The application provides T cell gene expression signatures that can be used to predict T cell therapy outcomes.

The present disclosure provides compositions with a modulating gene expression and methods for modulating transcription.

The present invention provides methods of systems and methods of site specific methylation.

Compositions and methods for carboxymethylation of cytosine containing DNA and applications thereof for direct sequencing of 5mC are disclosed.

A DNA methyltransferase is derived from Deinococcus radiodurans and has a typical conservative structural domain of DNA methyltransferase. The DNA methyltransferase includes: an AdoMet binding region containing a “FxGxG” conservative sequence, a target sequence recognition region and a catalytic region containing a “TSPPY” conservative sequence sequentially from N-terminal to C-terminal; and belongs to α-type DNA methyltransferase category. The recognized substrate DNA conservative sequence is 5′-CCGCGG-3′, a methylation modified position is N4 site of second cytosine to generate a 4mC type modified base, and an optimum temperature for methylated reaction is in a range of 25-37° C. The DNA methyltransferase can specific-recognize the conservative motif of “CCGCGG” and methylate the N4 site of the second cytosine to produce the 4mC modified base, which is a N4-Cytosine DNA methyltransferase.

The present disclosure provides compositions with a modulating gene expression and methods for modulating transcription.

The present disclosure relates to methods of treating AML, associated with DNMT3A mutations by administering one or more DOT1L inhibitors or related pharmaceutical compositions to subjects in need thereof.

Methods, compositions and kits are provided to amplify the amount of genomic methylated DNA can by subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

A method for treating cancer in a subject in need thereof includes administering to cancer cells of the subject an agent effective to modulate the level of DNMT1-associated RNA and/or the interaction of DNMT1-associated RNA and DNMT1 in the cancer cells of the subject. Embodiments described herein relate to RNAs (e.g., IncRNAs) associated with DNA methyltransferase 1 (DNMTI-associated RNA) in human cancer cells, methods and compositions of modulating the levels of DNMTI-associated RNA and/or the interaction of DNMT1-associated RNA and DNMT1 in cancer cells of the subject to treat cancer cells or a subject in need thereof, and/or methods of measuring the expression profile of DNMT1 associated RNA to determine whether the subject has cancer or an increased risk of cancer and/or the efficacy of a therapeutic regimen agent.

Methods and systems for obtaining inhibitors of human DNA methyltransferase 1 (DNMT1) are disclosed where the methods involve designing compounds that resemble the DNMT1 transition state.