biology, Developmental Genetics, Molecular & Cellular Biology

Genetic, biochemical, and computational approaches in RNA biology; how do animals make, use, and destroy RNAs; small RNAs in insects and mammals

Relaxed targeting rules help PIWI proteins silence transposons.

Gainetdinov I, Vega-Badillo J, Cecchini K, Bagci A, Colpan C, De D, Bailey S, Arif A, Wu PH, MacRae IJ, Zamore PD.

Nature. 2023 Jul;619(7969):394-402.

A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila.

Venkei ZG*, Gainetdinov I*, Bagci A, Starostik MR, Choi CP, Fingerhut JM, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, Yamashita YM. *co-first authors.

Nat Cell Biol. 2023; doi.org/10.1038/s41556-023-01227-4

The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice.

Cecchini K, Biasini A, Yu T, Säflund M, Mou H, Arif A, Eghbali A, Colpan C, Gainetdinov I, de Rooij DG, Weng Z, Zamore PD, Özata DM.

Reproduction. 2023 Jan 4;165(2):183-196.

GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins.

Arif A, Bailey S, Izumi N, Anzelon TA, Ozata DM, Andersson C, Gainetdinov I, MacRae IJ, Tomari Y, Zamore PD.

Nature. 2022 Aug;608(7923):618-625.

Terminal modification, sequence, length, and PIWI-protein identity determine piRNA stability.

Gainetdinov I, Colpan C, Cecchini K, Arif A, Jouravleva K, Albosta P, Vega-Badillo J, Lee Y, Özata DM, Zamore PD.

Mol Cell. 2021 Dec 2;81(23):4826-4842.

Thermus thermophilus Argonaute Functions in the Completion of DNA Replication.

Jolly SM, Gainetdinov I, Jouravleva K, Zhang H, Strittmatter L, Bailey SM, Hendricks GM, Dhabaria A, Ueberheide B, Zamore PD.

Cell. 2020 Sep 17;182(6):1545-1559.e18.

The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility.

Wu PH, Fu Y, Cecchini K, Özata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD.

Nat Genet. 2020 Jul;52(7):728-739.

Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans.

Özata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD.

Nat Ecol Evol. 2020 Jan;4(1):156-168.

The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria.

Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD.

Mol Cell. 2019 Jun 6;74(5):982-995.e6.

A Compact, High-Accuracy Cas9 with a Dinucleotide PAM for In Vivo Genome Editing.

Edraki A, Mir A, Ibraheim R, Gainetdinov I, Yoon Y, Song CQ, Cao Y, Gallant J, Xue W, Rivera-Pérez JA, Sontheimer EJ.

Mol Cell. 2019 Feb 21;73(4):714-726.e4.

Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster.

Chang TH, Mattei E, Gainetdinov I, Colpan C, Weng Z, Zamore PD.

Mol Cell. 2019 Jan 17;73(2):291-303.e6.

PIWI-interacting RNAs: small RNAs with big functions.

Ozata DM*, Gainetdinov I*, Zoch A, O'Carroll D, Zamore PD. *co-first authors.

Nat Rev Genet. 2019 Feb;20(2):89-108.

Potent Cas9 Inhibition in Bacterial and Human Cells by AcrIIC4 and AcrIIC5 Anti-CRISPR Proteins.

Lee J, Mir A, Edraki A, Garcia B, Amrani N, Lou HE, Gainetdinov I, Pawluk A, Ibraheim R, Gao XD, Liu P, Davidson AR, Maxwell KL, Sontheimer EJ.

mBio. 2018 Dec 4;9(6):e02321-18.

A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals.

Gainetdinov I*, Colpan C*, Arif A, Cecchini K, Zamore PD. *co-first authors.

Mol Cell. 2018 Sep 6;71(5):775-790.e5.

Assessment of piRNA biogenesis and function in testicular germ cell tumors and their precursor germ cell neoplasia in situ.

Gainetdinov IV, Skvortsova YV, Kondratieva SA, Klimov A, Tryakin AA, Azhikina TL.

BMC Cancer. 2018 Jan 4;18(1):20.

Two modes of targeting transposable elements by piRNA pathway in human testis.

Gainetdinov I, Skvortsova Y, Kondratieva S, Funikov S, Azhikina T.

RNA. 2017 Nov;23(11):1614-1625.

Hypomethylation of human-specific family of LINE-1 retrotransposons in circulating DNA of lung cancer patients.

Gainetdinov IV, Kapitskaya KY, Rykova EY, Ponomaryova AA, Cherdyntseva NV, Vlassov VV, Laktionov PP, Azhikina TL.

Lung Cancer. 2016 Sep;99:127-30.

Intragenic Locus in Human PIWIL2 Gene Shares Promoter and Enhancer Functions.

Skvortsova YV, Kondratieva SA, Zinovyeva MV, Nikolaev LG, Azhikina TL, Gainetdinov IV.

PLoS One. 2016 Jun 1;11(6):e0156454.

Distinguishing epigenetic features of preneoplastic testis tissues adjacent to seminomas and nonseminomas.

Gainetdinov IV, Kondratieva SA, Skvortsova YV, Zinovyeva MV, Stukacheva EA, Klimov A, Tryakin AA, Azhikina TL.

Oncotarget. 2016 Apr 19;7(16):22439-47.

Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes.

Gainetdinov IV, Skvortsova YV, Stukacheva EA, Bychenko OS, Kondratieva SA, Zinovieva MV, Azhikina TL.

PLoS One. 2014 Nov 10;9(11):e112528.

Use of short representative sequences for structural and functional genomic studies.

Gainetdinov IV, Azhikina TL, Sverdlov ED.

Biochemistry (Mosc). 2007 Nov;72(11):1179-86.

Methylation-free site patterns along a 1-Mb locus on Chr19 in cancerous and normal cells are similar. A new fast approach for analyzing unmethylated CCGG sites distribution.

Azhikina T, Gainetdinov I, Skvortsova Y, Sverdlov E.

Mol Genet Genomics. 2006 Jun;275(6):615-22.

Non-methylated Genomic Sites Coincidence Cloning (NGSCC): an approach to large scale analysis of hypomethylated CpG patterns at predetermined genomic loci.

Azhikina T, Gainetdinov I, Skvortsova Y, Batrak A, Dmitrieva N, Sverdlov E.

Mol Genet Genomics. 2004 Feb;271(1):22-32.